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Shin JE, Shin N, Park T, Park M. Multipartite network analysis to identify environmental and genetic associations of metabolic syndrome in the Korean population. Sci Rep 2024; 14:20283. [PMID: 39217223 PMCID: PMC11366034 DOI: 10.1038/s41598-024-71217-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
Network analysis has become a crucial tool in genetic research, enabling the exploration of associations between genes and diseases. Its utility extends beyond genetics to include the assessment of environmental factors. Unipartite network analysis is commonly used in genomics to visualize initial insights and relationships among variables. Syndromic diseases, such as metabolic syndrome, are characterized by the simultaneous occurrence of various signs, symptoms, and clinicopathological features. Metabolic syndrome encompasses hypertension, diabetes, obesity, and dyslipidemia, and both genetic and environmental factors contribute to its development. Given that relevant data often consist of distinct sets of variables, a more intuitive visualization method is needed. This study applied multipartite network analysis as an effective method to understand the associations among genetic, environmental, and disease components in syndromic diseases. We considered three distinct variable sets: genetic factors, environmental factors, and disease components. The process involved projecting a tripartite network onto a two-mode bipartite network and then simplifying it into a one-mode network. This approach facilitated the visualization of relationships among factors across different sets and within individual sets. To transition from multipartite to unipartite networks, we suggest both sequential and concurrent projection methods. Data from the Korean Association Resource (KARE) project were utilized, including 352,228 SNPs from 8840 individuals, alongside information on environmental factors such as lifestyle, dietary, and socioeconomic factors. The single-SNP analysis step filtered SNPs, supplemented by reference SNPs reported in a genome-wide association study catalog. The resulting network patterns differed significantly by sex: demographic factors and fat intake were crucial for women, while alcohol consumption was central for men. Indirect relationships were identified through projected bipartite networks, revealing that SNPs such as rs4244457, rs2156552, and rs10899345 had lifestyle interactions on metabolic components. Our approach offers several advantages: it simplifies the visualization of complex relationships among different datasets, identifies environmental interactions, and provides insights into SNP clusters sharing common environmental factors and metabolic components. This framework provides a comprehensive approach to elucidate the mechanisms underlying complex diseases like metabolic syndrome.
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Affiliation(s)
- Ji-Eun Shin
- Department of Biomedical Informatics, Konyang University, Daejeon, Republic of Korea
| | - Nari Shin
- Department of Statistics, Korea University, Seoul, Republic of Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Mira Park
- Department of Preventive Medicine, Eulji University, Daejeon, Republic of Korea.
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Cañadas-Garre M, Maqueda JJ, Baños-Jaime B, Hill C, Skelly R, Cappa R, Brennan E, Doyle R, Godson C, Maxwell AP, McKnight AJ. Mitochondrial related variants associated with cardiovascular traits. Front Physiol 2024; 15:1395371. [PMID: 39258111 PMCID: PMC11385366 DOI: 10.3389/fphys.2024.1395371] [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: 03/03/2024] [Accepted: 08/05/2024] [Indexed: 09/12/2024] Open
Abstract
Introduction Cardiovascular disease (CVD) is responsible for over 30% of mortality worldwide. CVD arises from the complex influence of molecular, clinical, social, and environmental factors. Despite the growing number of autosomal genetic variants contributing to CVD, the cause of most CVDs is still unclear. Mitochondria are crucial in the pathophysiology, development and progression of CVDs; the impact of mitochondrial DNA (mtDNA) variants and mitochondrial haplogroups in the context of CVD has recently been highlighted. Aims We investigated the role of genetic variants in both mtDNA and nuclear-encoded mitochondrial genes (NEMG) in CVD, including coronary artery disease (CAD), hypertension, and serum lipids in the UK Biobank, with sub-group analysis for diabetes. Methods We investigated 371,542 variants in 2,527 NEMG, along with 192 variants in 32 mitochondrial genes in 381,994 participants of the UK Biobank, stratifying by presence of diabetes. Results Mitochondrial variants showed associations with CVD, hypertension, and serum lipids. Mitochondrial haplogroup J was associated with CAD and serum lipids, whereas mitochondrial haplogroups T and U were associated with CVD. Among NEMG, variants within Nitric Oxide Synthase 3 (NOS3) showed associations with CVD, CAD, hypertension, as well as diastolic and systolic blood pressure. We also identified Translocase Of Outer Mitochondrial Membrane 40 (TOMM40) variants associated with CAD; Solute carrier family 22 member 2 (SLC22A2) variants associated with CAD and CVD; and HLA-DQA1 variants associated with hypertension. Variants within these three genes were also associated with serum lipids. Conclusion Our study demonstrates the relevance of mitochondrial related variants in the context of CVD. We have linked mitochondrial haplogroup U to CVD, confirmed association of mitochondrial haplogroups J and T with CVD and proposed new markers of hypertension and serum lipids in the context of diabetes. We have also evidenced connections between the etiological pathways underlying CVDs, blood pressure and serum lipids, placing NOS3, SLC22A2, TOMM40 and HLA-DQA1 genes as common nexuses.
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Affiliation(s)
- Marisa Cañadas-Garre
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol Oakfield House, Belfast, United Kingdom
| | - Joaquín J Maqueda
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Blanca Baños-Jaime
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Claire Hill
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
| | - Ryan Skelly
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
| | - Ruaidhri Cappa
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
| | - Eoin Brennan
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Ross Doyle
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Catherine Godson
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
- Regional Nephrology Unit, Belfast City Hospital Belfast, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, United Kingdom
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Vialle RA, de Paiva Lopes K, Li Y, Ng B, Schneider JA, Buchman AS, Wang Y, Farfel JM, Barnes LL, Wingo AP, Wingo TS, Seyfried NT, De Jager PL, Gaiteri C, Tasaki S, Bennett DA. Structural variants linked to Alzheimer's Disease and other common age-related clinical and neuropathologic traits. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.12.24311887. [PMID: 39185527 PMCID: PMC11343262 DOI: 10.1101/2024.08.12.24311887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Advances have led to a greater understanding of the genetics of Alzheimer's Disease (AD). However, the gap between the predicted and observed genetic heritability estimates when using single nucleotide polymorphisms (SNPs) and small indel data remains. Large genomic rearrangements, known as structural variants (SVs), have the potential to account for this missing genetic heritability. By leveraging data from two ongoing cohort studies of aging and dementia, the Religious Orders Study and Rush Memory and Aging Project (ROS/MAP), we performed genome-wide association analysis testing around 20,000 common SVs from 1,088 participants with whole genome sequencing (WGS) data. A range of Alzheimer's Disease and Related Disorders (AD/ADRD) clinical and pathologic traits were examined. Given the limited sample size, no genome-wide significant association was found, but we mapped SVs across 81 AD risk loci and discovered 22 SVs in linkage disequilibrium (LD) with GWAS lead variants and directly associated with AD/ADRD phenotypes (nominal P < 0.05). The strongest association was a deletion of an Alu element in the 3'UTR of the TMEM106B gene. This SV was in high LD with the respective AD GWAS locus and was associated with multiple AD/ADRD phenotypes, including tangle density, TDP-43, and cognitive resilience. The deletion of this element was also linked to lower TMEM106B protein abundance. We also found a 22 kb deletion associated with depression in ROSMAP and bearing similar association patterns as AD GWAS SNPs at the IQCK locus. In addition, genome-wide scans allowed the identification of 7 SVs, with no LD with SNPs and nominally associated with AD/ADRD traits. This result suggests potentially new ADRD risk loci not discoverable using SNP data. Among these findings, we highlight a 5.6 kb duplication of coding regions of the gene C1orf186 at chromosome 1 associated with indices of cognitive impairment, decline, and resilience. While further replication in independent datasets is needed to validate these findings, our results support the potential roles of common structural variations in the pathogenesis of AD/ADRD.
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Affiliation(s)
- Ricardo A Vialle
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yan Li
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Bernard Ng
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jose M Farfel
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Aliza P Wingo
- Department of Psychiatry, University of California, Davis CA, USA
- VA Northern California Health Care System, McClellan Park, CA, USA
| | - Thomas S Wingo
- Department of Neurology, University of California, Davis, CA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Department of Neurology and Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Philip L De Jager
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
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Altmann A, Aksman LM, Oxtoby NP, Young AL, Alexander DC, Barkhof F, Shoai M, Hardy J, Schott JM. Towards cascading genetic risk in Alzheimer's disease. Brain 2024; 147:2680-2690. [PMID: 38820112 PMCID: PMC11292901 DOI: 10.1093/brain/awae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024] Open
Abstract
Alzheimer's disease typically progresses in stages, which have been defined by the presence of disease-specific biomarkers: amyloid (A), tau (T) and neurodegeneration (N). This progression of biomarkers has been condensed into the ATN framework, in which each of the biomarkers can be either positive (+) or negative (-). Over the past decades, genome-wide association studies have implicated ∼90 different loci involved with the development of late-onset Alzheimer's disease. Here, we investigate whether genetic risk for Alzheimer's disease contributes equally to the progression in different disease stages or whether it exhibits a stage-dependent effect. Amyloid (A) and tau (T) status was defined using a combination of available PET and CSF biomarkers in the Alzheimer's Disease Neuroimaging Initiative cohort. In 312 participants with biomarker-confirmed A-T- status, we used Cox proportional hazards models to estimate the contribution of APOE and polygenic risk scores (beyond APOE) to convert to A+T- status (65 conversions). Furthermore, we repeated the analysis in 290 participants with A+T- status and investigated the genetic contribution to conversion to A+T+ (45 conversions). Both survival analyses were adjusted for age, sex and years of education. For progression from A-T- to A+T-, APOE-e4 burden showed a significant effect [hazard ratio (HR) = 2.88; 95% confidence interval (CI): 1.70-4.89; P < 0.001], whereas polygenic risk did not (HR = 1.09; 95% CI: 0.84-1.42; P = 0.53). Conversely, for the transition from A+T- to A+T+, the contribution of APOE-e4 burden was reduced (HR = 1.62; 95% CI: 1.05-2.51; P = 0.031), whereas the polygenic risk showed an increased contribution (HR = 1.73; 95% CI: 1.27-2.36; P < 0.001). The marginal APOE effect was driven by e4 homozygotes (HR = 2.58; 95% CI: 1.05-6.35; P = 0.039) as opposed to e4 heterozygotes (HR = 1.74; 95% CI: 0.87-3.49; P = 0.12). The genetic risk for late-onset Alzheimer's disease unfolds in a disease stage-dependent fashion. A better understanding of the interplay between disease stage and genetic risk can lead to a more mechanistic understanding of the transition between ATN stages and a better understanding of the molecular processes leading to Alzheimer's disease, in addition to opening therapeutic windows for targeted interventions.
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Affiliation(s)
- Andre Altmann
- UCL Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, WC1E 6BT, UK
| | - Leon M Aksman
- Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Neil P Oxtoby
- UCL Centre for Medical Image Computing, Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Alexandra L Young
- UCL Centre for Medical Image Computing, Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Daniel C Alexander
- UCL Centre for Medical Image Computing, Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Frederik Barkhof
- UCL Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, WC1E 6BT, UK
- UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Amsterdam, 1081 HV, The Netherlands
| | - Maryam Shoai
- UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - John Hardy
- UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
| | - Jonathan M Schott
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
- Dementia Research Centre, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3AR, UK
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Ray NR, Kunkle BW, Hamilton‐Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean‐Francois M, Cuccaro M, Reyes‐Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee W, Martin ER, Wang L, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak‐Vance MA, Reitz C. Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. Alzheimers Dement 2024; 20:5247-5261. [PMID: 38958117 PMCID: PMC11350055 DOI: 10.1002/alz.13880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Despite a two-fold risk, individuals of African ancestry have been underrepresented in Alzheimer's disease (AD) genomics efforts. METHODS Genome-wide association studies (GWAS) of 2,903 AD cases and 6,265 controls of African ancestry. Within-dataset results were meta-analyzed, followed by functional genomics analyses. RESULTS A novel AD-risk locus was identified in MPDZ on chromosome (chr) 9p23 (rs141610415, MAF = 0.002, p = 3.68×10-9). Two additional novel common and nine rare loci were identified with suggestive associations (P < 9×10-7). Comparison of association and linkage disequilibrium (LD) patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 (ASCL1), suggesting that this association is modulated by regional origin of local African ancestry. DISCUSSION These analyses identified novel AD-associated loci in individuals of African ancestry and suggest that degree of African ancestry modulates some associations. Increased sample sets covering as much African genetic diversity as possible will be critical to identify additional loci and deconvolute local genetic ancestry effects. HIGHLIGHTS Genetic ancestry significantly impacts risk of Alzheimer's Disease (AD). Although individuals of African ancestry are twice as likely to develop AD, they are vastly underrepresented in AD genomics studies. The Alzheimer's Disease Genetics Consortium has previously identified 16 common and rare genetic loci associated with AD in African American individuals. The current analyses significantly expand this effort by increasing the sample size and extending ancestral diversity by including populations from continental Africa. Single variant meta-analysis identified a novel genome-wide significant AD-risk locus in individuals of African ancestry at the MPDZ gene, and 11 additional novel loci with suggestive genome-wide significance at p < 9×10-7. Comparison of African American datasets with samples of higher degree of African ancestry demonstrated differing patterns of association and linkage disequilibrium at one of these loci, suggesting that degree and/or geographic origin of African ancestry modulates the effect at this locus. These findings illustrate the importance of increasing number and ancestral diversity of African ancestry samples in AD genomics studies to fully disentangle the genetic architecture underlying AD, and yield more effective ancestry-informed genetic screening tools and therapeutic interventions.
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Grants
- P30 AG013854 NIA NIH HHS
- International Parkinson Fonds
- P50 MH060451 NIMH NIH HHS
- P30 AG066444 NIA NIH HHS
- R01 AG28786-01A1 North Carolina A&T University
- U01AG46161 NIA NIH HHS
- AG05128 Duke University
- Medical Research Council
- U01AG057659 NIH HHS
- R01 AG022374 NIA NIH HHS
- U19 AG074865 NIA NIH HHS
- P50 AG023501 NIA NIH HHS
- U01 AG046152 NIA NIH HHS
- P30 AG010124 NIA NIH HHS
- U01 HG006375 NHGRI NIH HHS
- Biogen
- U01 AG058654 NIA NIH HHS
- NIMH MH60451 NINDS NIH HHS
- U54 AG052427 NIA NIH HHS
- UO1 HG004610 Group Health Research Institute
- RC2 AG036528 NIA NIH HHS
- P30 AG028377 NIA NIH HHS
- R01AG048927 NIH HHS
- UO1 HG006375 Group Health Research Institute
- R01 AG22018 Rush University
- U01AG46152 NIA NIH HHS
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- P30 AG10133 Indiana University
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- U01 AG10483 Boston University
- Higher Education Funding Council for England
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- 5R01AG012101 New York University
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- U01AG058654 NIH HHS
- AG025688 Emory University
- P30AG10161 NIA NIH HHS
- Alzheimer's Drug Discovery Foundation
- U01 AG061356 NIA NIH HHS
- RC2 AG036650 NIA NIH HHS
- Servier
- Janssen Alzheimer Immunotherapy Research & Development, LLC.
- U01 AG032984 NIA NIH HHS
- U01 HG008657 NHGRI NIH HHS
- Brain Net Europe
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- Lumosity
- R01 AG013616 NIA NIH HHS
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- Translational Genomics Research Institute
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- Bristol-Myers Squibb Company
- R01 AG030146 NIA NIH HHS
- R01AG041797 NIA FBS (Columbia University)
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- Piramal Imaging
- DeNDRoN
- UL1 RR029893 NCRR NIH HHS
- Takeda Pharmaceutical Company
- 1R01AG035137 New York University
- R01 AG15819 Rush University
- R01AG30146 NIA NIH HHS
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- P50 NS039764 NINDS NIH HHS
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- Office of Research and Development
- Genentech, Inc.
- U01 AG016976 NIA NIH HHS
- US Department of Veterans Affairs Administration
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- Hersenstichting Nederland Breinbrekend Werk
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- Internationale Stiching Alzheimer Onderzoek
- P30AG066462 NIH HHS
- U24 AG026390 NIA FBS (Columbia University)
- Novartis Pharmaceuticals Corporation
- P50 AG005136 NIA NIH HHS
- Meso Scale Diagnostics, LLC.
- CereSpir, Inc.
- P30 AG012300 NIA NIH HHS
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- Canadian Institute of Health Research
- RF1 AG059018 NIA NIH HHS
- BioClinica, Inc.
- U01 AG062943 NIA NIH HHS
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- P50 AG016573 NIA NIH HHS
- U24 AG21886 National Cell Repository for Alzheimer's Disease (NCRAD)
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- Stichting MS Research
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- AG019757 University of Miami
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- P30 AG08051 New York University
- IIRG-05-14147 Alzheimer's Association
- AG010491 University of Miami
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- IIRG-08-89720 Alzheimer's Association
- AbbVie
- R37 AG015473 NIA NIH HHS
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- NIBIB NIH HHS
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- P50 AG005144 NIA NIH HHS
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- Glaxo Smith Kline
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- Biomedical Laboratory Research Program
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- Alzheimer's Research Trust
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- Illinois Department of Public Health
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- NHS trusts
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- Eli Lilly and Company
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- 5R01AG022374 New York University
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- ADGC National Institutes of Health, National Institute on Aging (NIH-NIA)
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- Eisai Inc.
- 5R01AG013616 New York University
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- NIH
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- Columbia University
- Duke University
- Emory University
- Indiana University
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- Massachusetts General Hospital
- Mayo Clinic
- New York University
- Northwestern University
- Oregon Health & Science University
- Rush University
- NIA
- University of Alabama at Birmingham
- University of Arizona
- University of California, Davis
- University of California, Irvine
- University of California, Los Angeles
- University of California, San Diego
- University of California, San Francisco
- University of Kentucky
- University of Michigan
- University of Pittsburgh
- University of Southern California
- University of Miami
- University of Washington
- Vanderbilt University
- NINDS
- Alzheimer's Association
- Office of Research and Development
- BrightFocus Foundation
- Wellcome Trust
- Howard Hughes Medical Institute
- Medical Research Council
- Newcastle University
- Higher Education Funding Council for England
- Alzheimer's Research Trust
- BRACE
- Stichting MS Research
- Department of Defense
- National Institute of Biomedical Imaging and Bioengineering
- AbbVie
- Alzheimer's Drug Discovery Foundation
- BioClinica, Inc.
- Biogen
- Bristol‐Myers Squibb Company
- Eli Lilly and Company
- Genentech, Inc.
- Fujirebio
- GE Healthcare
- Lundbeck
- Merck & Co., Inc.
- Novartis Pharmaceuticals Corporation
- Pfizer Inc.
- Servier
- Takeda Pharmaceutical Company
- Illinois Department of Public Health
- Translational Genomics Research Institute
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6
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Nguyen Ho PT, Hoepel SJW, Rodriguez-Ayllon M, Luik AI, Vernooij MW, Neitzel J. Sleep, 24-Hour Activity Rhythms, and Subsequent Amyloid-β Pathology. JAMA Neurol 2024; 81:824-834. [PMID: 38913396 PMCID: PMC11197458 DOI: 10.1001/jamaneurol.2024.1755] [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: 12/21/2023] [Accepted: 04/15/2024] [Indexed: 06/25/2024]
Abstract
Importance Sleep disturbances are common among older adults and have been associated with the development of Alzheimer disease (AD), such as amyloid-β (Aβ) pathology. For effective AD prevention, it is essential to pinpoint the specific disturbances in sleep and the underlying 24-hour activity rhythms that confer the highest risk of Aβ deposition. Objective To determine the associations of 24-hour activity rhythms and sleep with Aβ deposition in adults without dementia, to evaluate whether disrupted 24-hour activity and sleep may precede Aβ deposition, and to assess the role of the apolipoprotein E ε4 (APOE4) genotype. Design, Setting, and Participants This was an observational cohort study using data from the Rotterdam Study. Of 639 participants without dementia who underwent Aβ positron emission tomography (PET) from September 2018 to November 2021, 319 were included in the current study. Exclusion criteria were no APOE genotyping and no valid actigraphy data at the baseline visits from 2004 to 2006 or from 2012 to 2014. The mean (SD) follow-up was 7.8 (2.4) years. Data were analyzed from March 2023 to April 2024. Exposures Actigraphy (7 days and nights, objective sleep, and 24-hour activity rhythms), sleep diaries (self-reported sleep), Aβ42/40, phosphorylated tau (p-tau)181 and p-tau217 plasma assays, 18F-florbetaben PET (mean standard uptake value ratio [SUVR] in a large cortical region of interest), and APOE4 genotype. Main Outcomes and Measures Association of objective and self-reported sleep and 24-hour activity rhythms at baseline with brain Aβ PET burden at follow-up. Results The mean (range) age in the study population was 61.5 (48-80) years at baseline and 69.2 (60-88) years at follow-up; 150 (47%) were women. Higher intradaily variability at baseline, an indicator of fragmented 24-hour activity rhythms, was associated with higher Aβ PET burden at follow-up (β, 0.15; bootstrapped 95% CI, 0.04 to 0.26; bootstrapped P = .02, false discovery rate [FDR] P = .048). APOE genotype modified this association, which was stronger in APOE4 carriers (β, 0.38; bootstrapped 95% CI, 0.05 to 0.64; bootstrapped P = .03) compared to noncarriers (β, 0.07; bootstrapped 95% CI, -0.04 to 0.18; bootstrapped P = .19). The findings remained largely similar after excluding participants with AD pathology at baseline, suggesting that a fragmented 24-hour activity rhythm may have preceded Aβ deposition. No other objective or self-reported measure of sleep was associated with Aβ. Conclusions and Relevance Among community-dwelling adults included in this study, higher fragmentation of the 24-hour activity rhythms was associated with greater subsequent Aβ burden, especially in APOE4 carriers. These results suggest that rest-activity fragmentation could represent a modifiable risk factor for AD.
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Affiliation(s)
- Phuong Thuy Nguyen Ho
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Sanne J. W. Hoepel
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maria Rodriguez-Ayllon
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Annemarie I. Luik
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, the Netherlands
- Trimbos Institute—the Netherlands Institute of Mental Health and Addiction, Utrecht, the Netherlands
| | - Meike W. Vernooij
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Julia Neitzel
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, the Netherlands
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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7
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Timsina J, Ali M, Do A, Wang L, Western D, Sung YJ, Cruchaga C. Harmonization of CSF and imaging biomarkers in Alzheimer's disease: Need and practical applications for genetics studies and preclinical classification. Neurobiol Dis 2024; 190:106373. [PMID: 38072165 DOI: 10.1016/j.nbd.2023.106373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
In Alzheimer's disease (AD) research, cerebrospinal fluid (CSF) Amyloid beta (Aβ), Tau and pTau are the most accepted and well validated biomarkers. Several methods and platforms exist to measure those biomarkers, leading to challenges in combining data across studies. Thus, there is a need to identify methods that harmonize and standardize these values. We used a Z-score based approach to harmonize CSF and amyloid imaging data from multiple cohorts and compared GWAS results using this approach with currently accepted methods. We also used a generalized mixture model to calculate the threshold for biomarker-positivity. Based on our findings, our normalization approach performed as well as meta-analysis and did not lead to any spurious results. In terms of dichotomization, cutoffs calculated with this approach were very similar to those reported previously. These findings show that the Z-score based harmonization approach can be applied to heterogeneous platforms and provides biomarker cut-offs consistent with the classical approaches without requiring any additional data.
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Affiliation(s)
- Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anh Do
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA.
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8
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Lancaster T, Creese B, Escott-Price V, Driver I, Menzies G, Khan Z, Corbett A, Ballard C, Williams J, Murphy K, Chandler H. Proof-of-concept recall-by-genotype study of extremely low and high Alzheimer's polygenic risk reveals autobiographical deficits and cingulate cortex correlates. Alzheimers Res Ther 2023; 15:213. [PMID: 38087383 PMCID: PMC10714651 DOI: 10.1186/s13195-023-01362-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Genome-wide association studies demonstrate that Alzheimer's disease (AD) has a highly polygenic architecture, where thousands of independent genetic variants explain risk with high classification accuracy. This AD polygenic risk score (AD-PRS) has been previously linked to preclinical cognitive and neuroimaging features observed in asymptomatic individuals. However, shared variance between AD-PRS and neurocognitive features are small, suggesting limited preclinical utility. METHODS Here, we recruited sixteen clinically asymptomatic individuals (mean age 67; range 58-76) with either extremely low / high AD-PRS (defined as at least 2 standard deviations from the wider sample mean (N = 4504; N EFFECTIVE = 90)) with comparable age sex and education level. We assessed group differences in autobiographical memory and T1-weighted structural neuroimaging features. RESULTS We observed marked reductions in autobiographical recollection (Cohen's d = - 1.66; P FDR = 0.014) and midline structure (cingulate) thickness (Cohen's d = - 1.55, P FDR = 0.05), with no difference in hippocampal volume (P > 0.3). We further confirm the negative association between AD-PRS and cingulate thickness in a larger study with a comparable age (N = 31,966, β = - 0.002, P = 0.011), supporting the validity of our approach. CONCLUSIONS These observations conform with multiple streams of prior evidence suggesting alterations in cingulate structures may occur in individuals with higher AD genetic risk. We were able to use a genetically informed research design strategy that significantly improved the efficiency and power of the study. Thus, we further demonstrate that the recall-by-genotype of AD-PRS from wider samples is a promising approach for the detection, assessment, and intervention in specific individuals with increased AD genetic risk.
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Affiliation(s)
- Thomas Lancaster
- Department of Psychology, University of Bath, Bath, UK.
- School of Physics and Astronomy, Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, UK.
- Dementia Research Institute (UKDRI), Cardiff University, Cardiff, UK.
| | - Byron Creese
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- Department of Life Sciences, Brunel University London, Uxbridge, west London, UK
| | - Valentina Escott-Price
- Division of Neuroscience and Mental Health, School of Medicine, Cardiff University, Cardiff, UK
| | - Ian Driver
- School of Physics and Astronomy, Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, UK
| | - Georgina Menzies
- Dementia Research Institute (UKDRI), Cardiff University, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Zunera Khan
- Institute of Psychiatry, King's College London, Psychology & Neuroscience, London, UK
| | - Anne Corbett
- Deptartment of Health & Community Sciences, University of Exeter, Exeter, UK
| | - Clive Ballard
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Julie Williams
- Dementia Research Institute (UKDRI), Cardiff University, Cardiff, UK
| | - Kevin Murphy
- School of Physics and Astronomy, Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, UK
| | - Hannah Chandler
- School of Physics and Astronomy, Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, UK
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9
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Bettencourt C, Skene N, Bandres-Ciga S, Anderson E, Winchester LM, Foote IF, Schwartzentruber J, Botia JA, Nalls M, Singleton A, Schilder BM, Humphrey J, Marzi SJ, Toomey CE, Kleifat AA, Harshfield EL, Garfield V, Sandor C, Keat S, Tamburin S, Frigerio CS, Lourida I, Ranson JM, Llewellyn DJ. Artificial intelligence for dementia genetics and omics. Alzheimers Dement 2023; 19:5905-5921. [PMID: 37606627 PMCID: PMC10841325 DOI: 10.1002/alz.13427] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 08/23/2023]
Abstract
Genetics and omics studies of Alzheimer's disease and other dementia subtypes enhance our understanding of underlying mechanisms and pathways that can be targeted. We identified key remaining challenges: First, can we enhance genetic studies to address missing heritability? Can we identify reproducible omics signatures that differentiate between dementia subtypes? Can high-dimensional omics data identify improved biomarkers? How can genetics inform our understanding of causal status of dementia risk factors? And which biological processes are altered by dementia-related genetic variation? Artificial intelligence (AI) and machine learning approaches give us powerful new tools in helping us to tackle these challenges, and we review possible solutions and examples of best practice. However, their limitations also need to be considered, as well as the need for coordinated multidisciplinary research and diverse deeply phenotyped cohorts. Ultimately AI approaches improve our ability to interrogate genetics and omics data for precision dementia medicine. HIGHLIGHTS: We have identified five key challenges in dementia genetics and omics studies. AI can enable detection of undiscovered patterns in dementia genetics and omics data. Enhanced and more diverse genetics and omics datasets are still needed. Multidisciplinary collaborative efforts using AI can boost dementia research.
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Affiliation(s)
- Conceicao Bettencourt
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Nathan Skene
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Emma Anderson
- Department of Mental Health of Older People, Division of Psychiatry, University College London, London, UK
| | | | - Isabelle F Foote
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jeremy Schwartzentruber
- Open Targets, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, California, USA
| | - Juan A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Mike Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Andrew Singleton
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian M Schilder
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Christina E Toomey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Ahmad Al Kleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Eric L Harshfield
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Victoria Garfield
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Cynthia Sandor
- UK Dementia Research Institute. School of Medicine, Cardiff University, Cardiff, UK
| | - Samuel Keat
- UK Dementia Research Institute. School of Medicine, Cardiff University, Cardiff, UK
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, Neurology Section, University of Verona, Verona, Italy
| | - Carlo Sala Frigerio
- UK Dementia Research Institute, Queen Square Institute of Neurology, University College London, London, UK
| | | | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- The Alan Turing Institute, London, UK
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10
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Vicidomini C, Borbone N, Roviello V, Roviello GN, Oliviero G. Summary of the Current Status of DNA Vaccination for Alzheimer Disease. Vaccines (Basel) 2023; 11:1706. [PMID: 38006038 PMCID: PMC10674988 DOI: 10.3390/vaccines11111706] [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: 10/08/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Alzheimer disease (AD) is one of the most common and disabling neuropathies in the ever-growing aged population around the world, that especially affects Western countries. We are in urgent need of finding an effective therapy but also a valid prophylactic means of preventing AD. There is a growing attention currently paid to DNA vaccination, a technology particularly used during the COVID-19 era, which can be used also to potentially prevent or modify the course of neurological diseases, including AD. This paper aims to discuss the main features and hurdles encountered in the immunization and therapy against AD using DNA vaccine technology. Ultimately, this work aims to effectively promote the efforts in research for the development of safe and effective DNA and RNA vaccines for AD.
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Affiliation(s)
- Caterina Vicidomini
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Valentina Roviello
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via Tommaso De Amicis 95, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
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11
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Aslam MM, Fan KH, Lawrence E, Bedison MA, Snitz BE, DeKosky ST, Lopez OL, Feingold E, Kamboh MI. Genome-wide analysis identifies novel loci influencing plasma apolipoprotein E concentration and Alzheimer's disease risk. Mol Psychiatry 2023; 28:4451-4462. [PMID: 37666928 PMCID: PMC10827653 DOI: 10.1038/s41380-023-02170-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 09/06/2023]
Abstract
The APOE 2/3/4 polymorphism is the greatest genetic risk factor for Alzheimer's disease (AD). This polymorphism is also associated with variation in plasma ApoE level; while APOE*4 lowers, APOE*2 increases ApoE level. Lower plasma ApoE level has also been suggested to be a risk factor for incident dementia. To our knowledge, no large genome-wide association study (GWAS) has been reported on plasma ApoE level. This study aimed to identify new genetic variants affecting plasma ApoE level as well as to test if baseline ApoE level is associated with cognitive function and incident dementia in a longitudinally followed cohort of the Ginkgo Evaluation of Memory (GEM) study. Baseline plasma ApoE concentration was measured in 3031 participants (95.4% European Americans (EAs)). GWAS analysis was performed on 2580 self-identified EAs where both genotype and plasma ApoE data were available. Lower ApoE concentration was associated with worse cognitive function, but not with incident dementia. As expected, the risk for AD increased from E2/2 through to E4/4 genotypes (P for trend = 4.8E-75). In addition to confirming the expected and opposite associations of APOE*2 (P = 4.73E-79) and APOE*4 (P = 8.73E-12) with ApoE level, GWAS analysis revealed nine additional independent signals in the APOE region, and together they explained about 22% of the variance in plasma ApoE level. We also identified seven new loci on chromosomes 1, 4, 5, 7, 11, 12 and 20 (P range = 5.49E-08 to 5.36E-10) that explained about 9% of the variance in ApoE level. Plasma ApoE level-associated independent variants, especially in the APOE region, were also associated with AD risk and amyloid deposition in the brain, indicating that genetically determined ApoE level variation may be a risk factor for developing AD. These results improve our understanding of the genetic determinants of plasma ApoE level and their potential value in affecting AD risk.
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Affiliation(s)
- M Muaaz Aslam
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kang-Hsien Fan
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elizabeth Lawrence
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Margaret Anne Bedison
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Beth E Snitz
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven T DeKosky
- McKnight Brain Institute and Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oscar L Lopez
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleanor Feingold
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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12
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Escott‐Price V, Schmidt KM. Pitfalls of predicting age-related traits by polygenic risk scores. Ann Hum Genet 2023; 87:203-209. [PMID: 37416935 PMCID: PMC10952323 DOI: 10.1111/ahg.12520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Polygenic risk scores (PRS) are a method increasingly used to capture the combined effect of genome-wide significant variants and those which individually do not show genome-wide significant association but are likely to contribute to the risk of developing diseases. However, their practical use incurs complications and inconsistencies that so far limit their clinical applicability. The aims of the present review are to discuss the PRS for age-related diseases and to highlight pitfalls and limitations of PRS prediction accuracy due to ageing and mortality effects. We argue that the PRS is widely used but the individual's PRS values differ substantially depending on the number of genetic variants included, the discovery GWAS and the method employed to generate them. Moreover, for neurodegenerative disorders, although an individual's genetics do not change with age, the actual score depends on the age of the sample used in the discovery GWAS and is likely to reflect the individual's disease risk at this particular age. Improvement of PRS prediction accuracy for neurodegenerative disorders will come from two sides, both the precision of clinical diagnoses, and a careful attention to the age distribution in the underlying samples and validation of the prediction in longitudinal studies.
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Affiliation(s)
- Valentina Escott‐Price
- Centre for Neuropsychiatric Genetics and GenomicsSchool of Medicine, Cardiff UniversityCardiffUK
- UK Dementia Research InstituteCardiff UniversityCardiffUK
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13
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Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer's Disease in individuals of African ancestry. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.29.23294774. [PMID: 37693582 PMCID: PMC10491365 DOI: 10.1101/2023.08.29.23294774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Despite a two-fold increased risk, individuals of African ancestry have been significantly underrepresented in Alzheimer's Disease (AD) genomics efforts. METHODS GWAS of 2,903 AD cases and 6,265 cognitive controls of African ancestry. Within-dataset results were meta-analyzed, followed by gene-based and pathway analyses, and analysis of RNAseq and whole-genome sequencing data. RESULTS A novel AD risk locus was identified in MPDZ on chromosome 9p23 (rs141610415, MAF=.002, P =3.68×10 -9 ). Two additional novel common and nine novel rare loci approached genome-wide significance at P <9×10 -7 . Comparison of association and LD patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 ( ASCL1 ), suggesting that the association is modulated by regional origin of local African ancestry. DISCUSSION Increased sample sizes and sample sets from Africa covering as much African genetic diversity as possible will be critical to identify additional disease-associated loci and improve deconvolution of local genetic ancestry effects.
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14
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Kang M, Ang TFA, Devine SA, Sherva R, Mukherjee S, Trittschuh EH, Gibbons LE, Scollard P, Lee M, Choi SE, Klinedinst B, Nakano C, Dumitrescu LC, Durant A, Hohman TJ, Cuccaro ML, Saykin AJ, Kukull WA, Bennett DA, Wang LS, Mayeux RP, Haines JL, Pericak-Vance MA, Schellenberg GD, Crane PK, Au R, Lunetta KL, Mez JB, Farrer LA. A genome-wide search for pleiotropy in more than 100,000 harmonized longitudinal cognitive domain scores. Mol Neurodegener 2023; 18:40. [PMID: 37349795 PMCID: PMC10286470 DOI: 10.1186/s13024-023-00633-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND More than 75 common variant loci account for only a portion of the heritability for Alzheimer's disease (AD). A more complete understanding of the genetic basis of AD can be deduced by exploring associations with AD-related endophenotypes. METHODS We conducted genome-wide scans for cognitive domain performance using harmonized and co-calibrated scores derived by confirmatory factor analyses for executive function, language, and memory. We analyzed 103,796 longitudinal observations from 23,066 members of community-based (FHS, ACT, and ROSMAP) and clinic-based (ADRCs and ADNI) cohorts using generalized linear mixed models including terms for SNP, age, SNP × age interaction, sex, education, and five ancestry principal components. Significance was determined based on a joint test of the SNP's main effect and interaction with age. Results across datasets were combined using inverse-variance meta-analysis. Genome-wide tests of pleiotropy for each domain pair as the outcome were performed using PLACO software. RESULTS Individual domain and pleiotropy analyses revealed genome-wide significant (GWS) associations with five established loci for AD and AD-related disorders (BIN1, CR1, GRN, MS4A6A, and APOE) and eight novel loci. ULK2 was associated with executive function in the community-based cohorts (rs157405, P = 2.19 × 10-9). GWS associations for language were identified with CDK14 in the clinic-based cohorts (rs705353, P = 1.73 × 10-8) and LINC02712 in the total sample (rs145012974, P = 3.66 × 10-8). GRN (rs5848, P = 4.21 × 10-8) and PURG (rs117523305, P = 1.73 × 10-8) were associated with memory in the total and community-based cohorts, respectively. GWS pleiotropy was observed for language and memory with LOC107984373 (rs73005629, P = 3.12 × 10-8) in the clinic-based cohorts, and with NCALD (rs56162098, P = 1.23 × 10-9) and PTPRD (rs145989094, P = 8.34 × 10-9) in the community-based cohorts. GWS pleiotropy was also found for executive function and memory with OSGIN1 (rs12447050, P = 4.09 × 10-8) and PTPRD (rs145989094, P = 3.85 × 10-8) in the community-based cohorts. Functional studies have previously linked AD to ULK2, NCALD, and PTPRD. CONCLUSION Our results provide some insight into biological pathways underlying processes leading to domain-specific cognitive impairment and AD, as well as a conduit toward a syndrome-specific precision medicine approach to AD. Increasing the number of participants with harmonized cognitive domain scores will enhance the discovery of additional genetic factors of cognitive decline leading to AD and related dementias.
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Affiliation(s)
- Moonil Kang
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
| | - Ting Fang Alvin Ang
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Sherral A. Devine
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
| | - Shubhabrata Mukherjee
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Emily H. Trittschuh
- Geriatric Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA USA
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Laura E. Gibbons
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Phoebe Scollard
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Michael Lee
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Seo-Eun Choi
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Brandon Klinedinst
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Connie Nakano
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Logan C. Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Alaina Durant
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, Miami, FL USA
| | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Services, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Walter A. Kukull
- Department of Epidemiology, University of Washington, Seattle, WA USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Richard P. Mayeux
- Department of Neurology, Columbia University School of Medicine, New York, NY USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH USA
| | | | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Paul K. Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Rhoda Au
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Slone Epidemiology Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA USA
| | - Kathryn L. Lunetta
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Jesse B. Mez
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street E200, Boston, MA 02118 USA
- Framingham Heart Study, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Boston University Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
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15
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Timsina J, Ali M, Do A, Wang L, Sung YJ, Cruchaga C. Harmonization of CSF and imaging biomarkers for Alzheimer's disease biomarkers: need and practical applications for genetics studies and preclinical classification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542118. [PMID: 37292823 PMCID: PMC10245826 DOI: 10.1101/2023.05.24.542118] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
INTRODUCTION In Alzheimer's disease (AD) research, cerebrospinal fluid (CSF) Amyloid beta (Aβ), Tau and pTau are the most accepted and well validated biomarkers. Several methods and platforms exist to measure those biomarkers which leads to challenges in combining data across studies. Thus, there is a need to identify methods that harmonize and standardize these values. METHODS We used a Z-score based approach to harmonize CSF and amyloid imaging data from multiple cohorts and compared GWAS result using this method with currently accepted methods. We also used a generalized mixture modelling to calculate the threshold for biomarker-positivity. RESULTS Z-scores method performed as well as meta-analysis and did not lead to any spurious results. Cutoffs calculated with this approach were found to be very similar to those reported previously. DISCUSSION This approach can be applied to heterogeneous platforms and provides biomarker cut-offs consistent with the classical approaches without requiring any additional data.
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Affiliation(s)
- Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anh Do
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
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16
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Seyedsalehi A, Warrier V, Bethlehem RAI, Perry BI, Burgess S, Murray GK. Educational attainment, structural brain reserve and Alzheimer's disease: a Mendelian randomization analysis. Brain 2023; 146:2059-2074. [PMID: 36310536 PMCID: PMC10151197 DOI: 10.1093/brain/awac392] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 11/13/2022] Open
Abstract
Higher educational attainment is observationally associated with lower risk of Alzheimer's disease. However, the biological mechanisms underpinning this association remain unclear. The protective effect of education on Alzheimer's disease may be mediated via increased brain reserve. We used two-sample Mendelian randomization to explore putative causal relationships between educational attainment, structural brain reserve as proxied by MRI phenotypes and Alzheimer's disease. Summary statistics were obtained from genome-wide association studies of educational attainment (n = 1 131 881), late-onset Alzheimer's disease (35 274 cases, 59 163 controls) and 15 measures of grey or white matter macro- or micro-structure derived from structural or diffusion MRI (nmax = 33 211). We conducted univariable Mendelian randomization analyses to investigate bidirectional associations between (i) educational attainment and Alzheimer's disease; (ii) educational attainment and imaging-derived phenotypes; and (iii) imaging-derived phenotypes and Alzheimer's disease. Multivariable Mendelian randomization was used to assess whether brain structure phenotypes mediated the effect of education on Alzheimer's disease risk. Genetically proxied educational attainment was inversely associated with Alzheimer's disease (odds ratio per standard deviation increase in genetically predicted years of schooling = 0.70, 95% confidence interval 0.60, 0.80). There were positive associations between genetically predicted educational attainment and four cortical metrics (standard deviation units change in imaging phenotype per one standard deviation increase in genetically predicted years of schooling): surface area 0.30 (95% confidence interval 0.20, 0.40); volume 0.29 (95% confidence interval 0.20, 0.37); intrinsic curvature 0.18 (95% confidence interval 0.11, 0.25); local gyrification index 0.21 (95% confidence interval 0.11, 0.31)]; and inverse associations with cortical intracellular volume fraction [-0.09 (95% confidence interval -0.15, -0.03)] and white matter hyperintensities volume [-0.14 (95% confidence interval -0.23, -0.05)]. Genetically proxied levels of surface area, cortical volume and intrinsic curvature were positively associated with educational attainment [standard deviation units change in years of schooling per one standard deviation increase in respective genetically predicted imaging phenotype: 0.13 (95% confidence interval 0.10, 0.16); 0.15 (95% confidence interval 0.11, 0.19) and 0.12 (95% confidence interval 0.04, 0.19)]. We found no evidence of associations between genetically predicted imaging-derived phenotypes and Alzheimer's disease. The inverse association of genetically predicted educational attainment with Alzheimer's disease did not attenuate after adjusting for imaging-derived phenotypes in multivariable analyses. Our results provide support for a protective causal effect of educational attainment on Alzheimer's disease risk, as well as potential bidirectional causal relationships between education and brain macro- and micro-structure. However, we did not find evidence that these structural markers affect risk of Alzheimer's disease. The protective effect of education on Alzheimer's disease may be mediated via other measures of brain reserve not included in the present study, or by alternative mechanisms.
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Affiliation(s)
- Aida Seyedsalehi
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0SR, UK
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford OX3 7JX, UK
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Richard A I Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Benjamin I Perry
- Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- CAMEO, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge CB4 1PX, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 0BB, UK
| | - Graham K Murray
- Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- CAMEO, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge CB4 1PX, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
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17
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Ali M, Archer DB, Gorijala P, Western D, Timsina J, Fernández MV, Wang TC, Satizabal CL, Yang Q, Beiser AS, Wang R, Chen G, Gordon B, Benzinger TLS, Xiong C, Morris JC, Bateman RJ, Karch CM, McDade E, Goate A, Seshadri S, Mayeux RP, Sperling RA, Buckley RF, Johnson KA, Won HH, Jung SH, Kim HR, Seo SW, Kim HJ, Mormino E, Laws SM, Fan KH, Kamboh MI, Vemuri P, Ramanan VK, Yang HS, Wenzel A, Rajula HSR, Mishra A, Dufouil C, Debette S, Lopez OL, DeKosky ST, Tao F, Nagle MW, Hohman TJ, Sung YJ, Dumitrescu L, Cruchaga C. Large multi-ethnic genetic analyses of amyloid imaging identify new genes for Alzheimer disease. Acta Neuropathol Commun 2023; 11:68. [PMID: 37101235 PMCID: PMC10134547 DOI: 10.1186/s40478-023-01563-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
Amyloid PET imaging has been crucial for detecting the accumulation of amyloid beta (Aβ) deposits in the brain and to study Alzheimer's disease (AD). We performed a genome-wide association study on the largest collection of amyloid imaging data (N = 13,409) to date, across multiple ethnicities from multicenter cohorts to identify variants associated with brain amyloidosis and AD risk. We found a strong APOE signal on chr19q.13.32 (top SNP: APOE ɛ4; rs429358; β = 0.35, SE = 0.01, P = 6.2 × 10-311, MAF = 0.19), driven by APOE ɛ4, and five additional novel associations (APOE ε2/rs7412; rs73052335/rs5117, rs1081105, rs438811, and rs4420638) independent of APOE ɛ4. APOE ɛ4 and ε2 showed race specific effect with stronger association in Non-Hispanic Whites, with the lowest association in Asians. Besides the APOE, we also identified three other genome-wide loci: ABCA7 (rs12151021/chr19p.13.3; β = 0.07, SE = 0.01, P = 9.2 × 10-09, MAF = 0.32), CR1 (rs6656401/chr1q.32.2; β = 0.1, SE = 0.02, P = 2.4 × 10-10, MAF = 0.18) and FERMT2 locus (rs117834516/chr14q.22.1; β = 0.16, SE = 0.03, P = 1.1 × 10-09, MAF = 0.06) that all colocalized with AD risk. Sex-stratified analyses identified two novel female-specific signals on chr5p.14.1 (rs529007143, β = 0.79, SE = 0.14, P = 1.4 × 10-08, MAF = 0.006, sex-interaction P = 9.8 × 10-07) and chr11p.15.2 (rs192346166, β = 0.94, SE = 0.17, P = 3.7 × 10-08, MAF = 0.004, sex-interaction P = 1.3 × 10-03). We also demonstrated that the overall genetic architecture of brain amyloidosis overlaps with that of AD, Frontotemporal Dementia, stroke, and brain structure-related complex human traits. Overall, our results have important implications when estimating the individual risk to a population level, as race and sex will needed to be taken into account. This may affect participant selection for future clinical trials and therapies.
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Affiliation(s)
- Muhammad Ali
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Derek B Archer
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Daniel Western
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Maria V Fernández
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Ting-Chen Wang
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health, San Antonio, TX, 78229, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alexa S Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Gengsheng Chen
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
- Mallinckrodt Institute of Radiology, Washington University, St Louis, MO, USA
| | - Brian Gordon
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
- Mallinckrodt Institute of Radiology, Washington University, St Louis, MO, USA
| | - Tammie L S Benzinger
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
- Mallinckrodt Institute of Radiology, Washington University, St Louis, MO, USA
| | - Chengjie Xiong
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
| | - John C Morris
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
- Department of Neurology, Washington University, St Louis, MO, USA
| | - Randall J Bateman
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA
- Department of Neurology, Washington University, St Louis, MO, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
| | - Eric McDade
- Department of Neurology, Washington University, St Louis, MO, USA
| | - Alison Goate
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Richard P Mayeux
- The Department of Neurology, Columbia University, New York, NY, USA
| | - Reisa A Sperling
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital and Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rachel F Buckley
- Brigham and Women's Hospital and Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, MA, USA
| | - Keith A Johnson
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hong-Hee Won
- Department of Digital Health, Samsung Medical Center, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Digital Health, Samsung Medical Center, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hang-Rai Kim
- Department of Neurology, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Republic of Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jin Kim
- Department of Digital Health, Samsung Medical Center, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Kang-Hsien Fan
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Prashanthi Vemuri
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Vijay K Ramanan
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Hyun-Sik Yang
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Allen Wenzel
- Wisconsin Alzheimer's Institute, Madison, WI, USA
| | - Hema Sekhar Reddy Rajula
- UMR 1219, University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, 33000, Bordeaux, France
| | - Aniket Mishra
- UMR 1219, University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, 33000, Bordeaux, France
| | - Carole Dufouil
- UMR 1219, University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, 33000, Bordeaux, France
| | - Stephanie Debette
- UMR 1219, University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, 33000, Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, MA, 2115, USA
- Department of Neurology, CHU de Bordeaux, 33000, Bordeaux, France
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven T DeKosky
- Department of Neurology and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Feifei Tao
- Neurogenomics, Genetics-Guided Dementia Discovery, Eisai, Inc, Cambridge, MA, USA
| | - Michael W Nagle
- Neurogenomics, Genetics-Guided Dementia Discovery, Eisai, Inc, Cambridge, MA, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, 63110, USA.
- NeuroGenomics and Informatics, Washington University, St. Louis, MO, 63110, USA.
- Knight Alzheimer's Disease Research Center, Washington University, St Louis, MO, USA.
- Hope Center for Neurologic Diseases, Washington University, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, USA.
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18
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Barrio-Alonso E, Lituma PJ, Notaras MJ, Albero R, Bouchekioua Y, Wayland N, Stankovic IN, Jain T, Gao S, Calderon DP, Castillo PE, Colak D. Circadian protein TIMELESS regulates synaptic function and memory by modulating cAMP signaling. Cell Rep 2023; 42:112375. [PMID: 37043347 PMCID: PMC10564971 DOI: 10.1016/j.celrep.2023.112375] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
The regulation of neurons by circadian clock genes is thought to contribute to the maintenance of neuronal functions that ultimately underlie animal behavior. However, the impact of specific circadian genes on cellular and molecular mechanisms controlling synaptic plasticity and cognitive function remains elusive. Here, we show that the expression of the circadian protein TIMELESS displays circadian rhythmicity in the mammalian hippocampus. We identify TIMELESS as a chromatin-bound protein that targets synaptic-plasticity-related genes such as phosphodiesterase 4B (Pde4b). By promoting Pde4b transcription, TIMELESS negatively regulates cAMP signaling to modulate AMPA receptor GluA1 function and influence synaptic plasticity. Conditional deletion of Timeless in the adult forebrain impairs working and contextual fear memory in mice. These cognitive phenotypes were accompanied by attenuation of hippocampal Schaffer-collateral synapse long-term potentiation. Together, these data establish a neuron-specific function of mammalian TIMELESS by defining a mechanism that regulates synaptic plasticity and cognitive function.
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Affiliation(s)
- Estibaliz Barrio-Alonso
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Pablo J Lituma
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Michael J Notaras
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Robert Albero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Youcef Bouchekioua
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Natalie Wayland
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Isidora N Stankovic
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Tanya Jain
- Program of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Sijia Gao
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | | | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dilek Colak
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York, NY, USA; Gale & Ira Drukier Institute for Children's Health, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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19
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Andrews SJ, Renton AE, Fulton-Howard B, Podlesny-Drabiniok A, Marcora E, Goate AM. The complex genetic architecture of Alzheimer's disease: novel insights and future directions. EBioMedicine 2023; 90:104511. [PMID: 36907103 PMCID: PMC10024184 DOI: 10.1016/j.ebiom.2023.104511] [Citation(s) in RCA: 83] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a complex multifactorial neurodegenerative disorder and the most common form of dementia. AD is highly heritable, with heritability estimates of ∼70% from twin studies. Progressively larger genome-wide association studies (GWAS) have continued to expand our knowledge of AD/dementia genetic architecture. Until recently these efforts had identified 39 disease susceptibility loci in European ancestry populations. RECENT DEVELOPMENTS Two new AD/dementia GWAS have dramatically expanded the sample sizes and the number of disease susceptibility loci. The first increased total sample size to 1,126,563-with an effective sample size of 332,376-by predominantly including new biobank and population-based dementia datasets. The second, expands on an earlier GWAS from the International Genomics of Alzheimer's Project (IGAP) by increasing the number of clinically-defined AD cases/controls in addition to incorporating biobank dementia datasets, resulting in a total sample size to 788,989 and an effective sample size of 382,472. Collectively both GWAS identified 90 independent variants across 75 AD/dementia susceptibility loci, including 42 novel loci. Pathway analyses indicate the susceptibility loci are enriched for genes involved in amyloid plaque and neurofibrillary tangle formation, cholesterol metabolism, endocytosis/phagocytosis, and the innate immune system. Gene prioritization efforts for the novel loci identified 62 candidate causal genes. Many of the candidate genes from known and newly discovered loci play key roles in macrophages and highlight phagocytic clearance of cholesterol-rich brain tissue debris by microglia (efferocytosis) as a core pathogenetic hub and putative therapeutic target for AD. WHERE NEXT?: While GWAS in European ancestry populations have substantially enhanced our understanding of AD genetic architecture, heritability estimates from population based GWAS cohorts are markedly smaller than those from twin studies. While this missing heritability is likely due to a combination of factors, it highlights that our understanding of AD genetic architecture and genetic risk mechanisms remains incomplete. These knowledge gaps result from several underexplored areas in AD research. First, rare variants remain understudied due to methodological issues in identifying them and the cost of generating sufficiently powered whole exome/genome sequencing datasets. Second, sample sizes of non-European ancestry populations in AD GWAS remain small. Third, GWAS of AD neuroimaging and cerebrospinal fluid endophenotypes remains limited due to low compliance and high costs associated with measuring amyloid-β and tau levels and other disease-relevant biomarkers. Studies generating sequencing data, including diverse populations, and incorporating blood-based AD biomarkers are set to substantially improve our knowledge of AD genetic architecture.
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Affiliation(s)
- Shea J Andrews
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA.
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna Podlesny-Drabiniok
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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20
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Zhang X, Hao Y, Zhang J, Ji Y, Zou S, Zhao S, Xie S, Du L. A multi-task SCCA method for brain imaging genetics and its application in neurodegenerative diseases. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 232:107450. [PMID: 36905750 DOI: 10.1016/j.cmpb.2023.107450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND OBJECTIVES In brain imaging genetics, multi-task sparse canonical correlation analysis (MTSCCA) is effective to study the bi-multivariate associations between genetic variations such as single nucleotide polymorphisms (SNPs) and multi-modal imaging quantitative traits (QTs). However, most existing MTSCCA methods are neither supervised nor capable of distinguishing the shared patterns of multi-modal imaging QTs from the specific patterns. METHODS A new diagnosis-guided MTSCCA (DDG-MTSCCA) with parameter decomposition and graph-guided pairwise group lasso penalty was proposed. Specifically, the multi-tasking modeling paradigm enables us to comprehensively identify risk genetic loci by jointly incorporating multi-modal imaging QTs. The regression sub-task was raised to guide the selection of diagnosis-related imaging QTs. To reveal the diverse genetic mechanisms, the parameter decomposition and different constraints were utilized to facilitate the identification of modality-consistent and -specific genotypic variations. Besides, a network constraint was added to find out meaningful brain networks. The proposed method was applied to synthetic data and two real neuroimaging data sets respectively from Alzheimer's disease neuroimaging initiative (ADNI) and Parkinson's progression marker initiative (PPMI) databases. RESULTS Compared with the competitive methods, the proposed method exhibited higher or comparable canonical correlation coefficients (CCCs) and better feature selection results. In particular, in the simulation study, DDG-MTSCCA showed the best anti-noise ability and achieved the highest average hit rate, about 25% higher than MTSCCA. On the real data of Alzheimer's disease (AD) and Parkinson's disease (PD), our method obtained the highest average testing CCCs, about 40% ∼ 50% higher than MTSCCA. Especially, our method could select more comprehensive feature subsets, and the top five SNPs and imaging QTs were all disease-related. The ablation experimental results also demonstrated the significance of each component in the model, i.e., the diagnosis guidance, parameter decomposition, and network constraint. CONCLUSIONS These results on simulated data, ADNI and PPMI cohorts suggested the effectiveness and generalizability of our method in identifying meaningful disease-related markers. DDG-MTSCCA could be a powerful tool in brain imaging genetics, worthy of in-depth study.
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Affiliation(s)
- Xin Zhang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Yipeng Hao
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Jin Zhang
- School of Automation, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Yanuo Ji
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Shihong Zou
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Shijie Zhao
- School of Automation, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Songyun Xie
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China
| | - Lei Du
- School of Automation, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China.
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Nho K, Risacher SL, Apostolova L, Bice PJ, Brosch J, Deardorff R, Faber K, Farlow MR, Foroud T, Gao S, Rosewood T, Kim JP, Nudelman K, Yu M, Aisen P, Sperling R, Hooli B, Shcherbinin S, Svaldi D, Jack CR, Jagust WJ, Landau S, Vasanthakumar A, Waring JF, Doré V, Laws SM, Masters CL, Porter T, Rowe CC, Villemagne VL, Dumitrescu L, Hohman TJ, Libby JB, Mormino E, Buckley RF, Johnson K, Yang HS, Petersen RC, Ramanan VK, Vemuri P, Cohen AD, Fan KH, Kamboh MI, Lopez OL, Bennett DA, Ali M, Benzinger T, Cruchaga C, Hobbs D, De Jager PL, Fujita M, Jadhav V, Lamb BT, Tsai AP, Castanho I, Mill J, Weiner MW, Saykin AJ. Novel CYP1B1-RMDN2 Alzheimer's disease locus identified by genome-wide association analysis of cerebral tau deposition on PET. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23286048. [PMID: 36993271 PMCID: PMC10055458 DOI: 10.1101/2023.02.27.23286048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aβ positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aβ. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.
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22
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Oatman SR, Reddy JS, Quicksall Z, Carrasquillo MM, Wang X, Liu CC, Yamazaki Y, Nguyen TT, Malphrus K, Heckman M, Biswas K, Nho K, Baker M, Martens YA, Zhao N, Kim JP, Risacher SL, Rademakers R, Saykin AJ, DeTure M, Murray ME, Kanekiyo T, Dickson DW, Bu G, Allen M, Ertekin-Taner N. Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins. Mol Neurodegener 2023; 18:2. [PMID: 36609403 PMCID: PMC9825010 DOI: 10.1186/s13024-022-00592-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is neuropathologically characterized by amyloid-beta (Aβ) plaques and neurofibrillary tangles. The main protein components of these hallmarks include Aβ40, Aβ42, tau, phosphor-tau, and APOE. We hypothesize that genetic variants influence the levels and solubility of these AD-related proteins in the brain; identifying these may provide key insights into disease pathogenesis. METHODS Genome-wide genotypes were collected from 441 AD cases, imputed to the haplotype reference consortium (HRC) panel, and filtered for quality and frequency. Temporal cortex levels of five AD-related proteins from three fractions, buffer-soluble (TBS), detergent-soluble (Triton-X = TX), and insoluble (Formic acid = FA), were available for these same individuals. Variants were tested for association with each quantitative biochemical measure using linear regression, and GSA-SNP2 was used to identify enriched Gene Ontology (GO) terms. Implicated variants and genes were further assessed for association with other relevant variables. RESULTS We identified genome-wide significant associations at seven novel loci and the APOE locus. Genes and variants at these loci also associate with multiple AD-related measures, regulate gene expression, have cell-type specific enrichment, and roles in brain health and other neuropsychiatric diseases. Pathway analysis identified significant enrichment of shared and distinct biological pathways. CONCLUSIONS Although all biochemical measures tested reflect proteins core to AD pathology, our results strongly suggest that each have unique genetic architecture and biological pathways that influence their specific biochemical states in the brain. Our novel approach of deep brain biochemical endophenotype GWAS has implications for pathophysiology of proteostasis in AD that can guide therapeutic discovery efforts focused on these proteins.
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Affiliation(s)
- Stephanie R. Oatman
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | | | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Thuy T. Nguyen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kimberly Malphrus
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Michael Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Kristi Biswas
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kwangsik Nho
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
| | - Matthew Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yuka A. Martens
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Jun Pyo Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Shannon L. Risacher
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Saykin
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
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23
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Kim HR, Jung SH, Kim B, Kim J, Jang H, Kim JP, Kim SY, Na DL, Kim HJ, Nho K, Won HH, Seo SW. Identifying genetic variants for amyloid β in subcortical vascular cognitive impairment. Front Aging Neurosci 2023; 15:1160536. [PMID: 37143691 PMCID: PMC10151714 DOI: 10.3389/fnagi.2023.1160536] [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: 02/07/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Background The genetic basis of amyloid β (Aβ) deposition in subcortical vascular cognitive impairment (SVCI) is still unknown. Here, we investigated genetic variants involved in Aβ deposition in patients with SVCI. Methods We recruited a total of 110 patients with SVCI and 424 patients with Alzheimer's disease-related cognitive impairment (ADCI), who underwent Aβ positron emission tomography and genetic testing. Using candidate AD-associated single nucleotide polymorphisms (SNPs) that were previously identified, we investigated Aβ-associated SNPs that were shared or distinct between patients with SVCI and those with ADCI. Replication analyses were performed using the Alzheimer's Disease Neuroimaging Initiative (ADNI) and Religious Orders Study and Rush Memory and Aging Project cohorts (ROS/MAP). Results We identified a novel SNP, rs4732728, which showed distinct associations with Aβ positivity in patients with SVCI (P interaction = 1.49 × 10-5); rs4732728 was associated with increased Aβ positivity in SVCI but decreased Aβ positivity in ADCI. This pattern was also observed in ADNI and ROS/MAP cohorts. Prediction performance for Aβ positivity in patients with SVCI increased (area under the receiver operating characteristic curve = 0.780; 95% confidence interval = 0.757-0.803) when rs4732728 was included. Cis-expression quantitative trait loci analysis demonstrated that rs4732728 was associated with EPHX2 expression in the brain (normalized effect size = -0.182, P = 0.005). Conclusion The novel genetic variants associated with EPHX2 showed a distinct effect on Aβ deposition between SVCI and ADCI. This finding may provide a potential pre-screening marker for Aβ positivity and a candidate therapeutic target for SVCI.
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Affiliation(s)
- Hang-Rai Kim
- Department of Neurology, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Beomsu Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Jaeho Kim
- Department of Neurology, Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Republic of Korea
| | - Hyemin Jang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Jun Pyo Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, United States
| | - So Yeon Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Artificial Intelligence, Ajou University, Suwon, Republic of Korea
- Department of Software and Computer Engineering, Ajou University, Suwon, Republic of Korea
| | - Duk L. Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Cell and Gene Therapy Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Hee Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Hong-Hee Won
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Hong-Hee Won,
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Seoul, Republic of Korea
- Hong-Hee Won,
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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Ciobanu LG, Stankov L, Schubert KO, Amare AT, Jawahar MC, Lawrence-Wood E, Mills NT, Knight M, Clark SR, Aidman E. General intelligence and executive functioning are overlapping but separable at genetic and molecular pathway levels: An analytical review of existing GWAS findings. PLoS One 2022; 17:e0272368. [PMID: 36251633 PMCID: PMC9576059 DOI: 10.1371/journal.pone.0272368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022] Open
Abstract
Understanding the genomic architecture and molecular mechanisms of cognitive functioning in healthy individuals is critical for developing tailored interventions to enhance cognitive functioning, as well as for identifying targets for treating impaired cognition. There has been substantial progress in uncovering the genetic composition of the general cognitive ability (g). However, there is an ongoing debate whether executive functioning (EF)–another key predictor of cognitive health and performance, is separable from general g. To provide an analytical review on existing findings on genetic influences on the relationship between g and EF, we re-analysed a subset of genome-wide association studies (GWAS) from the GWAS catalogue that used measures of g and EF as outcomes in non-clinical populations. We identified two sets of single nucleotide polymorphisms (SNPs) associated with g (1,372 SNPs across 12 studies), and EF (300 SNPs across 5 studies) at p<5x10-6. A comparative analysis of GWAS-identified g and EF SNPs in high linkage disequilibrium (LD), followed by pathway enrichment analyses suggest that g and EF are overlapping but separable at genetic variant and molecular pathway levels, however more evidence is required to characterize the genetic overlap/distinction between the two constructs. While not without limitations, these findings may have implications for navigating further research towards translatable genetic findings for cognitive remediation, enhancement, and augmentation.
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Affiliation(s)
- Liliana G. Ciobanu
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
- * E-mail:
| | - Lazar Stankov
- School of Psychology, The University of Sydney, Sydney, NSW, Australia
| | - K. Oliver Schubert
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
- Northern Adelaide Mental Health Services, Adelaide, SA, Australia
| | - Azmeraw T. Amare
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
- National Health and Medical Research Council (NHMRC) Centre of Research Excellence in Frailty and Healthy Ageing, University of Adelaide, Adelaide, Australia
| | | | | | - Natalie T. Mills
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Knight
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
- Weapons and Combat Systems Division, Defence Science & Technology Group, Edinburgh, SA, Australia
| | - Scott R. Clark
- Discipline of Psychiatry, University of Adelaide, Adelaide, SA, Australia
| | - Eugene Aidman
- School of Psychology, The University of Sydney, Sydney, NSW, Australia
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Land Division, Defence Science & Technology Group, Edinburgh, SA, Australia
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Li L, Yu X, Sheng C, Jiang X, Zhang Q, Han Y, Jiang J. A review of brain imaging biomarker genomics in Alzheimer’s disease: implementation and perspectives. Transl Neurodegener 2022; 11:42. [PMID: 36109823 PMCID: PMC9476275 DOI: 10.1186/s40035-022-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease with phenotypic changes closely associated with both genetic variants and imaging pathology. Brain imaging biomarker genomics has been developed in recent years to reveal potential AD pathological mechanisms and provide early diagnoses. This technique integrates multimodal imaging phenotypes with genetic data in a noninvasive and high-throughput manner. In this review, we summarize the basic analytical framework of brain imaging biomarker genomics and elucidate two main implementation scenarios of this technique in AD studies: (1) exploring novel biomarkers and seeking mutual interpretability and (2) providing a diagnosis and prognosis for AD with combined use of machine learning methods and brain imaging biomarker genomics. Importantly, we highlight the necessity of brain imaging biomarker genomics, discuss the strengths and limitations of current methods, and propose directions for development of this research field.
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Foote IF, Jacobs BM, Mathlin G, Watson CJ, Bothongo PLK, Waters S, Dobson R, Noyce AJ, Bhui KS, Korszun A, Marshall CR. The shared genetic architecture of modifiable risk for Alzheimer's disease: a genomic structural equation modelling study. Neurobiol Aging 2022; 117:222-235. [DOI: 10.1016/j.neurobiolaging.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
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Ali M, Sung YJ, Wang F, Fernández MV, Morris JC, Fagan AM, Blennow K, Zetterberg H, Heslegrave A, Johansson PM, Svensson J, Nellgård B, Lleó A, Alcolea D, Clarimon J, Rami L, Molinuevo JL, Suárez-Calvet M, Morenas-Rodríguez E, Kleinberger G, Haass C, Ewers M, Levin J, Farlow MR, Perrin RJ, Cruchaga C. Leveraging large multi-center cohorts of Alzheimer disease endophenotypes to understand the role of Klotho heterozygosity on disease risk. PLoS One 2022; 17:e0267298. [PMID: 35617280 PMCID: PMC9135221 DOI: 10.1371/journal.pone.0267298] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
Two genetic variants in strong linkage disequilibrium (rs9536314 and rs9527025) in the Klotho (KL) gene, encoding a transmembrane protein, implicated in longevity and associated with brain resilience during normal aging, were recently shown to be associated with Alzheimer disease (AD) risk in cognitively normal participants who are APOE ε4 carriers. Specifically, the participants heterozygous for this variant (KL-SVHET+) showed lower risk of developing AD. Furthermore, a neuroprotective effect of KL-VSHET+ has been suggested against amyloid burden for cognitively normal participants, potentially mediated via the regulation of redox pathways. However, inconsistent associations and a smaller sample size of existing studies pose significant hurdles in drawing definitive conclusions. Here, we performed a well-powered association analysis between KL-VSHET+ and five different AD endophenotypes; brain amyloidosis measured by positron emission tomography (PET) scans (n = 5,541) or cerebrospinal fluid Aβ42 levels (CSF; n = 5,093), as well as biomarkers associated with tau pathology: the CSF Tau (n = 5,127), phosphorylated Tau (pTau181; n = 4,778) and inflammation: CSF soluble triggering receptor expressed on myeloid cells 2 (sTREM2; n = 2,123) levels. Our results found nominally significant associations of KL-VSHET+ status with biomarkers for brain amyloidosis (e.g., CSF Aβ positivity; odds ratio [OR] = 0.67 [95% CI, 0.55-0.78], β = 0.72, p = 0.007) and tau pathology (e.g., biomarker positivity for CSF Tau; OR = 0.39 [95% CI, 0.19-0.77], β = -0.94, p = 0.007, and pTau; OR = 0.50 [95% CI, 0.27-0.96], β = -0.68, p = 0.04) in cognitively normal participants, 60-80 years old, who are APOE e4-carriers. Our work supports previous findings, suggesting that the KL-VSHET+ on an APOE ε4 genotype background may modulate Aβ and tau pathology, thereby lowering the intensity of neurodegeneration and incidence of cognitive decline in older controls susceptible to AD.
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Affiliation(s)
- Muhammad Ali
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Maria V. Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Anne M. Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - 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, University of Gothenburg, Sahlgrenska University Hospital, 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, University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, United Kingdom
- UK Dementia Research Institute at UCL, London, United Kingdom
| | - Amanda Heslegrave
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, United Kingdom
- UK Dementia Research Institute at UCL, London, United Kingdom
| | - Per M. Johansson
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, United Kingdom
- UK Dementia Research Institute at UCL, London, United Kingdom
- Department of Anesthesiology and Intensive Care Medicine, Sahlgrenska University Hospital, Mölndal, Sweden
- Institute of Clinical Sciences, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Johan Svensson
- Department of Internal Medicine, Institute of Medicine, The Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Bengt Nellgård
- Department of Internal Medicine, Institute of Medicine, The Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Alberto Lleó
- Neurology Department, Hospital de Sant Pau, Barcelona, Spain
| | - Daniel Alcolea
- Neurology Department, Hospital de Sant Pau, Barcelona, Spain
| | - Jordi Clarimon
- Neurology Department, Hospital de Sant Pau, Barcelona, Spain
| | - Lorena Rami
- IDIBAPS, Alzheimer´s Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
| | - José Luis Molinuevo
- IDIBAPS, Alzheimer´s Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
- Alzheimer´s Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic i Universitari, Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Marc Suárez-Calvet
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Biomedical Center (BMC), Biochemistry, Ludwig‐Maximilians‐Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Estrella Morenas-Rodríguez
- Biomedical Center (BMC), Biochemistry, Ludwig‐Maximilians‐Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gernot Kleinberger
- Biomedical Center (BMC), Biochemistry, Ludwig‐Maximilians‐Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Haass
- Biomedical Center (BMC), Biochemistry, Ludwig‐Maximilians‐Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Michael Ewers
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Levin
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin R. Farlow
- Indiana Alzheimer Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Richard J. Perrin
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | | | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Ragno D, De Risi C, Massi A, Di Carmine G, Toldo S, Leonardi C, Bortolini O. Regiodivergent Synthesis of Benzothiazole‐based Isosorbide Imidates by Oxidative N‐Heterocyclic Carbene Catalysis. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniele Ragno
- University of Ferrara: Universita degli Studi di Ferrara Chemical, Pharmaceutical and Agricultural Sciences ITALY
| | - Carmela De Risi
- University of Ferrara: Universita degli Studi di Ferrara Chemical, Pharmaceutical and Agricultural Sciences ITALY
| | - Alessandro Massi
- University of Ferrara: Universita degli Studi di Ferrara DepartmentEnvironmental and Prevention Sciences ITALY
| | - Graziano Di Carmine
- University of Ferrara: Universita degli Studi di Ferrara Chemical, Pharmaceutical and Agricultural Sciences ITALY
| | - Sofia Toldo
- University of Ferrara: Universita degli Studi di Ferrara Environmental and Prevention Sciences ITALY
| | - Costanza Leonardi
- University of Ferrara: Universita degli Studi di Ferrara Chemical, Pharmaceutical and Agricultural Sciences ITALY
| | - Olga Bortolini
- Universita of Ferrara DepartmentEnvironmental and Prevention Sciences Via Borsari 46 44121 Ferrara ITALY
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30
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Ramanan VK, Heckman MG, Lesnick TG, Przybelski SA, Cahn EJ, Kosel ML, Murray ME, Mielke MM, Botha H, Graff-Radford J, Jones DT, Lowe VJ, Machulda MM, Jack CR, Knopman DS, Petersen RC, Ross OA, Vemuri P. Tau polygenic risk scoring: a cost-effective aid for prognostic counseling in Alzheimer's disease. Acta Neuropathol 2022; 143:571-583. [PMID: 35412102 PMCID: PMC9109940 DOI: 10.1007/s00401-022-02419-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
Abstract
Tau deposition is one of two hallmark features of biologically defined Alzheimer's disease (AD) and is more closely related to cognitive decline than amyloidosis. Further, not all amyloid-positive individuals develop tauopathy, resulting in wide heterogeneity in clinical outcomes across the population with AD. We hypothesized that a polygenic risk score (PRS) based on tau PET (tau PRS) would capture the aggregate inherited susceptibility/resistance architecture influencing tau accumulation, beyond solely the measurement of amyloid-β burden. Leveraging rich multimodal data from a population-based sample of older adults, we found that this novel tau PRS was a strong surrogate of tau PET deposition and captured a significant proportion of the variance in tau PET levels as compared with amyloid PET burden, APOE (apolipoprotein E) ε4 (the most common risk allele for AD), and a non-APOE PRS of clinical case-control AD risk variants. In independent validation samples, the tau PRS was associated with cerebrospinal fluid phosphorylated tau levels in one cohort and with postmortem Braak neurofibrillary tangle stage in another. We also observed an association of the tau PRS with longitudinal cognitive trajectories, including a statistical interaction of the tau PRS with amyloid burden on cognitive decline. Although additional study is warranted, these findings demonstrate the potential utility of a tau PRS for capturing the collective genetic background influencing tau deposition in the general population. In the future, a tau PRS could be leveraged for cost-effective screening and risk stratification to guide trial enrollment and clinical interventions in AD.
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Affiliation(s)
- Vijay K Ramanan
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Michael G Heckman
- Department of Quantitative Health Sciences, Mayo Clinic-Florida, Jacksonville, FL, 32224, USA
| | - Timothy G Lesnick
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Scott A Przybelski
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Elliot J Cahn
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Matthew L Kosel
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic-Florida, Jacksonville, FL, 32224, USA
| | - Michelle M Mielke
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Hugo Botha
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jonathan Graff-Radford
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - David T Jones
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Radiology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - Val J Lowe
- Department of Radiology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mary M Machulda
- Department of Psychiatry and Psychology, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Clifford R Jack
- Department of Radiology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - David S Knopman
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ronald C Petersen
- Department of Neurology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, MN, 55905, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic-Florida, Jacksonville, FL, 32224, USA
- Department of Clinical Genomics, Mayo Clinic-Florida, Jacksonville, FL, 32224, USA
| | - Prashanthi Vemuri
- Department of Neuroscience, Mayo Clinic-Florida, Jacksonville, FL, 32224, USA.
- Department of Radiology, Mayo Clinic-Minnesota, 200 First Street SW, Rochester, MN, 55905, USA.
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31
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Zhao B, Li T, Smith SM, Xiong D, Wang X, Yang Y, Luo T, Zhu Z, Shan Y, Matoba N, Sun Q, Yang Y, Hauberg ME, Bendl J, Fullard JF, Roussos P, Lin W, Li Y, Stein JL, Zhu H. Common variants contribute to intrinsic human brain functional networks. Nat Genet 2022; 54:508-517. [PMID: 35393594 DOI: 10.1038/s41588-022-01039-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/28/2022] [Indexed: 01/01/2023]
Abstract
The human brain forms functional networks of correlated activity, which have been linked with both cognitive and clinical outcomes. However, the genetic variants affecting brain function are largely unknown. Here, we used resting-state functional magnetic resonance images from 47,276 individuals to discover and validate common genetic variants influencing intrinsic brain activity. We identified 45 new genetic regions associated with brain functional signatures (P < 2.8 × 10-11), including associations to the central executive, default mode, and salience networks involved in the triple-network model of psychopathology. A number of brain activity-associated loci colocalized with brain disorders (e.g., the APOE ε4 locus with Alzheimer's disease). Variation in brain function was genetically correlated with brain disorders, such as major depressive disorder and schizophrenia. Together, our study provides a step forward in understanding the genetic architecture of brain functional networks and their genetic links to brain-related complex traits and disorders.
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Affiliation(s)
- Bingxin Zhao
- Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Di Xiong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tianyou Luo
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ziliang Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Shan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nana Matoba
- 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
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mads E Hauberg
- 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.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Jaroslav Bendl
- 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.,Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Fullard
- 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.,Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panagiotis Roussos
- 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.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Weili Lin
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason L Stein
- 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
| | - Hongtu Zhu
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Abstract
Alzheimer's disease (AD) is a complex and multifactorial neurodegenerative disease. Due to its long clinical course and lack of an effective treatment, AD has become a major public health problem in the USA and worldwide. Due to variation in age-at-onset, AD is classified into early-onset (< 60 years) and late-onset (≥ 60 years) forms with early-onset accounting for only 5-10% of all cases. With the exception of a small number of early-onset cases that are afflicted because of high penetrant single gene mutations in APP, PSEN1, and PSEN2 genes, AD is genetically heterogeneous, especially the late-onset form having a polygenic or oligogenic risk inheritance. Since the identification of APOE as the most significant risk factor for late-onset AD in 1993, the path to the discovery of additional AD risk genes had been arduous until 2009 when the use of large genome-wide association studies opened up the discovery gateways that led the identification of ~ 95 additional risk loci from 2009 to early 2022. This article reviews the history of AD genetics followed by the potential molecular pathways and recent application of functional genomics methods to identify the causal AD gene(s) among the many genes that reside within a single locus. The ultimate goal of integrating genomics and functional genomics is to discover novel pathways underlying the AD pathobiology in order to identify drug targets for the therapeutic treatment of this heterogeneous disorder.
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Affiliation(s)
- M Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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Ramanan VK, Heckman MG, Przybelski SA, Lesnick TG, Lowe VJ, Graff-Radford J, Mielke MM, Jack CR, Knopman DS, Petersen RC, Ross OA, Vemuri P. Polygenic Scores of Alzheimer's Disease Risk Genes Add Only Modestly to APOE in Explaining Variation in Amyloid PET Burden. J Alzheimers Dis 2022; 88:1615-1625. [PMID: 35811524 PMCID: PMC9534315 DOI: 10.3233/jad-220164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Brain accumulation of amyloid-β is a hallmark event in Alzheimer's disease (AD) whose underlying mechanisms are incompletely understood. Case-control genome-wide association studies have implicated numerous genetic variants in risk of clinically diagnosed AD dementia. OBJECTIVE To test for associations between case-control AD risk variants and amyloid PET burden in older adults, and to assess whether a polygenic measure encompassing these factors would account for a large proportion of the unexplained variance in amyloid PET levels in the wider population. METHODS We analyzed data from the Mayo Clinic Study of Aging (MCSA) and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Global cortical amyloid PET burden was the primary outcome. The 38 gene variants from Wightman et al. (2021) were analyzed as predictors, with PRSice-2 used to assess the collective phenotypic variance explained. RESULTS Known AD risk variants in APOE, PICALM, CR1, and CLU were associated with amyloid PET levels. In aggregate, the AD risk variants were strongly associated with amyloid PET levels in the MCSA (p = 1.51×10-50) and ADNI (p = 3.21×10-64). However, in both cohorts the non-APOE variants uniquely contributed only modestly (MCSA = 2.1%, ADNI = 4.4%) to explaining variation in amyloid PET levels. CONCLUSION Additional case-control AD risk variants added only modestly to APOE in accounting for individual variation in amyloid PET burden, results which were consistent across independent cohorts with distinct recruitment strategies and subject characteristics. Our findings suggest that advancing precision medicine for dementia may require integration of strategies complementing case-control approaches, including biomarker-specific genetic associations, gene-by-environment interactions, and markers of disease progression and heterogeneity.
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Affiliation(s)
- Vijay K Ramanan
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Michael G. Heckman
- Department of Quantitative Health Sciences, Mayo Clinic-Florida, Jacksonville, Florida, 32224, USA
| | - Scott A. Przybelski
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Timothy G. Lesnick
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Val J. Lowe
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | | | - Michelle M. Mielke
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Clifford R. Jack
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - David S. Knopman
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Ronald C. Petersen
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic-Florida, Jacksonville, Florida, 32224, USA
- Department of Clinical Genomics, Mayo Clinic-Florida, Jacksonville, Florida, 32224, USA
| | - Prashanthi Vemuri
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, Minnesota, 55905, USA
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34
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Kim HR, Jung SH, Kim J, Jang H, Kang SH, Hwangbo S, Kim JP, Kim SY, Kim B, Kim S, Jeong JH, Yoon SJ, Park KW, Kim EJ, Yoon B, Jang JW, Hong JY, Choi SH, Noh Y, Kim KW, Kim SE, Lee JS, Jung NY, Lee J, Kim BC, Son SJ, Hong CH, Na DL, Seo SW, Won HH, Kim HJ. Identifying novel genetic variants for brain amyloid deposition: a genome-wide association study in the Korean population. Alzheimers Res Ther 2021; 13:117. [PMID: 34154648 PMCID: PMC8215820 DOI: 10.1186/s13195-021-00854-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified a number of genetic variants for Alzheimer's disease (AD). However, most GWAS were conducted in individuals of European ancestry, and non-European populations are still underrepresented in genetic discovery efforts. Here, we performed GWAS to identify single nucleotide polymorphisms (SNPs) associated with amyloid β (Aβ) positivity using a large sample of Korean population. METHODS One thousand four hundred seventy-four participants of Korean ancestry were recruited from multicenters in South Korea. Discovery dataset consisted of 1190 participants (383 with cognitively unimpaired [CU], 330 with amnestic mild cognitive impairment [aMCI], and 477 with AD dementia [ADD]) and replication dataset consisted of 284 participants (46 with CU, 167 with aMCI, and 71 with ADD). GWAS was conducted to identify SNPs associated with Aβ positivity (measured by amyloid positron emission tomography). Aβ prediction models were developed using the identified SNPs. Furthermore, bioinformatics analysis was conducted for the identified SNPs. RESULTS In addition to APOE, we identified nine SNPs on chromosome 7, which were associated with a decreased risk of Aβ positivity at a genome-wide suggestive level. Of these nine SNPs, four novel SNPs (rs73375428, rs2903923, rs3828947, and rs11983537) were associated with a decreased risk of Aβ positivity (p < 0.05) in the replication dataset. In a meta-analysis, two SNPs (rs7337542 and rs2903923) reached a genome-wide significant level (p < 5.0 × 10-8). Prediction performance for Aβ positivity increased when rs73375428 were incorporated (area under curve = 0.75; 95% CI = 0.74-0.76) in addition to clinical factors and APOE genotype. Cis-eQTL analysis demonstrated that the rs73375428 was associated with decreased expression levels of FGL2 in the brain. CONCLUSION The novel genetic variants associated with FGL2 decreased risk of Aβ positivity in the Korean population. This finding may provide a candidate therapeutic target for AD, highlighting the importance of genetic studies in diverse populations.
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Affiliation(s)
- Hang-Rai Kim
- Department of Neurology, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Jaeho Kim
- Department of Neurology, Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, Republic of Korea
| | - Hyemin Jang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Sung Hoon Kang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Song Hwangbo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Jun Pyo Kim
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - So Yeon Kim
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Beomsu Kim
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Soyeon Kim
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Jee Hyang Jeong
- Department of Neurology, Ewha Womans University Seoul Hospital, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Soo Jin Yoon
- Department of Neurology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, Republic of Korea
| | - Kyung Won Park
- Department of Neurology, Dong-A University College of Medicine, Department of Translational Biomedical Sciences, Graduate School of Dong-A University, Busan, Republic of Korea
| | - Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Busan, Republic of Korea
| | - Bora Yoon
- Department of Neurology, Konyang University College of Medicine, Daejeon, Republic of Korea
| | - Jae-Won Jang
- Department of Neurology, Kangwon National University Hospital, Kangwon National University College of Medicine, Chuncheon, Republic of Korea
| | - Jin Yong Hong
- Department of Neurology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Seong Hye Choi
- Department of Neurology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Young Noh
- Department of Neurology, Gachon University College of Medicine, Gil Medical Center, Incheon, Republic of Korea
| | - Ko Woon Kim
- Department of Neurology, School of Medicine, Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | - Si Eun Kim
- Department of Neurology, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Republic of Korea
| | - Jin San Lee
- Department of Neurology, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Na-Yeon Jung
- Department of Neurology, Pusan National University Yangsan Hospital, Pusan National University School of Medicine and Medical Research Institute, Busan, Republic of Korea
| | - Juyoun Lee
- Department of Neurology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Byeong C Kim
- Departmet of Neurology, Chonnam National University School of Medicine, Gwangju, Republic of Korea
| | - Sang Joon Son
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Chang Hyung Hong
- Department of Psychiatry, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Duk L Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hong-Hee Won
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.
| | - Hee Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea.
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.
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Da Mesquita S, Papadopoulos Z, Dykstra T, Brase L, Farias FG, Wall M, Jiang H, Kodira CD, de Lima KA, Herz J, Louveau A, Goldman DH, Salvador AF, Onengut-Gumuscu S, Farber E, Dabhi N, Kennedy T, Milam MG, Baker W, Smirnov I, Rich SS, Benitez BA, Karch CM, Perrin RJ, Farlow M, Chhatwal JP, Holtzman DM, Cruchaga C, Harari O, Kipnis J. Meningeal lymphatics affect microglia responses and anti-Aβ immunotherapy. Nature 2021; 593:255-260. [PMID: 33911285 PMCID: PMC8817786 DOI: 10.1038/s41586-021-03489-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/25/2021] [Indexed: 02/02/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent cause of dementia1. Although there is no effective treatment for AD, passive immunotherapy with monoclonal antibodies against amyloid beta (Aβ) is a promising therapeutic strategy2,3. Meningeal lymphatic drainage has an important role in the accumulation of Aβ in the brain4, but it is not known whether modulation of meningeal lymphatic function can influence the outcome of immunotherapy in AD. Here we show that ablation of meningeal lymphatic vessels in 5xFAD mice (a mouse model of amyloid deposition that expresses five mutations found in familial AD) worsened the outcome of mice treated with anti-Aβ passive immunotherapy by exacerbating the deposition of Aβ, microgliosis, neurovascular dysfunction, and behavioural deficits. By contrast, therapeutic delivery of vascular endothelial growth factor C improved clearance of Aβ by monoclonal antibodies. Notably, there was a substantial overlap between the gene signature of microglia from 5xFAD mice with impaired meningeal lymphatic function and the transcriptional profile of activated microglia from the brains of individuals with AD. Overall, our data demonstrate that impaired meningeal lymphatic drainage exacerbates the microglial inflammatory response in AD and that enhancement of meningeal lymphatic function combined with immunotherapies could lead to better clinical outcomes.
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Affiliation(s)
- Sandro Da Mesquita
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA.
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
| | - Zachary Papadopoulos
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, Washington University in St. Louis, St. Louis, MO, USA
| | - Taitea Dykstra
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Logan Brase
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Morgan Wall
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Hong Jiang
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Kalil Alves de Lima
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jasmin Herz
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Antoine Louveau
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dylan H Goldman
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Andrea Francesca Salvador
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nisha Dabhi
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Tatiana Kennedy
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Mary Grace Milam
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Wendy Baker
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Igor Smirnov
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Jasmeer P Chhatwal
- Massachusetts General Hospital, Harvard Medical School, Department of Neurology, Boston, MA, USA
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Jonathan Kipnis
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA.
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA.
- Neuroscience Graduate Program, Washington University in St. Louis, St. Louis, MO, USA.
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA.
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Kim S, Kim K, Nho K, Myung W, Won HH. Shared Genetic Background Between Cerebrospinal Fluid Biomarkers and Risk for Alzheimer's Disease: A Two-Sample Mendelian Randomization Study. J Alzheimers Dis 2021; 80:1197-1207. [PMID: 33646147 DOI: 10.3233/jad-200671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Whether the epidemiological association of amyloid-β (Aβ) and tau pathology in late-onset Alzheimer's disease (LOAD) is causal remains unclear. OBJECTIVE We aimed to investigate the shared genetic background between the cerebrospinal fluid (CSF) biomarkers for Aβ and tau pathology and the risk of LOAD. METHODS We conducted a two-sample Mendelian randomization (MR) analysis. We used summary statistics of genome-wide association studies for CSF biomarkers (Aβ1-42 [Aβ], phosphorylated tau181 [p-tau], and total tau [t-tau]) in 3,146 individuals and for LOAD in 21,982 cases and 41,944 controls. We tested the association between changes in the genetically predicted CSF biomarkers and LOAD risk. RESULTS We found a decrease in LOAD risk per one-standard-deviation (SD) increase in the genetically predicted CSF Aβ (odds ratio [OR], 2.87×10-3 for AD; 95%confidence interval [CI], 1.54×10-4-0.05; p = 8.91×10-5). Conversely, we observed an increase in LOAD risk per one-SD increase in the genetically predicted CSF p-tau (OR, 19.46; 95%CI, 1.50-2.52×102; p = 0.02) and t-tau (OR, 33.80; 95%CI, 1.57-7.29×102; p = 0.02). However, only the association between p-tau and the risk for LOAD remained significant after the exclusion of the APOE variant (rs769449). CONCLUSION We found the causal association between CSF biomarkers and the risk for LOAD. Our results suggest that the etiology of LOAD involves multiple biological processes, including the pathways of Aβ and tau proteins. Further MR studies using large-scale data of multiple candidate biomarkers are needed to elucidate the pathophysiology of LOAD.
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Affiliation(s)
- Soyeon Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Kiwon Kim
- Department of Psychiatry, Veteran Health Service Medical Center, Seoul, South Korea
| | - Kwangsik Nho
- Department of Radiology & Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Woojae Myung
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
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Mentis AFA, Dardiotis E, Chrousos GP. Apolipoprotein E4 and meningeal lymphatics in Alzheimer disease: a conceptual framework. Mol Psychiatry 2021; 26:1075-1097. [PMID: 32355332 PMCID: PMC7985019 DOI: 10.1038/s41380-020-0731-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/01/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022]
Abstract
The potential existence and roles of the meningeal lymphatic system in normal and pathological brain function have been a long-standing enigma. Recent evidence suggests that meningeal lymphatic vessels are present in both the mouse and human brain; in mice, they seem to play a role in clearing toxic amyloid-beta peptides, which have been connected with Alzheimer disease (AD). Here, we review the evidence linking the meningeal lymphatic system with human AD. Novel findings suggest that the recently described meningeal lymphatic vessels could be linked to, and possibly drain, the efferent paravascular glial lymphatic (glymphatic) system carrying cerebrospinal fluid, after solute and immune cell exchange with brain interstitial fluid. In so doing, the glymphatic system could contribute to the export of toxic solutes and immune cells from the brain (an exported fluid we wish to describe as glymph, similarly to lymph) to the meningeal lymphatic system; the latter, by being connected with downstream anatomic regions, carries the glymph to the conventional cervical lymphatic vessels and nodes. Thus, abnormal function in the meningeal lymphatic system could, in theory, lead to the accumulation, in the brain, of amyloid-beta, cellular debris, and inflammatory mediators, as well as immune cells, resulting in damage of the brain parenchyma and, in turn, cognitive and other neurologic dysfunctions. In addition, we provide novel insights into APOE4-the leading genetic risk factor for AD-and its relation to the meningeal lymphatic system. In this regard, we have reanalyzed previously published RNA-Seq data to show that induced pluripotent stem cells (iPSCs) carrying the APOE4 allele (either as APOE4 knock-in or stemming from APOE4 patients) express lower levels of (a) genes associated with lymphatic markers, and (b) genes for which well-characterized missense mutations have been linked to peripheral lymphedema. Taking into account this evidence, we propose a new conceptual framework, according to which APOE4 could play a novel role in the premature shrinkage of meningeal lymphatic vessels (meningeal lymphosclerosis), leading to abnormal meningeal lymphatic functions (meningeal lymphedema), and, in turn, reduction in the clearance of amyloid-beta and other macromolecules and inflammatory mediators, as well as immune cells, from the brain, exacerbation of AD manifestations, and progression of the disease. Altogether, these findings and their potential interpretations may herald novel diagnostic tools and therapeutic approaches in patients with AD.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Vas. Sofias Avenue 127, 115 21, Athens, Greece.
- Department of Microbiology, University of Thessaly, Panepistimiou 3, Viopolis, 41 500, Larissa, Greece.
| | - Efthimios Dardiotis
- Department of Neurology, University of Thessaly, Panepistimiou 3, Viopolis, 41 500, Larissa, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Medical School, Aghia Sophia Children's Hospital, Livadias 8, 115 27, Athens, Greece
- UNESCO Chair on Adolescent Health Care, Athens, Greece
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38
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Du L, Liu F, Liu K, Yao X, Risacher SL, Han J, Saykin AJ, Shen L. Associating Multi-Modal Brain Imaging Phenotypes and Genetic Risk Factors via a Dirty Multi-Task Learning Method. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:3416-3428. [PMID: 32746095 PMCID: PMC7705646 DOI: 10.1109/tmi.2020.2995510] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Brain imaging genetics becomes more and more important in brain science, which integrates genetic variations and brain structures or functions to study the genetic basis of brain disorders. The multi-modal imaging data collected by different technologies, measuring the same brain distinctly, might carry complementary information. Unfortunately, we do not know the extent to which the phenotypic variance is shared among multiple imaging modalities, which further might trace back to the complex genetic mechanism. In this paper, we propose a novel dirty multi-task sparse canonical correlation analysis (SCCA) to study imaging genetic problems with multi-modal brain imaging quantitative traits (QTs) involved. The proposed method takes advantages of the multi-task learning and parameter decomposition. It can not only identify the shared imaging QTs and genetic loci across multiple modalities, but also identify the modality-specific imaging QTs and genetic loci, exhibiting a flexible capability of identifying complex multi-SNP-multi-QT associations. Using the state-of-the-art multi-view SCCA and multi-task SCCA, the proposed method shows better or comparable canonical correlation coefficients and canonical weights on both synthetic and real neuroimaging genetic data. In addition, the identified modality-consistent biomarkers, as well as the modality-specific biomarkers, provide meaningful and interesting information, demonstrating the dirty multi-task SCCA could be a powerful alternative method in multi-modal brain imaging genetics.
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Affiliation(s)
- Lei Du
- School of Automation, Northwestern Polytechnical University, Xi’an 710072, China
| | - Fang Liu
- School of Automation, Northwestern Polytechnical University, Xi’an 710072, China
| | - Kefei Liu
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xiaohui Yao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shannon L. Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Junwei Han
- School of Automation, Northwestern Polytechnical University, Xi’an 710072, China
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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Raghavan NS, Dumitrescu L, Mormino E, Mahoney ER, Lee AJ, Gao Y, Bilgel M, Goldstein D, Harrison T, Engelman CD, Saykin AJ, Whelan CD, Liu JZ, Jagust W, Albert M, Johnson SC, Yang HS, Johnson K, Aisen P, Resnick SM, Sperling R, De Jager PL, Schneider J, Bennett DA, Schrag M, Vardarajan B, Hohman TJ, Mayeux R. Association Between Common Variants in RBFOX1, an RNA-Binding Protein, and Brain Amyloidosis in Early and Preclinical Alzheimer Disease. JAMA Neurol 2020; 77:1288-1298. [PMID: 32568366 PMCID: PMC7309575 DOI: 10.1001/jamaneurol.2020.1760] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 01/27/2023]
Abstract
Importance Genetic studies of Alzheimer disease have focused on the clinical or pathologic diagnosis as the primary outcome, but little is known about the genetic basis of the preclinical phase of the disease. Objective To examine the underlying genetic basis for brain amyloidosis in the preclinical phase of Alzheimer disease. Design, Setting, and Participants In the first stage of this genetic association study, a meta-analysis was conducted using genetic and imaging data acquired from 6 multicenter cohort studies of healthy older individuals between 1994 and 2019: the Anti-Amyloid Treatment in Asymptomatic Alzheimer Disease Study, the Berkeley Aging Cohort Study, the Wisconsin Registry for Alzheimer's Prevention, the Biomarkers of Cognitive Decline Among Normal Individuals cohort, the Baltimore Longitudinal Study of Aging, and the Alzheimer Disease Neuroimaging Initiative, which included Alzheimer disease and mild cognitive impairment. The second stage was designed to validate genetic observations using pathologic and clinical data from the Religious Orders Study and Rush Memory and Aging Project. Participants older than 50 years with amyloid positron emission tomographic (PET) imaging data and DNA from the 6 cohorts were included. The largest cohort, the Anti-Amyloid Treatment in Asymptomatic Alzheimer Disease Study (n = 3154), was the PET screening cohort used for a secondary prevention trial designed to slow cognitive decline associated with brain amyloidosis. Six smaller, longitudinal cohort studies (n = 1160) provided additional amyloid PET imaging data with existing genetic data. The present study was conducted from March 29, 2019, to February 19, 2020. Main Outcomes and Measures A genome-wide association study of PET imaging amyloid levels. Results From the 4314 analyzed participants (age, 52-96 years; 2478 participants [57%] were women), a novel locus for amyloidosis was noted within RBFOX1 (β = 0.61, P = 3 × 10-9) in addition to APOE. The RBFOX1 protein localized around plaques, and reduced expression of RBFOX1 was correlated with higher amyloid-β burden (β = -0.008, P = .002) and worse cognition (β = 0.007, P = .006) during life in the Religious Orders Study and Rush Memory and Aging Project cohort. Conclusions and Relevance RBFOX1 encodes a neuronal RNA-binding protein known to be expressed in neuronal tissues and may play a role in neuronal development. The findings of this study suggest that RBFOX1 is a novel locus that may be involved in the pathogenesis of Alzheimer disease.
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Affiliation(s)
- Neha S. Raghavan
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
- The Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California
| | - Emily R. Mahoney
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Annie J. Lee
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
| | - Yizhe Gao
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - David Goldstein
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
| | - Theresa Harrison
- Helen Wills Neuroscience Institute, University of California, Berkeley
| | - Corinne D. Engelman
- Department of Population Health Sciences, University of Wisconsin, School of Medicine and Public Health, Madison
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, School of Medicine, Indiana University, Indianapolis
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis
| | | | - Jimmy Z. Liu
- Research and Early Development, Biogen Inc, Cambridge, Massachusetts
| | - William Jagust
- Helen Wills Neuroscience Institute, University of California, Berkeley
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sterling C. Johnson
- Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison
| | - Hyun-Sik Yang
- Department of Neurology, Massachusetts General Hospital, Boston
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Keith Johnson
- Department of Neurology, Massachusetts General Hospital, Boston
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Paul Aisen
- Alzheimer’s Therapeutic Research Institute, Keck School of Medicine, University of Southern California, San Diego
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Reisa Sperling
- Department of Neurology, Massachusetts General Hospital, Boston
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Philip L. De Jager
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts
| | - Julie Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Matthew Schrag
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Badri Vardarajan
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
- The Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Richard Mayeux
- Department of Neurology, Columbia University Medical Center, New York, New York
- Department of Neurology, The New York Presbyterian Hospital, New York
- Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University Medical Center, New York, New York
- The Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
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40
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Ramanan VK, Wang X, Przybelski SA, Raghavan S, Heckman MG, Batzler A, Kosel ML, Hohman TJ, Knopman DS, Graff-Radford J, Lowe VJ, Mielke MM, Jack CR, Petersen RC, Ross OA, Vemuri P. Variants in PPP2R2B and IGF2BP3 are associated with higher tau deposition. Brain Commun 2020; 2:fcaa159. [PMID: 33426524 PMCID: PMC7780444 DOI: 10.1093/braincomms/fcaa159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/29/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Tau deposition is a key biological feature of Alzheimer's disease that is closely related to cognitive impairment. However, it remains poorly understood why certain individuals may be more susceptible to tau deposition while others are more resistant. The recent availability of in vivo assessment of tau burden through positron emission tomography provides an opportunity to test the hypothesis that common genetic variants may influence tau deposition. We performed a genome-wide association study of tau-positron emission tomography on a sample of 754 individuals over age 50 (mean age 72.4 years, 54.6% men, 87.6% cognitively unimpaired) from the population-based Mayo Clinic Study of Aging. Linear regression was performed to test nucleotide polymorphism associations with AV-1451 (18F-flortaucipir) tau-positron emission tomography burden in an Alzheimer's-signature composite region of interest, using an additive genetic model and covarying for age, sex and genetic principal components. Genome-wide significant associations with higher tau were identified for rs76752255 (P = 9.91 × 10-9, β = 0.20) in the tau phosphorylation regulatory gene PPP2R2B (protein phosphatase 2 regulatory subunit B) and for rs117402302 (P = 4.00 × 10-8, β = 0.19) near IGF2BP3 (insulin-like growth factor 2 mRNA-binding protein 3). The PPP2R2B association remained genome-wide significant after additionally covarying for global amyloid burden and cerebrovascular disease risk, while the IGF2BP3 association was partially attenuated after accounting for amyloid load. In addition to these discoveries, three single nucleotide polymorphisms within MAPT (microtubule-associated protein tau) displayed nominal associations with tau-positron emission tomography burden, and the association of the APOE (apolipoprotein E) ɛ4 allele with tau-positron emission tomography was marginally nonsignificant (P = 0.06, β = 0.07). No associations with tau-positron emission tomography burden were identified for other single nucleotide polymorphisms associated with Alzheimer's disease clinical diagnosis in prior large case-control studies. Our findings nominate PPP2R2B and IGF2BP3 as novel potential influences on tau pathology which warrant further functional characterization. Our data are also supportive of previous literature on the associations of MAPT genetic variation with tau, and more broadly supports the inference that tau accumulation may have a genetic architecture distinct from known Alzheimer's susceptibility genes, which may have implications for improved risk stratification and therapeutic targeting.
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Affiliation(s)
- Vijay K Ramanan
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Xuewei Wang
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Scott A Przybelski
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | | | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic-Florida, Jacksonville, FL 32224, USA
| | - Anthony Batzler
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Matthew L Kosel
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Timothy J Hohman
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David S Knopman
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | | | - Val J Lowe
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Michelle M Mielke
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Clifford R Jack
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Ronald C Petersen
- Department of Neurology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
- Department of Health Sciences Research, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic-Florida, Jacksonville, FL 32224, USA
- Department of Clinical Genomics, Mayo Clinic-Florida, Jacksonville, FL 32224, USA
| | - Prashanthi Vemuri
- Department of Radiology, Mayo Clinic-Minnesota, Rochester, MN 55905, USA
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41
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Sullivan KJ, Liu A, Chang CCH, Cohen AD, Lopresti BJ, Minhas DS, Laymon CM, Klunk WE, Aizenstein H, Nadkarni NK, Loewenstein D, Kamboh MI, Ganguli M, Snitz BE. Alzheimer's disease pathology in a community-based sample of older adults without dementia: The MYHAT neuroimaging study. Brain Imaging Behav 2020; 15:1355-1363. [PMID: 32748322 DOI: 10.1007/s11682-020-00334-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/07/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
A true understanding of the distribution and functional correlates of Alzheimer's disease pathology in dementia-free older adults requires a population-based perspective. Here we report initial findings from a sample of 102 cognitively unimpaired participants (average age 77.2 years, 54.9% women, 13.7% APOE*4 carriers) recruited for neuroimaging from a larger representative population-based cohort participating in an ongoing longitudinal study of aging, the Monongahela-Youghiogheny Healthy Aging Team (MYHAT). All participants scored < 1.0 on the Clinical Dementia Rating (CDR) Scale, with 8 participants (7.8%) scoring CDR = 0.5. Participants completed a positron emission tomography scan using the tracers [C-11]Pittsburgh Compound-B (PiB) and [F-18]AV-1451 to estimate amyloid and tau deposition. PiB positivity was defined on a regional basis using established standardized uptake value ratio cutoffs (SUVR; cerebellar gray matter reference), with 39 participants (38.2%) determined to be PiB(+). Health history, lifestyle, and cognitive abilities were assessed cross-sectionally at the nearest annual parent MYHAT study visit. A series of adjusted regression analyses modeled cognitive performance as a function of global PiB SUVR and [F-18]AV-1451 SUVR in Braak associated regions 1, 3/4, and 5/6. In comparison to PiB(-) participants (n = 63), PiB(+) participants were older, less educated, and were more likely to be APOE*4 carriers. Global PiB SUVR was significantly correlated with [F-18]AV-1451 SUVR in all Braak-associated regions (r = .38-0.53, p < .05). In independent models, higher Global PiB SUVR and Braak 1 [F-18]AV-1451 SUVR were associated with worse performance on a semantic interference verbal memory test. Our findings suggest that brain amyloid is common in a community-based setting, and is associated with tau deposition, but both pathologies show few associations with concurrent cognitive performance in a dementia-free sample.
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Affiliation(s)
- Kevin J Sullivan
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Anran Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ann D Cohen
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian J Lopresti
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Davneet S Minhas
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles M Laymon
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - William E Klunk
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Howard Aizenstein
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neelesh K Nadkarni
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - David Loewenstein
- Department of Psychiatry and Behavioral Science, University of Miami, FL, Coral Gables, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, PA, Pittsburgh, USA
| | - Mary Ganguli
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Beth E Snitz
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
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42
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Influence of apolipoprotein-E genotype on brain amyloid load and longitudinal trajectories. Neurobiol Aging 2020; 94:111-120. [PMID: 32603776 DOI: 10.1016/j.neurobiolaging.2020.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 12/23/2022]
Abstract
To characterize the influence of apolipoprotein-E (APOE) genotype on cerebral Aβ load and longitudinal Aβ trajectories, [11C]Pittsburgh compound-B (PiB) positron emission tomography (PET) imaging was used to assess amyloid load in a clinically heterogeneous cohort of 428 elderly participants with known APOE genotype. Serial [11C]PiB data and a repeated measures model were used to model amyloid trajectories in a subset of 235 participants classified on the basis of APOE genotype. We found that APOE-ε4 was associated with increased Aβ burden and an earlier age of onset of Aβ positivity, whereas APOE-ε2 appeared to have modest protective effects against Aβ. APOE class did not predict rates of Aβ accumulation. The present study suggests that APOE modifies Alzheimer's disease risk through a direct influence on amyloidogenic processes, which manifests as an earlier age of onset of Aβ positivity, although it is likely that other genetic, environmental, and lifestyle factors are important.
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43
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Altmann A, Scelsi MA, Shoai M, de Silva E, Aksman LM, Cash DM, Hardy J, Schott JM. A comprehensive analysis of methods for assessing polygenic burden on Alzheimer's disease pathology and risk beyond APOE. Brain Commun 2019; 2:fcz047. [PMID: 32226939 PMCID: PMC7100005 DOI: 10.1093/braincomms/fcz047] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies have identified dozens of loci that alter the risk to develop Alzheimer's disease. However, with the exception of the APOE-ε4 allele, most variants bear only little individual effect and have, therefore, limited diagnostic and prognostic value. Polygenic risk scores aim to collate the disease risk distributed across the genome in a single score. Recent works have demonstrated that polygenic risk scores designed for Alzheimer's disease are predictive of clinical diagnosis, pathology confirmed diagnosis and changes in imaging biomarkers. Methodological innovations in polygenic risk modelling include the polygenic hazard score, which derives effect estimates for individual single nucleotide polymorphisms from survival analysis, and methods that account for linkage disequilibrium between genomic loci. In this work, using data from the Alzheimer's disease neuroimaging initiative, we compared different approaches to quantify polygenic disease burden for Alzheimer's disease and their association (beyond the APOE locus) with a broad range of Alzheimer's disease-related traits: cross-sectional CSF biomarker levels, cross-sectional cortical amyloid burden, clinical diagnosis, clinical progression, longitudinal loss of grey matter and longitudinal decline in cognitive function. We found that polygenic scores were associated beyond APOE with clinical diagnosis, CSF-tau levels and, to a minor degree, with progressive atrophy. However, for many other tested traits such as clinical disease progression, CSF amyloid, cognitive decline and cortical amyloid load, the additional effects of polygenic burden beyond APOE were of minor nature. Overall, polygenic risk scores and the polygenic hazard score performed equally and given the ease with which polygenic risk scores can be derived; they constitute the more practical choice in comparison with polygenic hazard scores. Furthermore, our results demonstrate that incomplete adjustment for the APOE locus, i.e. only adjusting for APOE-ε4 carrier status, can lead to overestimated effects of polygenic scores due to APOE-ε4 homozygous participants. Lastly, on many of the tested traits, the major driving factor remained the APOE locus, with the exception of quantitative CSF-tau and p-tau measures.
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Affiliation(s)
- Andre Altmann
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC), University College London (UCL), London WC1V 6LJ, UK
| | - Marzia A Scelsi
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC), University College London (UCL), London WC1V 6LJ, UK
| | - Maryam Shoai
- Reta Lilla Research Laboratories, Department of Neurodegeneration, Queen Square Institute of Neurology, University College London (UCL), London WC1V 6LJ, UK.,UK Dementia Research Institute, University College London (UCL), London WC1V 6LJ, UK
| | - Eric de Silva
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC), University College London (UCL), London WC1V 6LJ, UK.,Institute for Health Informatics, University College London (UCL), London WC1V 6LJ, UK
| | - Leon M Aksman
- Department of Medical Physics and Biomedical Engineering, Centre for Medical Image Computing (CMIC), University College London (UCL), London WC1V 6LJ, UK
| | - David M Cash
- UK Dementia Research Institute, University College London (UCL), London WC1V 6LJ, UK.,Dementia Research Centre, Queen Square Institute of Neurology, University College London (UCL), London WC1V 6LJ, UK
| | - John Hardy
- Reta Lilla Research Laboratories, Department of Neurodegeneration, Queen Square Institute of Neurology, University College London (UCL), London WC1V 6LJ, UK.,UK Dementia Research Institute, University College London (UCL), London WC1V 6LJ, UK
| | - Jonathan M Schott
- UK Dementia Research Institute, University College London (UCL), London WC1V 6LJ, UK.,Dementia Research Centre, Queen Square Institute of Neurology, University College London (UCL), London WC1V 6LJ, UK
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44
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Liu YS, Yan WJ, Tan CC, Li JQ, Xu W, Cao XP, Tan L, Yu JT. Common Variant in TREM1 Influencing Brain Amyloid Deposition in Mild Cognitive Impairment and Alzheimer’s Disease. Neurotox Res 2019; 37:661-668. [DOI: 10.1007/s12640-019-00105-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 10/25/2022]
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45
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Genetics influences development of AD pathology. Nat Rev Neurol 2018; 14:689. [PMID: 30449889 DOI: 10.1038/s41582-018-0106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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