1
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Archer DB, Eissman JM, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Dumitrescu L, Hohman TJ. Longitudinal change in memory performance as a strong endophenotype for Alzheimer's disease. Alzheimers Dement 2024; 20:1268-1283. [PMID: 37985223 PMCID: PMC10896586 DOI: 10.1002/alz.13508] [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: 06/19/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 11/22/2023]
Abstract
INTRODUCTION Although large-scale genome-wide association studies (GWAS) have been conducted on AD, few have been conducted on continuous measures of memory performance and memory decline. METHODS We conducted a cross-ancestry GWAS on memory performance (in 27,633 participants) and memory decline (in 22,365 participants; 129,201 observations) by leveraging harmonized cognitive data from four aging cohorts. RESULTS We found high heritability for two ancestry backgrounds. Further, we found a novel ancestry locus for memory decline on chromosome 4 (rs6848524) and three loci in the non-Hispanic Black ancestry group for memory performance on chromosomes 2 (rs111471504), 7 (rs4142249), and 15 (rs74381744). In our gene-level analysis, we found novel genes for memory decline on chromosomes 1 (SLC25A44), 11 (BSX), and 15 (DPP8). Memory performance and memory decline shared genetic architecture with AD-related traits, neuropsychiatric traits, and autoimmune traits. DISCUSSION We discovered several novel loci, genes, and genetic correlations associated with late-life memory performance and decline. HIGHLIGHTS Late-life memory has high heritability that is similar across ancestries. We discovered four novel variants associated with late-life memory. We identified four novel genes associated with late-life memory. Late-life memory shares genetic architecture with psychiatric/autoimmune traits.
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2
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Albala B, Appelmans E, Burress R, De Santi S, Devins T, Klein G, Logovinsky V, Novak GP, Ribeiro K, Schmidt ME, Schwarz AJ, Scott D, Shcherbinin S, Siemers E, Travaglia A, Weber CJ, White L, Wolf‐Rodda J, Vasanthakumar A. The Alzheimer's Disease Neuroimaging Initiative and the role and contributions of the Private Partners Scientific Board (PPSB). Alzheimers Dement 2024; 20:695-708. [PMID: 37774088 PMCID: PMC10843521 DOI: 10.1002/alz.13483] [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: 06/16/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 10/01/2023]
Abstract
The Alzheimer's Disease Neuroimaging Initiative (ADNI) Private Partners Scientific Board (PPSB) encompasses members from industry, biotechnology, diagnostic, and non-profit organizations that have until recently been managed by the Foundation for the National Institutes of Health (FNIH) and provided financial and scientific support to ADNI programs. In this article, we review some of the major activities undertaken by the PPSB, focusing on those supporting the most recently completed National Institute on Aging grant, ADNI3, and the impact it has had on streamlining biomarker discovery and validation in Alzheimer's disease. We also provide a perspective on the gaps that may be filled with future PPSB activities as part of ADNI4 and beyond. HIGHLIGHTS: The Private Partners Scientific board (PPSB) continues to play a key role in enabling several Alzheimer's Disease Neuroimaging Initiative (ADNI) activities. PPSB working groups have led landscape assessments to provide valuable feedback on new technologies, platforms, and methods that may be taken up by ADNI in current or future iterations.
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Affiliation(s)
- Bruce Albala
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Program in Public HealthIrvine and Department of NeurologyUCI School of MedicineUniversity of California856 Health Sciences QuadIrvineCalifornia92697‐3957USA
| | - Eline Appelmans
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
| | - Ramona Burress
- Janssen Research & Development, LLCTitusvilleNew JerseyUSA
- Present address:
Takeda95, Hayden AvenueLexingtonMassachusetts02421USA
| | - Susan De Santi
- Eisai Inc.NutleyNew JerseyUSA
- Life Molecular ImagingBerlinGermany
- Present address:
Eisai Inc.NutleyNew JerseyUSA
| | - Theresa Devins
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Cognition Therapeutics2500 Westchester AvenuePurchaseNew York10577USA
| | | | - Veronika Logovinsky
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Lundbeck6 Parkway NDeerfieldIllinois60015USA
| | | | | | | | | | | | | | | | - Alessio Travaglia
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
| | | | - Leah White
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
- Present address:
Veranex5420 Wade Park Blvd Suite 204RaleighNorth Carolina27607USA
| | - Julie Wolf‐Rodda
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
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3
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Logue MW, Dasgupta S, Farrer LA. Genetics of Alzheimer's Disease in the African American Population. J Clin Med 2023; 12:5189. [PMID: 37629231 PMCID: PMC10455208 DOI: 10.3390/jcm12165189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Black/African American (AA) individuals have a higher risk of Alzheimer's disease (AD) than White non-Hispanic persons of European ancestry (EUR) for reasons that may include economic disparities, cardiovascular health, quality of education, and biases in the methods used to diagnose AD. AD is also heritable, and some of the differences in risk may be due to genetics. Many AD-associated variants have been identified by candidate gene studies, genome-wide association studies (GWAS), and genome-sequencing studies. However, most of these studies have been performed using EUR cohorts. In this paper, we review the genetics of AD and AD-related traits in AA individuals. Importantly, studies of genetic risk factors in AA cohorts can elucidate the molecular mechanisms underlying AD risk in AA and other populations. In fact, such studies are essential to enable reliable precision medicine approaches in persons with considerable African ancestry. Furthermore, genetic studies of AA cohorts allow exploration of the ways the impact of genes can vary by ancestry, culture, and economic and environmental disparities. They have yielded important gains in our knowledge of AD genetics, and increasing AA individual representation within genetic studies should remain a priority for inclusive genetic study design.
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Affiliation(s)
- Mark W. Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA 02130, USA;
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Shoumita Dasgupta
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Medical Sciences and Education, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
- Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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4
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Chakraborty S, Kahali B. Exome-wide analysis reveals role of LRP1 and additional novel loci in cognition. HGG ADVANCES 2023; 4:100208. [PMID: 37305557 PMCID: PMC10248556 DOI: 10.1016/j.xhgg.2023.100208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Cognitive functioning is heritable, with metabolic risk factors known to accelerate age-associated cognitive decline. Identifying genetic underpinnings of cognition is thus crucial. Here, we undertake single-variant and gene-based association analyses upon 6 neurocognitive phenotypes across 6 cognition domains in whole-exome sequencing data from 157,160 individuals of the UK Biobank cohort to expound the genetic architecture of human cognition. We report 20 independent loci associated with 5 cognitive domains while controlling for APOE isoform-carrier status and metabolic risk factors; 18 of which were not previously reported, and implicated genes relating to oxidative stress, synaptic plasticity and connectivity, and neuroinflammation. A subset of significant hits for cognition indicates mediating effects via metabolic traits. Some of these variants also exhibit pleiotropic effects on metabolic traits. We further identify previously unknown interactions of APOE variants with LRP1 (rs34949484 and others, suggestively significant), AMIGO1 (rs146766120; pAla25Thr, significant), and ITPR3 (rs111522866, significant), controlling for lipid and glycemic risks. Our gene-based analysis also suggests that APOC1 and LRP1 have plausible roles along shared pathways of amyloid beta (Aβ) and lipid and/or glucose metabolism in affecting complex processing speed and visual attention. In addition, we report pairwise suggestive interactions of variants harbored in these genes with APOE affecting visual attention. Our report based on this large-scale exome-wide study highlights the effects of neuronal genes, such as LRP1, AMIGO1, and other genomic loci, thus providing further evidence of the genetic underpinnings for cognition during aging.
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Affiliation(s)
- Shreya Chakraborty
- Centre for Brain Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Interdisciplinary Mathematical Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Bratati Kahali
- Centre for Brain Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
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5
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Bharthur Sanjay A, Patania A, Yan X, Svaldi D, Duran T, Shah N, Nemes S, Chen E, Apostolova LG. Characterization of gene expression patterns in mild cognitive impairment using a transcriptomics approach and neuroimaging endophenotypes. Alzheimers Dement 2022; 18:2493-2508. [PMID: 35142026 PMCID: PMC10078657 DOI: 10.1002/alz.12587] [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: 04/11/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Identification of novel therapeutics and risk assessment in early stages of Alzheimer's disease (AD) is a crucial aspect of addressing this complex disease. We characterized gene-expression patterns at the mild cognitive impairment (MCI) stage to identify critical mRNA measures and gene clusters associated with AD pathogenesis. METHODS We used a transcriptomics approach, integrating magnetic resonance imaging (MRI) and peripheral blood-based gene expression data using persistent homology (PH) followed by kernel-based clustering. RESULTS We identified three clusters of genes significantly associated with diagnosis of amnestic MCI. The biological processes associated with each cluster were mitochondrial function, NF-kB signaling, and apoptosis. Cluster-level associations with cortical thickness displayed canonical AD-like patterns. Driver genes from clusters were also validated in an external dataset for prediction of amyloidosis and clinical diagnosis. DISCUSSION We found a disease-relevant transcriptomic signature sensitive to prodromal AD and identified a subset of potential therapeutic targets associated with AD pathogenesis.
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Affiliation(s)
| | - Alice Patania
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Xiaoran Yan
- Indiana University Network Sciences InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Diana Svaldi
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Tugce Duran
- Department of Internal Medicine, Section of Gerontology & Geriatric MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Niraj Shah
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Sara Nemes
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eric Chen
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Liana G. Apostolova
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
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6
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Lahti J, Tuominen S, Yang Q, Pergola G, Ahmad S, Amin N, Armstrong NJ, Beiser A, Bey K, Bis JC, Boerwinkle E, Bressler J, Campbell A, Campbell H, Chen Q, Corley J, Cox SR, Davies G, De Jager PL, Derks EM, Faul JD, Fitzpatrick AL, Fohner AE, Ford I, Fornage M, Gerring Z, Grabe HJ, Grodstein F, Gudnason V, Simonsick E, Holliday EG, Joshi PK, Kajantie E, Kaprio J, Karell P, Kleineidam L, Knol MJ, Kochan NA, Kwok JB, Leber M, Lam M, Lee T, Li S, Loukola A, Luck T, Marioni RE, Mather KA, Medland S, Mirza SS, Nalls MA, Nho K, O'Donnell A, Oldmeadow C, Painter J, Pattie A, Reppermund S, Risacher SL, Rose RJ, Sadashivaiah V, Scholz M, Satizabal CL, Schofield PW, Schraut KE, Scott RJ, Simino J, Smith AV, Smith JA, Stott DJ, Surakka I, Teumer A, Thalamuthu A, Trompet S, Turner ST, van der Lee SJ, Villringer A, Völker U, Wilson RS, Wittfeld K, Vuoksimaa E, Xia R, Yaffe K, Yu L, Zare H, Zhao W, Ames D, Attia J, Bennett DA, Brodaty H, Chasman DI, Goldman AL, Hayward C, Ikram MA, Jukema JW, Kardia SLR, Lencz T, Loeffler M, Mattay VS, Palotie A, Psaty BM, Ramirez A, Ridker PM, Riedel-Heller SG, Sachdev PS, Saykin AJ, Scherer M, Schofield PR, Sidney S, Starr JM, Trollor J, Ulrich W, Wagner M, Weir DR, Wilson JF, Wright MJ, Weinberger DR, Debette S, Eriksson JG, Mosley TH, Launer LJ, van Duijn CM, Deary IJ, Seshadri S, Räikkönen K. Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning. Mol Psychiatry 2022; 27:4419-4431. [PMID: 35974141 PMCID: PMC9734053 DOI: 10.1038/s41380-022-01710-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022]
Abstract
Understanding the genomic basis of memory processes may help in combating neurodegenerative disorders. Hence, we examined the associations of common genetic variants with verbal short-term memory and verbal learning in adults without dementia or stroke (N = 53,637). We identified novel loci in the intronic region of CDH18, and at 13q21 and 3p21.1, as well as an expected signal in the APOE/APOC1/TOMM40 region. These results replicated in an independent sample. Functional and bioinformatic analyses supported many of these loci and further implicated POC1. We showed that polygenic score for verbal learning associated with brain activation in right parieto-occipital region during working memory task. Finally, we showed genetic correlations of these memory traits with several neurocognitive and health outcomes. Our findings suggest a role of several genomic loci in verbal memory processes.
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Affiliation(s)
- Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland.
- Turku Institute of Advanced Studies, University of Turku, Turku, Finland.
| | - Samuli Tuominen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Qiong Yang
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Giulio Pergola
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Basic Medical Science, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Murdoch University, Murdoch, WA, Australia
| | - Alexa Beiser
- Department of Biostatistics, Boston University, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Katharina Bey
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Janie Corley
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Eske M Derks
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Annette L Fitzpatrick
- Department of Family Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Institute of Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - Myriam Fornage
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zachary Gerring
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases, Greifswald, Germany
| | - Francine Grodstein
- Channing Laboratory, Brigham and Women's Hospital, Boston, MA, USA
- Harvard School of Public Health, Boston, MA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Assocation, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Eleanor Simonsick
- Translational Gerontology Branch, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Elizabeth G Holliday
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Institute of Social and Preventive Medicine, University of Lausanne, Lausanne, Switzerland
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Hospital for Children and Adolescents, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Pauliina Karell
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Luca Kleineidam
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Nicole A Kochan
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Markus Leber
- Department of Psychiatry, University of Cologne, Cologne, Germany
| | - Max Lam
- Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Teresa Lee
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Shuo Li
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki Central Hospital, Helsinki, Finland
| | - Tobias Luck
- Department of Economic and Social Sciences & Institute of Social Medicine, Rehabilitation Sciences and Healthcare Research, University of Applied Sciences Nordhausen, Nordhausen, Germany
- University of Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Leipzig, Germany
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Sunnybrook Health Sciences Centre, University of Toronto, Randwick, NSW, Australia
| | - Sarah Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Saira S Mirza
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Neurology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adrienne O'Donnell
- Department of Biostatistics, Boston University, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Christopher Oldmeadow
- Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Jodie Painter
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alison Pattie
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Simone Reppermund
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard J Rose
- Department of Psychological & Brain Sciences, Indiana University Bloomington, Bloomington, IN, USA
| | - Vijay Sadashivaiah
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Claudia L Satizabal
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Peter W Schofield
- Neuropsychiatry Service, Hunter New England Local Health District, Charlestown, NSW, Australia
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, Royal Infirmary of Edinburgh, University of Edinburgh, Edinburgh, UK
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Jeannette Simino
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Albert V Smith
- Icelandic Heart Assocation, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
- Institute of Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ida Surakka
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Neurology and Alzheimer Center, VU University Medical Center, Amsterdam, The Netherlands
| | - Arno Villringer
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Day Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Robert S Wilson
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases, Greifswald, Germany
| | - Eero Vuoksimaa
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Rui Xia
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kristine Yaffe
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Habil Zare
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, San Antonio, TX, USA
- University of Texas Health Sciences Center, Houston, NA, US
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - David Ames
- National Ageing Research Institute, Parkville, Melbourne, VIC, Australia
- University of Melbourne, Academic Unit for Psychiatry of Old Age, St George's Hospital, Melbourne, VIC, Australia
| | - John Attia
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
- Clinical Research Design, IT and Statistical Support Unit, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Henry Brodaty
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Dementia Collaborative Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aaron L Goldman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Todd Lencz
- Hofstra Northwell School of Medicine, Hempstead, NY, USA
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Venkata S Mattay
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Food and Drug Administration, Washington, DC, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology and Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Heath Research Institute, Seattle, WA, USA
| | - Alfredo Ramirez
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
- Department of Psychiatry, University of Cologne, Cologne, Germany
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steffi G Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Martin Scherer
- Institute of Primary Medical Care, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter R Schofield
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Stephen Sidney
- Kaiser Permanente Northern California, Division of Research, Oakland, CA, USA
| | - John M Starr
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Julian Trollor
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - William Ulrich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Michael Wagner
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie Debette
- Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, University of Bordeaux, Bordeaux, France
- Bordeaux University Hospital (CHU Bordeaux), Department of Neurology, Bordeaux, France
| | - Johan G Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, and Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Helsinki, Singapore
| | - Thomas H Mosley
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Public Health, Oxford University, Oxford, UK
| | - Ian J Deary
- Department of Psychology, Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
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7
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Abrishamcar S, Chen J, Feil D, Kilanowski A, Koen N, Vanker A, Wedderburn CJ, Donald KA, Zar HJ, Stein DJ, Hüls A. DNA methylation as a potential mediator of the association between prenatal tobacco and alcohol exposure and child neurodevelopment in a South African birth cohort. Transl Psychiatry 2022; 12:418. [PMID: 36180424 PMCID: PMC9525659 DOI: 10.1038/s41398-022-02195-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 01/12/2023] Open
Abstract
Prenatal tobacco exposure (PTE) and prenatal alcohol exposure (PAE) have been associated with an increased risk of delayed neurodevelopment in children as well as differential newborn DNA methylation (DNAm). However, the biological mechanisms connecting PTE and PAE, DNAm, and neurodevelopment are largely unknown. Here we aim to determine whether differential DNAm mediates the association between PTE and PAE and neurodevelopment at 6 (N = 112) and 24 months (N = 184) in children from the South African Drakenstein Child Health Study. PTE and PAE were assessed antenatally using urine cotinine measurements and the ASSIST questionnaire, respectively. Cord blood DNAm was measured using the EPIC and 450 K BeadChips. Neurodevelopment (cognitive, language, motor, adaptive behavior, socioemotional) was measured using the Bayley Scales of Infant and Toddler Development, Third Edition. We constructed methylation risk scores (MRS) for PTE and PAE and conducted causal mediation analysis (CMA) with these MRS as mediators. Next, we conducted a high-dimensional mediation analysis to identify individual CpG sites as potential mediators, followed by a CMA to estimate the average causal mediation effects (ACME) and total effect (TE). PTE and PAE were associated with neurodevelopment at 6 but not at 24 months. PTE MRS reached a prediction accuracy (R2) of 0.23 but did not significantly mediate the association between PTE and neurodevelopment. PAE MRS was not predictive of PAE (R2 = 0.006). For PTE, 31 CpG sites and eight CpG sites were identified as significant mediators (ACME and TE P < 0.05) for the cognitive and motor domains at 6 months, respectively. For PAE, 16 CpG sites and 1 CpG site were significant mediators for the motor and adaptive behavior domains at 6 months, respectively. Several of the associated genes, including MAD1L1, CAMTA1, and ALDH1A2 have been implicated in neurodevelopmental delay, suggesting that differential DNAm may partly explain the biological mechanisms underlying the relationship between PTE and PAE and child neurodevelopment.
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Affiliation(s)
- Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dakotah Feil
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Anna Kilanowski
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology, Pettenkofer School of Public Health, LMU Munich, Munich, Germany
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Aneesa Vanker
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Catherine J Wedderburn
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Kirsten A Donald
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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8
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Querfurth H, Lee HK. Mammalian/mechanistic target of rapamycin (mTOR) complexes in neurodegeneration. Mol Neurodegener 2021; 16:44. [PMID: 34215308 PMCID: PMC8252260 DOI: 10.1186/s13024-021-00428-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Novel targets to arrest neurodegeneration in several dementing conditions involving misfolded protein accumulations may be found in the diverse signaling pathways of the Mammalian/mechanistic target of rapamycin (mTOR). As a nutrient sensor, mTOR has important homeostatic functions to regulate energy metabolism and support neuronal growth and plasticity. However, in Alzheimer's disease (AD), mTOR alternately plays important pathogenic roles by inhibiting both insulin signaling and autophagic removal of β-amyloid (Aβ) and phospho-tau (ptau) aggregates. It also plays a role in the cerebrovascular dysfunction of AD. mTOR is a serine/threonine kinase residing at the core in either of two multiprotein complexes termed mTORC1 and mTORC2. Recent data suggest that their balanced actions also have implications for Parkinson's disease (PD) and Huntington's disease (HD), Frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). Beyond rapamycin; an mTOR inhibitor, there are rapalogs having greater tolerability and micro delivery modes, that hold promise in arresting these age dependent conditions.
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Affiliation(s)
- Henry Querfurth
- Department of Neurology, Tufts Medical Center, Boston, Massachusetts, USA.
| | - Han-Kyu Lee
- Department of Neurology, Tufts Medical Center, Boston, Massachusetts, USA
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9
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Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L. Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease. Nat Commun 2020; 11:6114. [PMID: 33257653 PMCID: PMC7704686 DOI: 10.1038/s41467-020-19791-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
DNA methylation differences in Alzheimer's disease (AD) have been reported. Here, we conducted a meta-analysis of more than 1000 prefrontal cortex brain samples to prioritize the most consistent methylation differences in multiple cohorts. Using a uniform analysis pipeline, we identified 3751 CpGs and 119 differentially methylated regions (DMRs) significantly associated with Braak stage. Our analysis identified differentially methylated genes such as MAMSTR, AGAP2, and AZU1. The most significant DMR identified is located on the MAMSTR gene, which encodes a cofactor that stimulates MEF2C. Notably, MEF2C cooperates with another transcription factor, PU.1, a central hub in the AD gene network. Our enrichment analysis highlighted the potential roles of the immune system and polycomb repressive complex 2 in pathological AD. These results may help facilitate future mechanistic and biomarker discovery studies in AD.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Brian W Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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10
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Nho K, Nudelman K, Allen M, Hodges A, Kim S, Risacher SL, Apostolova LG, Lin K, Lunnon K, Wang X, Burgess JD, Ertekin-Taner N, Petersen RC, Wang L, Qi Z, He A, Neuhaus I, Patel V, Foroud T, Faber KM, Lovestone S, Simmons A, Weiner MW, Saykin AJ. Genome-wide transcriptome analysis identifies novel dysregulated genes implicated in Alzheimer's pathology. Alzheimers Dement 2020; 16:1213-1223. [PMID: 32755048 DOI: 10.1002/alz.12092] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/23/2020] [Accepted: 02/21/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Abnormal gene expression patterns may contribute to the onset and progression of late-onset Alzheimer's disease (LOAD). METHODS We performed transcriptome-wide meta-analysis (N = 1440) of blood-based microarray gene expression profiles as well as neuroimaging and cerebrospinal fluid (CSF) endophenotype analysis. RESULTS We identified and replicated five genes (CREB5, CD46, TMBIM6, IRAK3, and RPAIN) as significantly dysregulated in LOAD. The most significantly altered gene, CREB5, was also associated with brain atrophy and increased amyloid beta (Aβ) accumulation, especially in the entorhinal cortex region. cis-expression quantitative trait loci mapping analysis of CREB5 detected five significant associations (P < 5 × 10-8 ), where rs56388170 (most significant) was also significantly associated with global cortical Aβ deposition measured by [18 F]Florbetapir positron emission tomography and CSF Aβ1-42 . DISCUSSION RNA from peripheral blood indicated a differential gene expression pattern in LOAD. Genes identified have been implicated in biological processes relevant to Alzheimer's disease. CREB, in particular, plays a key role in nervous system development, cell survival, plasticity, and learning and memory.
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Affiliation(s)
- Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kelly Nudelman
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.,National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University, Indiana
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida
| | - Angela Hodges
- Psychology & Neuroscience, Institute of Psychiatry, King's college London, London, UK
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Electrical and Computer Engineering, State University of New York, Oswego, New York
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Liana G Apostolova
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kuang Lin
- Psychology & Neuroscience, Institute of Psychiatry, King's college London, London, UK
| | | | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, Florida
| | - Jeremy D Burgess
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida.,Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida
| | - Ronald C Petersen
- Department of Neurology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - Lisu Wang
- Bristol-Meyers Squibb, Wallingford, Connecticut
| | - Zhenhao Qi
- Bristol-Meyers Squibb, Wallingford, Connecticut
| | - Aiqing He
- Bristol-Meyers Squibb, Wallingford, Connecticut
| | | | | | - Tatiana Foroud
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.,National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University, Indiana
| | - Kelley M Faber
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.,National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University, Indiana
| | | | - Andrew Simmons
- Psychology & Neuroscience, Institute of Psychiatry, King's college London, London, UK
| | - Michael W Weiner
- Departments of Radiology, Medicine, and Psychiatry, University of California-San Francisco, San Francisco, California.,Department of Veterans Affairs Medical Center, San Francisco, California
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
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11
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Wei X, Du M, Li D, Wen S, Xie J, Li Y, Chen A, Zhang K, Xu P, Jia M, Wen C, Zhou H, Lyu J, Yang Y, Fang H. Mutations in FASTKD2 are associated with mitochondrial disease with multi-OXPHOS deficiency. Hum Mutat 2020; 41:961-972. [PMID: 31944455 DOI: 10.1002/humu.23985] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 02/03/2023]
Abstract
Mutations in FASTKD2, a mitochondrial RNA binding protein, have been associated with mitochondrial encephalomyopathy with isolated complex IV deficiency. However, deficiencies related to other oxidative phosphorylation system (OXPHOS) complexes have not been reported. Here, we identified three novel FASTKD2 mutations, c.808_809insTTTCAGTTTTG, homoplasmic mutation c.868C>T, and heteroplasmic mutation c.1859delT/c.868C>T, in patients with mitochondrial encephalomyopathy. Cell-based complementation assay revealed that these three FASTKD2 mutations were pathogenic. Mitochondrial functional analysis revealed that mutations in FASTKD2 impaired the mitochondrial function in patient-derived lymphocytes due to the deficiency in multi-OXPHOS complexes, whereas mitochondrial complex II remained unaffected. Consistent results were also found in human primary muscle cell and zebrafish with knockdown of FASTKD2. Furthermore, we discovered that FASTKD2 mutation is not inherently associated with epileptic seizures, optic atrophy, and loss of visual function. Alternatively, a patient with FASTKD2 mutation can show sinus tachycardia and hypertrophic cardiomyopathy, which was partially confirmed in zebrafish with knockdown of FASTKD2. In conclusion, both in vivo and in vitro studies suggest that loss of function mutation in FASTKD2 is responsible for multi-OXPHOS complexes deficiency, and FASTKD2-associated mitochondrial disease has a high degree of clinical heterogenicity.
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Affiliation(s)
- Xiujuan Wei
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Miaomiao Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Dongxiao Li
- Department of Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Shumeng Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
- Department of Clinical Laboratory, Qingdao Municipal Hospital (Group), Qingdao, China
| | - Jie Xie
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Aolong Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Kun Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Pu Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Manli Jia
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Chaowei Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Huaibin Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, China
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12
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Shen L, Thompson PM. Brain Imaging Genomics: Integrated Analysis and Machine Learning. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2020; 108:125-162. [PMID: 31902950 PMCID: PMC6941751 DOI: 10.1109/jproc.2019.2947272] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Brain imaging genomics is an emerging data science field, where integrated analysis of brain imaging and genomics data, often combined with other biomarker, clinical and environmental data, is performed to gain new insights into the phenotypic, genetic and molecular characteristics of the brain as well as their impact on normal and disordered brain function and behavior. It has enormous potential to contribute significantly to biomedical discoveries in brain science. Given the increasingly important role of statistical and machine learning in biomedicine and rapidly growing literature in brain imaging genomics, we provide an up-to-date and comprehensive review of statistical and machine learning methods for brain imaging genomics, as well as a practical discussion on method selection for various biomedical applications.
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Affiliation(s)
- Li Shen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Institute for Neuroimaging & Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90232, USA
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13
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Dopamine perturbation of gene co-expression networks reveals differential response in schizophrenia for translational machinery. Transl Psychiatry 2018; 8:278. [PMID: 30546022 PMCID: PMC6293320 DOI: 10.1038/s41398-018-0325-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/13/2018] [Indexed: 12/02/2022] Open
Abstract
The dopaminergic hypothesis of schizophrenia (SZ) postulates that positive symptoms of SZ, in particular psychosis, are due to disturbed neurotransmission via the dopamine (DA) receptor D2 (DRD2). However, DA is a reactive molecule that yields various oxidative species, and thus has important non-receptor-mediated effects, with empirical evidence of cellular toxicity and neurodegeneration. Here we examine non-receptor-mediated effects of DA on gene co-expression networks and its potential role in SZ pathology. Transcriptomic profiles were measured by RNA-seq in B-cell transformed lymphoblastoid cell lines from 514 SZ cases and 690 controls, both before and after exposure to DA ex vivo (100 μM). Gene co-expression modules were identified using Weighted Gene Co-expression Network Analysis for both baseline and DA-stimulated conditions, with each module characterized for biological function and tested for association with SZ status and SNPs from a genome-wide panel. We identified seven co-expression modules under baseline, of which six were preserved in DA-stimulated data. One module shows significantly increased association with SZ after DA perturbation (baseline: P = 0.023; DA-stimulated: P = 7.8 × 10-5; ΔAIC = -10.5) and is highly enriched for genes related to ribosomal proteins and translation (FDR = 4 × 10-141), mitochondrial oxidative phosphorylation, and neurodegeneration. SNP association testing revealed tentative QTLs underlying module co-expression, notably at FASTKD2 (top P = 2.8 × 10-6), a gene involved in mitochondrial translation. These results substantiate the role of translational machinery in SZ pathogenesis, providing insights into a possible dopaminergic mechanism disrupting mitochondrial function, and demonstrates the utility of disease-relevant functional perturbation in the study of complex genetic etiologies.
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Lemche E. Early Life Stress and Epigenetics in Late-onset Alzheimer's Dementia: A Systematic Review. Curr Genomics 2018; 19:522-602. [PMID: 30386171 PMCID: PMC6194433 DOI: 10.2174/1389202919666171229145156] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/27/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022] Open
Abstract
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing. Discussed are relevant ELS studies, and findings from three mitogen-activated protein kinase pathways (JNK/SAPK pathway, ERK pathway, p38/MAPK pathway) relevant for mediating environmental stresses. Further considered were the roles of autophagy impairment, neuroinflammation, and brain insulin resistance. For the meta-analytic evaluation, 224 candidate gene loci were extracted from reviews of animal studies of LOAD pathophysiological mechanisms, of which 60 had no positive results in human LOAD association studies. These loci were combined with 89 gene loci confirmed as LOAD risk genes in previous GWAS and WES. Of the 313 risk gene loci evaluated, there were 35 human reports on epigenomic modifications in terms of methylation or histone acetylation. 64 microRNA gene regulation mechanisms were published for the compiled loci. Genomic association studies support close relations of both noradrenergic and glucocorticoid systems with LOAD. For HPA involvement, a CRHR1 haplotype with MAPT was described, but further association of only HSD11B1 with LOAD found; however, association of FKBP1 and NC3R1 polymorphisms was documented in support of stress influence to LOAD. In the brain insulin system, IGF2R, INSR, INSRR, and plasticity regulator ARC, were associated with LOAD. Pertaining to compromised myelin stability in LOAD, relevant associations were found for BIN1, RELN, SORL1, SORCS1, CNP, MAG, and MOG. Regarding epigenetic modifications, both methylation variability and de-acetylation were reported for LOAD. The majority of up-to-date epigenomic findings include reported modifications in the well-known LOAD core pathology loci MAPT, BACE1, APP (with FOS, EGR1), PSEN1, PSEN2, and highlight a central role of BDNF. Pertaining to ELS, relevant loci are FKBP5, EGR1, GSK3B; critical roles of inflammation are indicated by CRP, TNFA, NFKB1 modifications; for cholesterol biosynthesis, DHCR24; for myelin stability BIN1, SORL1, CNP; pertaining to (epi)genetic mechanisms, hTERT, MBD2, DNMT1, MTHFR2. Findings on gene regulation were accumulated for BACE1, MAPK signalling, TLR4, BDNF, insulin signalling, with most reports for miR-132 and miR-27. Unclear in epigenomic studies remains the role of noradrenergic signalling, previously demonstrated by neuropathological findings of childhood nucleus caeruleus degeneration for LOAD tauopathy.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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15
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Espinosa A, Hernández-Olasagarre B, Moreno-Grau S, Kleineidam L, Heilmann-Heimbach S, Hernández I, Wolfsgruber S, Wagner H, Rosende-Roca M, Mauleón A, Vargas L, Lafuente A, Rodríguez-Gómez O, Abdelnour C, Gil S, Marquié M, Santos-Santos MA, Sanabria Á, Ortega G, Monté-Rubio G, Pérez A, Ibarria M, Ruiz S, Kornhuber J, Peters O, Frölich L, Hüll M, Wiltfang J, Luck T, Riedel-Heller S, Montrreal L, Cañabate P, Moreno M, Preckler S, Aguilera N, de Rojas I, Orellana A, Alegret M, Valero S, Nöthen MM, Wagner M, Jessen F, Tárraga L, Boada M, Ramírez A, Ruiz A. Exploring Genetic Associations of Alzheimer's Disease Loci With Mild Cognitive Impairment Neurocognitive Endophenotypes. Front Aging Neurosci 2018; 10:340. [PMID: 30425636 PMCID: PMC6218590 DOI: 10.3389/fnagi.2018.00340] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/08/2018] [Indexed: 11/30/2022] Open
Abstract
The role of genetic risk markers for Alzheimer’s disease (AD) in mediating the neurocognitive endophenotypes (NEs) of subjects with mild cognitive impairment (MCI) has rarely been studied. The aim of the present study was to investigate the relationship between well-known AD-associated single-nucleotide polymorphisms (SNPs) and individual NEs routinely evaluated during diagnosis of MCI, AD, and other dementias. The Fundació ACE (ACE) dataset, comprising information from 1245 patients with MCI, was analyzed, including the total sample, amnestic MCI (aMCI) (n = 811), and non-amnestic MCI (naMCI) (n = 434). As probable-MCI (Pr-MCI) patients with memory impairment have a higher risk of AD, which could influence the statistical power to detect genetic associations, the MCI phenotype was also stratified into four related conditions: Pr-aMCI (n = 262), Pr-naMCI (n = 76), possible (Pss)-aMCI (n = 549), and Pss-naMCI (n = 358). Validation analyses were performed using data from the German study on Aging, Cognition, and Dementia in primary care patients (AgeCoDe), and the German Dementia Competence Network (DCN). SNP associations with NEs were calculated in PLINK using multivariate linear regression analysis adjusted for age, gender, and education. In the total MCI sample, APOE-ε4 was significantly associated with the memory function NEs “delayed recall (DR)” (β = -0.76, p = 4.1 × 10-10), “learning” (β = -1.35, p = 2.91 × 10-6), and “recognition memory” (β = -0.58, p = 9.67 × 10-5); and with “DR” in the aMCI group (β = -0.36, p = 2.96 × 10-5). These results were confirmed by validation in the AgeCoDe (n = 503) and DCN (n = 583) datasets. APOE-ε4 was also significantly associated with the NE “learning” in individuals classified as having Pss-aMCI (β = -1.37, p = 5.82 × 10-5). Moreover, there was a near study-wide significant association between the HS3ST1 locus (rs6448799) and the “backward digits” working memory NE (β = 0.52, p = 7.57 × 10-5) among individuals with Pr-aMCI, while the AP2A2 locus (rs10751667) was significantly associated with the language NE “repetition” (β = -0.19, p = 5.34 × 10-6). Overall, our findings support specific associations of established AD-associated SNPs with MCI NEs.
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Affiliation(s)
- Ana Espinosa
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Begoña Hernández-Olasagarre
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Sonia Moreno-Grau
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Luca Kleineidam
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Isabel Hernández
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Steffen Wolfsgruber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Holger Wagner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Maitée Rosende-Roca
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Ana Mauleón
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Liliana Vargas
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Asunción Lafuente
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Octavio Rodríguez-Gómez
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Carla Abdelnour
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Silvia Gil
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Marta Marquié
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Miguel A Santos-Santos
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Ángela Sanabria
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Gemma Ortega
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Gemma Monté-Rubio
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Alba Pérez
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Marta Ibarria
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Susana Ruiz
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University Clinic Erlangen, Erlangen, Germany
| | - Oliver Peters
- Department of Psychiatry, Charité University Medicine, Berlin, Germany
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Hüll
- Center for Geriatric Medicine and Section of Gerontopsychiatry and Neuropsychology, Medical School, University of Freiburg, Freiburg, Germany
| | - Jens Wiltfang
- Department of Psychiatry and Psychotherapy, University of Göttingen, Göttingen, Germany
| | - Tobias Luck
- Department of Economic and Social Sciences & Institute of Social Medicine, Rehabilitation Sciences and Healthcare Research (ISRV), University of Applied Sciences Nordhausen, Nordhausen, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Laura Montrreal
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Pilar Cañabate
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariola Moreno
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Silvia Preckler
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Nuria Aguilera
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Itziar de Rojas
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Adelina Orellana
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Montserrat Alegret
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Sergi Valero
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Wagner
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Frank Jessen
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Lluis Tárraga
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Alfredo Ramírez
- Department for Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany.,Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Agustín Ruiz
- Research Center and Memory Clinic, Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
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16
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Mitochondrial DNA transcription and translation: clinical syndromes. Essays Biochem 2018; 62:321-340. [PMID: 29980628 PMCID: PMC6056718 DOI: 10.1042/ebc20170103] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
Abstract
Diagnosing primary mitochondrial diseases is challenging in clinical practice. Although, defective oxidative phosphorylation (OXPHOS) is the common final pathway, it is unknown why different mtDNA or nuclear mutations result in largely heterogeneous and often tissue -specific clinical presentations. Mitochondrial tRNA (mt-tRNA) mutations are frequent causes of mitochondrial diseases both in children and adults. However numerous nuclear mutations involved in mitochondrial protein synthesis affecting ubiquitously expressed genes have been reported in association with very tissue specific clinical manifestations suggesting that there are so far unknown factors determining the tissue specificity in mitochondrial translation. Most of these gene defects result in histological abnormalities and multiple respiratory chain defects in the affected organs. The clinical phenotypes are usually early-onset, severe, and often fatal, implying the importance of mitochondrial translation from birth. However, some rare, reversible infantile mitochondrial diseases are caused by very specific defects of mitochondrial translation. An unbiased genetic approach (whole exome sequencing, RNA sequencing) combined with proteomics and functional studies revealed novel factors involved in mitochondrial translation which contribute to the clinical manifestation and recovery in these rare reversible mitochondrial conditions.
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17
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Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, Schneider JA. Religious Orders Study and Rush Memory and Aging Project. J Alzheimers Dis 2018; 64:S161-S189. [PMID: 29865057 PMCID: PMC6380522 DOI: 10.3233/jad-179939] [Citation(s) in RCA: 630] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Religious Orders Study and Rush Memory and Aging Project are both ongoing longitudinal clinical-pathologic cohort studies of aging and Alzheimer's disease (AD). OBJECTIVES To summarize progress over the past five years and its implications for understanding neurodegenerative diseases. METHODS Participants in both studies are older adults who enroll without dementia and agree to detailed longitudinal clinical evaluations and organ donation. The last review summarized findings through the end of 2011. Here we summarize progress and study findings over the past five years and discuss new directions for how these studies can inform on aging and AD in the future. RESULTS We summarize 1) findings on the relation of neurobiology to clinical AD; 2) neurobiologic pathways linking risk factors to clinical AD; 3) non-cognitive AD phenotypes including motor function and decision making; 4) the development of a novel drug discovery platform. CONCLUSION Complexity at multiple levels needs to be understood and overcome to develop effective treatments and preventions for cognitive decline and AD dementia.
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Affiliation(s)
- David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Patricia A. Boyle
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Robert S. Wilson
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL., USA
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18
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Maiese K. Forkhead transcription factors: new considerations for alzheimer's disease and dementia. JOURNAL OF TRANSLATIONAL SCIENCE 2016; 2:241-247. [PMID: 27390624 PMCID: PMC4932907 DOI: 10.15761/jts.1000146] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Life expectancy of individuals in both developed and undeveloped nations continues to rise at an unprecedented rate. Coupled to this increase in longevity for individuals is the rise in the incidence of chronic neurodegenerative disorders that includes Alzheimer's disease (AD). Currently, almost ten percent of the population over the age of 65 suffers from AD, a disorder that is presently without definitive therapy to prevent the onset or progression of cognitive loss. Yet, it is estimated that AD will continue to significantly increase throughout the world to impact millions of individuals and foster the escalation of healthcare costs. One potential target for the development of novel strategies against AD and other cognitive disorders involves the mammalian forkhead transcription factors of the O class (FoxOs). FoxOs are present in "cognitive centers" of the brain to include the hippocampus, the amygdala, and the nucleus accumbens and may be required for memory formation and consolidation. FoxOs play a critical role in determining survival of multiple cell types in the nervous system, drive pathways of apoptosis and autophagy, and control stem cell proliferation and differentiation. FoxOs also interface with multiple cellular pathways that include growth factors, Wnt signaling, Wnt1 inducible signaling pathway protein 1 (WISP1), and silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) that ultimately may control FoxOs and determine the fate and function of cells in the nervous system that control memory and cognition. Future work that can further elucidate the complex relationship FoxOs hold over cell fate and cognitive function could yield exciting prospects for the treatment of a number of neurodegenerative disorders including AD.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, Newark, New Jersey 07101
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19
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Garza-Lombó C, Gonsebatt ME. Mammalian Target of Rapamycin: Its Role in Early Neural Development and in Adult and Aged Brain Function. Front Cell Neurosci 2016; 10:157. [PMID: 27378854 PMCID: PMC4910040 DOI: 10.3389/fncel.2016.00157] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/30/2016] [Indexed: 01/14/2023] Open
Abstract
The kinase mammalian target of rapamycin (mTOR) integrates signals triggered by energy, stress, oxygen levels, and growth factors. It regulates ribosome biogenesis, mRNA translation, nutrient metabolism, and autophagy. mTOR participates in various functions of the brain, such as synaptic plasticity, adult neurogenesis, memory, and learning. mTOR is present during early neural development and participates in axon and dendrite development, neuron differentiation, and gliogenesis, among other processes. Furthermore, mTOR has been shown to modulate lifespan in multiple organisms. This protein is an important energy sensor that is present throughout our lifetime its role must be precisely described in order to develop therapeutic strategies and prevent diseases of the central nervous system. The aim of this review is to present our current understanding of the functions of mTOR in neural development, the adult brain and aging.
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Affiliation(s)
- Carla Garza-Lombó
- Departamento de Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México México
| | - María E Gonsebatt
- Departamento de Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México México
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20
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Tadayon SH, Vaziri-Pashkam M, Kahali P, Ansari Dezfouli M, Abbassian A. Common Genetic Variant in VIT Is Associated with Human Brain Asymmetry. Front Hum Neurosci 2016; 10:236. [PMID: 27252636 PMCID: PMC4877381 DOI: 10.3389/fnhum.2016.00236] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/04/2016] [Indexed: 11/22/2022] Open
Abstract
Brain asymmetry varies across individuals. However, genetic factors contributing to this normal variation are largely unknown. Here we studied variation of cortical surface area asymmetry in a large sample of subjects. We performed principal component analysis (PCA) to capture correlated asymmetry variation across cortical regions. We found that caudal and rostral anterior cingulate together account for a substantial part of asymmetry variation among individuals. To find SNPs associated with this subset of brain asymmetry variation we performed a genome-wide association study followed by replication in an independent cohort. We identified one SNP (rs11691187) that had genome-wide significant association (PCombined = 2.40e-08). The rs11691187 is in the first intron of VIT. In a follow-up analysis, we found that VIT gene expression is associated with brain asymmetry in six donors of the Allen Human Brain Atlas. Based on these findings we suggest that VIT contributes to normal brain asymmetry variation. Our results can shed light on disorders associated with altered brain asymmetry.
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Affiliation(s)
- Sayed H Tadayon
- School of Cognitive Sciences, Institute for Research in Fundamental SciencesTehran, Iran; School of Mathematics, Institute for Research in Fundamental SciencesTehran, Iran
| | - Maryam Vaziri-Pashkam
- Vision Sciences Laboratory, Department of Psychology, Harvard University Cambridge, MA, USA
| | - Pegah Kahali
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences Tehran, Iran
| | - Mitra Ansari Dezfouli
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran Tehran, Iran
| | - Abdolhossein Abbassian
- School of Cognitive Sciences, Institute for Research in Fundamental SciencesTehran, Iran; School of Mathematics, Institute for Research in Fundamental SciencesTehran, Iran
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21
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Maiese K. Targeting molecules to medicine with mTOR, autophagy and neurodegenerative disorders. Br J Clin Pharmacol 2015; 82:1245-1266. [PMID: 26469771 DOI: 10.1111/bcp.12804] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 10/11/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative disorders are significantly increasing in incidence as the age of the global population continues to climb with improved life expectancy. At present, more than 30 million individuals throughout the world are impacted by acute and chronic neurodegenerative disorders with limited treatment strategies. The mechanistic target of rapamycin (mTOR), also known as the mammalian target of rapamycin, is a 289 kDa serine/threonine protein kinase that offers exciting possibilities for novel treatment strategies for a host of neurodegenerative diseases that include Alzheimer's disease, Parkinson's disease, Huntington's disease, epilepsy, stroke and trauma. mTOR governs the programmed cell death pathways of apoptosis and autophagy that can determine neuronal stem cell development, precursor cell differentiation, cell senescence, cell survival and ultimate cell fate. Coupled to the cellular biology of mTOR are a number of considerations for the development of novel treatments involving the fine control of mTOR signalling, tumourigenesis, complexity of the apoptosis and autophagy relationship, functional outcome in the nervous system, and the intimately linked pathways of growth factors, phosphoinositide 3-kinase (PI 3-K), protein kinase B (Akt), AMP activated protein kinase (AMPK), silent mating type information regulation two homologue one (Saccharomyces cerevisiae) (SIRT1) and others. Effective clinical translation of the cellular signalling mechanisms of mTOR offers provocative avenues for new drug development in the nervous system tempered only by the need to elucidate further the intricacies of the mTOR pathway.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, Newark, New Jersey, 07101, USA.
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22
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DICER1 and microRNA regulation in post-traumatic stress disorder with comorbid depression. Nat Commun 2015; 6:10106. [PMID: 26632874 PMCID: PMC4686835 DOI: 10.1038/ncomms10106] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022] Open
Abstract
DICER1 is an enzyme that generates mature microRNAs (miRNAs), which regulate gene expression post-transcriptionally in brain and other tissues and is involved in synaptic maturation and plasticity. Here, through genome-wide differential gene expression survey of post-traumatic stress disorder (PTSD) with comorbid depression (PTSD&Dep), we find that blood DICER1 expression is significantly reduced in cases versus controls, and replicate this in two independent cohorts. Our follow-up studies find that lower blood DICER1 expression is significantly associated with increased amygdala activation to fearful stimuli, a neural correlate for PTSD. Additionally, a genetic variant in the 3′ un-translated region of DICER1, rs10144436, is significantly associated with DICER1 expression and with PTSD&Dep, and the latter is replicated in an independent cohort. Furthermore, genome-wide differential expression survey of miRNAs in blood in PTSD&Dep reveals miRNAs to be significantly downregulated in cases versus controls. Together, our novel data suggest DICER1 plays a role in molecular mechanisms of PTSD&Dep through the DICER1 and the miRNA regulation pathway. DICER1 is required for the maturation of miRNAs which regulate expression of thousands of genes. Here the authors show significantly reduced levels of DICER1 in individuals having post-traumatic stress disorder and comorbid depression suggestive of a role in the molecular mechanism of the condition.
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Ramanan VK, Risacher SL, Nho K, Kim S, Shen L, McDonald BC, Yoder KK, Hutchins GD, West JD, Tallman EF, Gao S, Foroud TM, Farlow MR, De Jager PL, Bennett DA, Aisen PS, Petersen RC, Jack CR, Toga AW, Green RC, Jagust WJ, Weiner MW, Saykin AJ. GWAS of longitudinal amyloid accumulation on 18F-florbetapir PET in Alzheimer's disease implicates microglial activation gene IL1RAP. Brain 2015; 138:3076-88. [PMID: 26268530 PMCID: PMC4671479 DOI: 10.1093/brain/awv231] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/24/2015] [Indexed: 12/30/2022] Open
Abstract
Brain amyloid deposition is thought to be a seminal event in Alzheimer's disease. To identify genes influencing Alzheimer's disease pathogenesis, we performed a genome-wide association study of longitudinal change in brain amyloid burden measured by (18)F-florbetapir PET. A novel association with higher rates of amyloid accumulation independent from APOE (apolipoprotein E) ε4 status was identified in IL1RAP (interleukin-1 receptor accessory protein; rs12053868-G; P = 1.38 × 10(-9)) and was validated by deep sequencing. IL1RAP rs12053868-G carriers were more likely to progress from mild cognitive impairment to Alzheimer's disease and exhibited greater longitudinal temporal cortex atrophy on MRI. In independent cohorts rs12053868-G was associated with accelerated cognitive decline and lower cortical (11)C-PBR28 PET signal, a marker of microglial activation. These results suggest a crucial role of activated microglia in limiting amyloid accumulation and nominate the IL-1/IL1RAP pathway as a potential target for modulating this process.
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Affiliation(s)
- Vijay K Ramanan
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shannon L. Risacher
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kwangsik Nho
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,5 Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sungeun Kim
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,5 Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Li Shen
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,5 Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brenna C. McDonald
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,6 Department of Neurology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Karmen K. Yoder
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gary D. Hutchins
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - John D. West
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eileen F. Tallman
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sujuan Gao
- 4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,7 Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Tatiana M. Foroud
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,5 Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Martin R. Farlow
- 4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,6 Department of Neurology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Philip L. De Jager
- 8 Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Brigham and Women’s Hospital, Boston, MA 02115, USA,9 Departments of Neurology and Psychiatry, Harvard Medical School, Boston, MA 02115, USA,10 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - David A. Bennett
- 11 Rush Alzheimer’s Disease Centre, Rush University Medical Centre, Chicago, IL 60612, USA
| | - Paul S. Aisen
- 12 University of Southern California Alzheimer's Therapeutic Research Institute, San Diego, CA 92121, USA
| | - Ronald C. Petersen
- 13 Department of Neurology, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | - Clifford R. Jack
- 14 Department of Radiology, Mayo Clinic Minnesota, Rochester, MN 55905, USA
| | - Arthur W. Toga
- 15 Laboratory of NeuroImaging, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Robert C. Green
- 16 Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - William J. Jagust
- 17 Department of Neurology, University of California, Berkeley, CA 94720, USA
| | - Michael W. Weiner
- 18 Departments of Radiology, Medicine, and Psychiatry, University of California-San Francisco, San Francisco, CA 94143, USA,19 Department of Veterans Affairs Medical Centre, San Francisco, CA 94121, USA
| | - Andrew J. Saykin
- 1 Centre for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA,4 Indiana Alzheimer Disease Centre, Indiana University School of Medicine, Indianapolis, IN 46202, USA,5 Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Maiese K. Stem cell guidance through the mechanistic target of rapamycin. World J Stem Cells 2015; 7:999-1009. [PMID: 26328016 PMCID: PMC4550632 DOI: 10.4252/wjsc.v7.i7.999] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/29/2015] [Accepted: 07/17/2015] [Indexed: 02/06/2023] Open
Abstract
Stem cells offer great promise for the treatment of multiple disorders throughout the body. Critical to this premise is the ability to govern stem cell pluripotency, proliferation, and differentiation. The mechanistic target of rapamycin (mTOR), 289-kDa serine/threonine protein kinase, that is a vital component of mTOR Complex 1 and mTOR Complex 2 represents a critical pathway for the oversight of stem cell maintenance. mTOR can control the programmed cell death pathways of autophagy and apoptosis that can yield variable outcomes in stem cell survival and be reliant upon proliferative pathways that include Wnt signaling, Wnt1 inducible signaling pathway protein 1 (WISP1), silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), and trophic factors. mTOR also is a necessary component for the early development and establishment of stem cells as well as having a significant impact in the regulation of the maturation of specific cell phenotypes. Yet, as a proliferative agent, mTOR can not only foster cancer stem cell development and tumorigenesis, but also mediate cell senescence under certain conditions to limit invasive cancer growth. mTOR offers an exciting target for the oversight of stem cell therapies but requires careful consideration of the diverse clinical outcomes that can be fueled by mTOR signaling pathways.
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Saykin AJ, Shen L, Yao X, Kim S, Nho K, Risacher SL, Ramanan VK, Foroud TM, Faber KM, Sarwar N, Munsie LM, Hu X, Soares HD, Potkin SG, Thompson PM, Kauwe JSK, Kaddurah-Daouk R, Green RC, Toga AW, Weiner MW. Genetic studies of quantitative MCI and AD phenotypes in ADNI: Progress, opportunities, and plans. Alzheimers Dement 2015; 11:792-814. [PMID: 26194313 PMCID: PMC4510473 DOI: 10.1016/j.jalz.2015.05.009] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Genetic data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) have been crucial in advancing the understanding of Alzheimer's disease (AD) pathophysiology. Here, we provide an update on sample collection, scientific progress and opportunities, conceptual issues, and future plans. METHODS Lymphoblastoid cell lines and DNA and RNA samples from blood have been collected and banked, and data and biosamples have been widely disseminated. To date, APOE genotyping, genome-wide association study (GWAS), and whole exome and whole genome sequencing data have been obtained and disseminated. RESULTS ADNI genetic data have been downloaded thousands of times, and >300 publications have resulted, including reports of large-scale GWAS by consortia to which ADNI contributed. Many of the first applications of quantitative endophenotype association studies used ADNI data, including some of the earliest GWAS and pathway-based studies of biospecimen and imaging biomarkers, as well as memory and other clinical/cognitive variables. Other contributions include some of the first whole exome and whole genome sequencing data sets and reports in healthy controls, mild cognitive impairment, and AD. DISCUSSION Numerous genetic susceptibility and protective markers for AD and disease biomarkers have been identified and replicated using ADNI data and have heavily implicated immune, mitochondrial, cell cycle/fate, and other biological processes. Early sequencing studies suggest that rare and structural variants are likely to account for significant additional phenotypic variation. Longitudinal analyses of transcriptomic, proteomic, metabolomic, and epigenomic changes will also further elucidate dynamic processes underlying preclinical and prodromal stages of disease. Integration of this unique collection of multiomics data within a systems biology framework will help to separate truly informative markers of early disease mechanisms and potential novel therapeutic targets from the vast background of less relevant biological processes. Fortunately, a broad swath of the scientific community has accepted this grand challenge.
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Affiliation(s)
- Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Li Shen
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaohui Yao
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; School of Informatics and Computing, Indiana University, Purdue University - Indianapolis, Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vijay K Ramanan
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana M Foroud
- 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
| | - Kelley M Faber
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | - Xiaolan Hu
- Bristol-Myers Squibb, Wallingford, CT, USA
| | | | - Steven G Potkin
- Department of Psychiatry and Human Behavior, University of California - Irvine, Irvine, CA, USA
| | - Paul M Thompson
- Department of Neurology, Keck School of Medicine of USC, University of Southern California, Marina del Rey, CA, USA; Imaging Genetics Center, Keck School of Medicine of USC, University of Southern California, Marina del Rey, CA, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA; Department of Neuroscience, Brigham Young University, Provo, UT, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Robert C Green
- Partners Center for Personalized Genetic Medicine, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute for Neuroimaging and Neuroinformatics, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Michael W Weiner
- Department of Radiology, University of California-San Francisco, San Francisco, CA, USA; Department of Medicine, University of California-San Francisco, San Francisco, CA, USA; Department of Psychiatry, University of California-San Francisco, San Francisco, CA, USA; Center for Imaging of Neurodegenerative Diseases, San Francisco VA Medical Center, San Francisco, CA, USA
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Yan J, Kim S, Nho K, Chen R, Risacher SL, Moore JH, Saykin AJ, Shen L. Hippocampal transcriptome-guided genetic analysis of correlated episodic memory phenotypes in Alzheimer's disease. Front Genet 2015; 6:117. [PMID: 25859259 PMCID: PMC4374536 DOI: 10.3389/fgene.2015.00117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/09/2015] [Indexed: 01/18/2023] Open
Abstract
As the most common type of dementia, Alzheimer's disease (AD) is a neurodegenerative disorder initially manifested by impaired memory performances. While the diagnosis information indicates a dichotomous status of a patient, memory scores have the potential to capture the continuous nature of the disease progression and may provide more insights into the underlying mechanism. In this work, we performed a targeted genetic study of memory scores on an AD cohort to identify the associations between a set of genes highly expressed in the hippocampal region and seven cognitive scores related to episodic memory. Both main effects and interaction effects of the targeted genetic markers on these correlated memory scores were examined. In addition to well-known AD genetic markers APOE and TOMM40, our analysis identified a new risk gene NAV2 through the gene-level main effect analysis. NAV2 was found to be significantly and consistently associated with all seven episodic memory scores. Genetic interaction analysis also yielded a few promising hits warranting further investigation, especially for the RAVLT list B Score.
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Affiliation(s)
- Jingwen Yan
- BioHealth, Indiana University School of Informatics and Computing Indianapolis, IN, USA ; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Rui Chen
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Computer Science, Dartmouth College Hanover, NH, USA
| | - Shannon L Risacher
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Jason H Moore
- Genetics, Community and Family Medicine, Geisel School of Medicine at Dartmouth Lebanon, NH, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA ; Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Li Shen
- BioHealth, Indiana University School of Informatics and Computing Indianapolis, IN, USA ; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis, IN, USA ; Indiana Alzheimer Disease Center, Indiana University School of Medicine Indianapolis, IN, USA ; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine Indianapolis, IN, USA
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Ramanan VK, Saykin AJ. FASTKD2 and human memory: functional pathways and prospects for novel therapeutic target development for Alzheimer's disease and age-associated memory decline. Pharmacogenomics 2015; 16:429-32. [PMID: 25916514 PMCID: PMC4478049 DOI: 10.2217/pgs.15.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Vijay K Ramanan
- Center for Neuroimaging, Department of Radiology & Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical & Molecular Genetics, Indiana University School of Medicine, IN, USA; Medical Scientist Training Program, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology & Imaging Sciences, Indiana University School of Medicine, 355 West 16th Street, Suite 4100, Indianapolis, IN 46202, USA; Department of Medical & Molecular Genetics, Indiana University School of Medicine, IN, USA; Medical Scientist Training Program, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA Tel.: +1 317 963 7501 Fax: +1 317 963 7547
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