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Homann J, Osburg T, Ohlei O, Dobricic V, Deecke L, Bos I, Vandenberghe R, Gabel S, Scheltens P, Teunissen CE, Engelborghs S, Frisoni G, Blin O, Richardson JC, Bordet R, Lleó A, Alcolea D, Popp J, Clark C, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Sleegers K, Van Broeckhoven C, Wittig M, Franke A, Lill CM, Blennow K, Zetterberg H, Lovestone S, Streffer J, ten Kate M, Vos SJB, Barkhof F, Visser PJ, Bertram L. Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset. Front Aging Neurosci 2022; 14:840651. [PMID: 35386118 PMCID: PMC8979334 DOI: 10.3389/fnagi.2022.840651] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) is the most frequent neurodegenerative disease with an increasing prevalence in industrialized, aging populations. AD susceptibility has an established genetic basis which has been the focus of a large number of genome-wide association studies (GWAS) published over the last decade. Most of these GWAS used dichotomized clinical diagnostic status, i.e., case vs. control classification, as outcome phenotypes, without the use of biomarkers. An alternative and potentially more powerful study design is afforded by using quantitative AD-related phenotypes as GWAS outcome traits, an analysis paradigm that we followed in this work. Specifically, we utilized genotype and phenotype data from n = 931 individuals collected under the auspices of the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study to perform a total of 19 separate GWAS analyses. As outcomes we used five magnetic resonance imaging (MRI) traits and seven cognitive performance traits. For the latter, longitudinal data from at least two timepoints were available in addition to cross-sectional assessments at baseline. Our GWAS analyses revealed several genome-wide significant associations for the neuropsychological performance measures, in particular those assayed longitudinally. Among the most noteworthy signals were associations in or near EHBP1 (EH domain binding protein 1; on chromosome 2p15) and CEP112 (centrosomal protein 112; 17q24.1) with delayed recall as well as SMOC2 (SPARC related modular calcium binding 2; 6p27) with immediate recall in a memory performance test. On the X chromosome, which is often excluded in other GWAS, we identified a genome-wide significant signal near IL1RAPL1 (interleukin 1 receptor accessory protein like 1; Xp21.3). While polygenic score (PGS) analyses showed the expected strong associations with SNPs highlighted in relevant previous GWAS on hippocampal volume and cognitive function, they did not show noteworthy associations with recent AD risk GWAS findings. In summary, our study highlights the power of using quantitative endophenotypes as outcome traits in AD-related GWAS analyses and nominates several new loci not previously implicated in cognitive decline.
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Affiliation(s)
- Jan Homann
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Tim Osburg
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Laura Deecke
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany
| | - Isabelle Bos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands,Department of Neurology, Alzheimer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium,Neurology Service, University Hospital Leuven, Leuven, Belgium
| | - Silvy Gabel
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Philip Scheltens
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, Netherlands
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium,Department of Neurology and Center for Neurosciences, Universitair Ziekenhuis Brussel and Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giovanni Frisoni
- Department of Psychiatry, University of Geneva, Geneva, Switzerland,IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Olivier Blin
- Institut Neurosciences Timone, AIX Marseille University, Marseille, France
| | - Jill C. Richardson
- Neurosciences Therapeutic Area, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Regis Bordet
- Lille Neuroscience and Cognition, University of Lille, Inserm, CHU Lille, Lille, France
| | - Alberto Lleó
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Julius Popp
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland,Old Age Psychiatry, Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Christopher Clark
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zurich, Zurich, Switzerland
| | - Gwendoline Peyratout
- Old Age Psychiatry, Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pablo Martinez-Lage
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Donostia-San Sebastian, Spain
| | - Mikel Tainta
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, Donostia-San Sebastian, Spain
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, United Kingdom,NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom,Health Data Research UK London, University College London, London, United Kingdom,Institute of Health Informatics, University College London, London, United Kingdom,NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Cristina Legido-Quigley
- Steno Diabetes Center, Copenhagen, Denmark,King’s College London, Institute of Pharmaceutical Sciences, London, United Kingdom
| | - Kristel Sleegers
- Complex Genetics of Alzheimer’s Disease Group, Center for Molecular Neurology, VIB, Antwerp, Belgium,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium,Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christina M. Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany,Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, United Kingdom
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden,Department of Neurodegenerative Disease, University College London, Queen Square Institute of Neurology, Queen Square, London, United Kingdom,UK Dementia Research Institute at University College London, London, United Kingdom
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Johannes Streffer
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium,Janssen R&D, LLC. Beerse, Belgium
| | - Mara ten Kate
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium,Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Stephanie J. B. Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, Netherlands,Institutes of Neurology and Healthcare Engineering, University College London, London, United Kingdom
| | - Pieter Jelle Visser
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands,Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium,Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Lübeck, Germany,Department of Psychology, University of Oslo, Oslo, Norway,*Correspondence: Lars Bertram,
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Pan Z, Yao Y, Yin H, Cai Z, Wang Y, Bai L, Kern C, Halstead M, Chanthavixay G, Trakooljul N, Wimmers K, Sahana G, Su G, Lund MS, Fredholm M, Karlskov-Mortensen P, Ernst CW, Ross P, Tuggle CK, Fang L, Zhou H. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 2021; 12:5848. [PMID: 34615879 PMCID: PMC8494738 DOI: 10.1038/s41467-021-26153-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hongwei Yin
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Lijing Bai
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Michelle Halstead
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Klaus Wimmers
- Leibniz-Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Tjele, 8300, Denmark
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederikgsberg C, 1870, Denmark
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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