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De La Fuente DC, Tamburini C, Stonelake E, Andrews R, Hall J, Owen MJ, Linden DEJ, Pocklington A, Li M. Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorder. Cell Rep 2024; 43:113946. [PMID: 38483902 DOI: 10.1016/j.celrep.2024.113946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 12/22/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
The mechanisms by which genomic risks contribute to the onset of neuropsychiatric conditions remain a key challenge and a prerequisite for successful development of effective therapies. 15q11.2 copy number variation (CNV) containing the CYFIP1 gene is associated with autism and schizophrenia. Using stem cell models, we show that 15q11.2 deletion (15q11.2del) and CYFIP1 loss of function (CYFIP1-LoF) lead to premature neuronal differentiation, while CYFIP1 gain of function (CYFIP1-GoF) favors neural progenitor maintenance. CYFIP1 dosage changes led to dysregulated cholesterol metabolism and altered levels of 24S,25-epoxycholesterol, which can mimic the 15q11.2del and CYFIP1-LoF phenotypes by promoting cortical neuronal differentiation and can restore the impaired neuronal differentiation of CYFIP1-GoF neural progenitors. Moreover, the neurogenic activity of 24S,25-epoxycholesterol is lost following genetic deletion of liver X receptor (LXRβ), while compound deletion of LXRβ in CYFIP1-/- background rescued their premature neurogenesis. This work delineates LXR-mediated oxysterol regulation of neurogenesis as a pathological mechanism in neural cells carrying 15q11.2 CNV and provides a potential target for therapeutic strategies for associated disorders.
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Affiliation(s)
| | - Claudia Tamburini
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
| | | | - Robert Andrews
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK; Division of Psychiatry and Clinical Neuroscience, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK; Division of Psychiatry and Clinical Neuroscience, Cardiff University, Cardiff, UK
| | - David E J Linden
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK; Division of Psychiatry and Clinical Neuroscience, Cardiff University, Cardiff, UK; School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Andrew Pocklington
- Division of Psychiatry and Clinical Neuroscience, Cardiff University, Cardiff, UK
| | - Meng Li
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK; Division of Psychiatry and Clinical Neuroscience, Cardiff University, Cardiff, UK; School of Bioscience, Cardiff University, Cardiff, UK.
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2
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Pocklington A, Wang YX, Clerk AA. Dissipative Pairing Interactions: Quantum Instabilities, Topological Light, and Volume-Law Entanglement. Phys Rev Lett 2023; 130:123602. [PMID: 37027846 DOI: 10.1103/physrevlett.130.123602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
We analyze an unusual class of bosonic dynamical instabilities that arise from dissipative (or non-Hermitian) pairing interactions. We show that, surprisingly, a completely stable dissipative pairing interaction can be combined with simple hopping or beam-splitter interactions (also stable) to generate instabilities. Further, we find that the dissipative steady state in such a situation remains completely pure up until the instability threshold (in clear distinction from standard parametric instabilities). These pairing-induced instabilities also exhibit an extremely pronounced sensitivity to wave function localization. This provides a simple yet powerful method for selectively populating and entangling edge modes of photonic (or more general bosonic) lattices having a topological band structure. The underlying dissipative pairing interaction is experimentally resource friendly, requiring the addition of a single additional localized interaction to an existing lattice, and is compatible with a number of existing platforms, including superconducting circuits.
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Affiliation(s)
- Andrew Pocklington
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, USA
- Department of Physics, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, USA
| | - Yu-Xin Wang
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, USA
| | - A A Clerk
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, USA
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3
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Dimitriadis SI, Perry G, Lancaster TM, Tansey KE, Singh KD, Holmans P, Pocklington A, Davey Smith G, Zammit S, Hall J, O’Donovan MC, Owen MJ, Jones DK, Linden DE. Genetic risk for schizophrenia is associated with increased proportion of indirect connections in brain networks revealed by a semi-metric analysis: evidence from population sample stratified for polygenic risk. Cereb Cortex 2023; 33:2997-3011. [PMID: 35830871 PMCID: PMC10016061 DOI: 10.1093/cercor/bhac256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/02/2023] Open
Abstract
Research studies based on tractography have revealed a prominent reduction of asymmetry in some key white-matter tracts in schizophrenia (SCZ). However, we know little about the influence of common genetic risk factors for SCZ on the efficiency of routing on structural brain networks (SBNs). Here, we use a novel recall-by-genotype approach, where we sample young adults from a population-based cohort (ALSPAC:N genotyped = 8,365) based on their burden of common SCZ risk alleles as defined by polygenic risk score (PRS). We compared 181 individuals at extremes of low (N = 91) or high (N = 90) SCZ-PRS under a robust diffusion MRI-based graph theoretical SBN framework. We applied a semi-metric analysis revealing higher SMR values for the high SCZ-PRS group compared with the low SCZ-PRS group in the left hemisphere. Furthermore, a hemispheric asymmetry index showed a higher leftward preponderance of indirect connections for the high SCZ-PRS group compared with the low SCZ-PRS group (PFDR < 0.05). These findings might indicate less efficient structural connectivity in the higher genetic risk group. This is the first study in a population-based sample that reveals differences in the efficiency of SBNs associated with common genetic risk variants for SCZ.
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Affiliation(s)
- S I Dimitriadis
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Neuroinformatics Group, School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - G Perry
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - T M Lancaster
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Department of Psychology, Bath University, Claverton Down BA2 7AY, Bath, Wales, UK
| | - K E Tansey
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Queens Road BS8 1QU, Bristol, Wales, UK
| | - K D Singh
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - P Holmans
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - A Pocklington
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - G Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Queens Road BS8 1QU, Bristol, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
| | - S Zammit
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
| | - J Hall
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - M C O’Donovan
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - M J Owen
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - D K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - D E Linden
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
- School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40 UNS40 6229 ER, Maastricht, The Netherlands
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4
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Hall LS, Medway CW, Pain O, Pardiñas AF, Rees EG, Escott-Price V, Pocklington A, Bray NJ, Holmans PA, Walters JTR, Owen MJ, O'Donovan MC. A transcriptome-wide association study implicates specific pre- and post-synaptic abnormalities in schizophrenia. Hum Mol Genet 2020; 29:159-167. [PMID: 31691811 PMCID: PMC7416679 DOI: 10.1093/hmg/ddz253] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/31/2019] [Accepted: 09/02/2019] [Indexed: 12/25/2022] Open
Abstract
Schizophrenia is a complex highly heritable disorder. Genome-wide association studies (GWAS) have identified multiple loci that influence the risk of developing schizophrenia, although the causal variants driving these associations and their impacts on specific genes are largely unknown. We identify a significant correlation between schizophrenia risk and expression at 89 genes in the dorsolateral prefrontal cortex (P ≤ 9.43 × 10-6), including 20 novel genes. Genes whose expression correlate with schizophrenia were enriched for those involved in abnormal CNS synaptic transmission (PFDR = 0.02) and antigen processing and presentation of peptide antigen via MHC class I (PFDR = 0.02). Within the CNS synaptic transmission set, we identify individual significant candidate genes to which we assign direction of expression changes in schizophrenia. The findings provide strong candidates for experimentally probing the molecular basis of synaptic pathology in schizophrenia.
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Affiliation(s)
- Lynsey S Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Christopher W Medway
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Oliver Pain
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Elliott G Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Andrew Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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5
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Sanders B, Steward T, Whitcomb D, Pocklington A, Shin EJ. Postsynaptic density protein DLG2 has a novel role in cortical neuronal development relevant to schizophrenia aetiology. IBRO Rep 2019. [DOI: 10.1016/j.ibror.2019.07.1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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Morgan SE, Seidlitz J, Whitaker KJ, Romero-Garcia R, Clifton NE, Scarpazza C, van Amelsvoort T, Marcelis M, van Os J, Donohoe G, Mothersill D, Corvin A, Pocklington A, Raznahan A, McGuire P, Vértes PE, Bullmore ET. Cortical patterning of abnormal morphometric similarity in psychosis is associated with brain expression of schizophrenia-related genes. Proc Natl Acad Sci U S A 2019; 116:9604-9609. [PMID: 31004051 PMCID: PMC6511038 DOI: 10.1073/pnas.1820754116] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [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] [Indexed: 12/05/2022] Open
Abstract
Schizophrenia has been conceived as a disorder of brain connectivity, but it is unclear how this network phenotype is related to the underlying genetics. We used morphometric similarity analysis of MRI data as a marker of interareal cortical connectivity in three prior case-control studies of psychosis: in total, n = 185 cases and n = 227 controls. Psychosis was associated with globally reduced morphometric similarity in all three studies. There was also a replicable pattern of case-control differences in regional morphometric similarity, which was significantly reduced in patients in frontal and temporal cortical areas but increased in parietal cortex. Using prior brain-wide gene expression data, we found that the cortical map of case-control differences in morphometric similarity was spatially correlated with cortical expression of a weighted combination of genes enriched for neurobiologically relevant ontology terms and pathways. In addition, genes that were normally overexpressed in cortical areas with reduced morphometric similarity were significantly up-regulated in three prior post mortem studies of schizophrenia. We propose that this combined analysis of neuroimaging and transcriptional data provides insight into how previously implicated genes and proteins as well as a number of unreported genes in their topological vicinity on the protein interaction network may drive structural brain network changes mediating the genetic risk of schizophrenia.
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Affiliation(s)
- Sarah E Morgan
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom;
| | - Jakob Seidlitz
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Developmental Neurogenomics Unit, National Institute of Mental Health, Bethesda, MD 20892
| | - Kirstie J Whitaker
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
| | - Rafael Romero-Garcia
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
| | - Nicholas E Clifton
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff CF24 4HQ, United Kingdom
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, United Kingdom
| | - Cristina Scarpazza
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
- Department of General Psychology, University of Padova, 35131 Padova, Italy
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, Maastricht University, 616 6200, Maastricht, The Netherlands
| | - Machteld Marcelis
- Department of Psychiatry and Neuropsychology, Maastricht University, 616 6200, Maastricht, The Netherlands
| | - Jim van Os
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
- Department of Psychiatry and Neuropsychology, Maastricht University, 616 6200, Maastricht, The Netherlands
- Department of Psychiatry, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, The Netherlands
| | - Gary Donohoe
- School of Psychology, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - David Mothersill
- School of Psychology, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Aiden Corvin
- Department of Psychiatry, Trinity College Dublin, Dublin 8, D08 W9RT, Ireland
| | - Andrew Pocklington
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, United Kingdom
| | - Armin Raznahan
- Developmental Neurogenomics Unit, National Institute of Mental Health, Bethesda, MD 20892
| | - Philip McGuire
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Petra E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- ImmunoPsychiatry, GlaxoSmithKline R&D, Stevenage SG1 2NY, United Kingdom
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7
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Lancaster TM, Dimitriadis SL, Tansey KE, Perry G, Ihssen N, Jones DK, Singh KD, Holmans P, Pocklington A, Davey Smith G, Zammit S, Hall J, O’Donovan MC, Owen MJ, Linden DE. Structural and Functional Neuroimaging of Polygenic Risk for Schizophrenia: A Recall-by-Genotype-Based Approach. Schizophr Bull 2019; 45:405-414. [PMID: 29608775 PMCID: PMC6403064 DOI: 10.1093/schbul/sby037] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Risk profile scores (RPS) derived from genome-wide association studies (GWAS) explain a considerable amount of susceptibility for schizophrenia (SCZ). However, little is known about how common genetic risk factors for SCZ influence the structure and function of the human brain, largely due to the constraints of imaging sample sizes. In the current study, we use a novel recall-by-genotype (RbG) methodological approach, where we sample young adults from a population cohort (Avon Longitudinal Study of Parents and Children: N genotyped = 8365) based on their SCZ-RPS. We compared 197 healthy individuals at extremes of low (N = 99) or high (N = 98) SCZ-RPS with behavioral tests, and structural and functional magnetic resonance imaging (fMRI). We first provide methodological details that will inform the design of future RbG studies for common SCZ genetic risk. We further provide an between group analysis of the RbG individuals (low vs high SCZ-RPS) who underwent structural neuroimaging data (T1-weighted scans) and fMRI data during a reversal learning task. While we found little evidence for morphometric differences between the low and high SCZ-RPS groups, we observed an impact of SCZ-RPS on blood oxygen level-dependent (BOLD) signal during reward processing in the ventral striatum (PFWE-VS-CORRECTED = .037), a previously investigated broader reward-related network (PFWE-ROIS-CORRECTED = .008), and across the whole brain (PFWE-WHOLE-BRAIN-CORRECTED = .013). We also describe the study strategy and discuss specific challenges of RbG for SCZ risk (such as SCZ-RPS related homoscedasticity). This study will help to elucidate the behavioral and imaging phenotypes that are associated with SCZ genetic risk.
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Affiliation(s)
- Thomas M Lancaster
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - Stavros L Dimitriadis
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - Katherine E Tansey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Gavin Perry
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
| | | | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
| | - Krish D Singh
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stan Zammit
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - Michael C O’Donovan
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
| | - David E Linden
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff School of Medicine, Cardiff University, Cardiff, UK
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8
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Vivian‐Griffiths T, Baker E, Schmidt KM, Bracher‐Smith M, Walters J, Artemiou A, Holmans P, O'Donovan MC, Owen MJ, Pocklington A, Escott‐Price V. Predictive modeling of schizophrenia from genomic data: Comparison of polygenic risk score with kernel support vector machines approach. Am J Med Genet B Neuropsychiatr Genet 2019; 180:80-85. [PMID: 30516002 PMCID: PMC6492016 DOI: 10.1002/ajmg.b.32705] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/03/2018] [Accepted: 11/09/2018] [Indexed: 11/07/2022]
Abstract
A major controversy in psychiatric genetics is whether nonadditive genetic interaction effects contribute to the risk of highly polygenic disorders. We applied a support vector machines (SVMs) approach, which is capable of building linear and nonlinear models using kernel methods, to classify cases from controls in a large schizophrenia case-control sample of 11,853 subjects (5,554 cases and 6,299 controls) and compared its prediction accuracy with the polygenic risk score (PRS) approach. We also investigated whether SVMs are a suitable approach to detecting nonlinear genetic effects, that is, interactions. We found that PRS provided more accurate case/control classification than either linear or nonlinear SVMs, and give a tentative explanation why PRS outperforms both multivariate regression and linear kernel SVMs. In addition, we observe that nonlinear kernel SVMs showed higher classification accuracy than linear SVMs when a large number of SNPs are entered into the model. We conclude that SVMs are a potential tool for assessing the presence of interactions, prior to searching for them explicitly.
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Affiliation(s)
- Timothy Vivian‐Griffiths
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Emily Baker
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Karl M. Schmidt
- School of MathematicsCardiff UniversityCardiffUnited Kingdom
| | - Matthew Bracher‐Smith
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - James Walters
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | | | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Michael C. O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Andrew Pocklington
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
| | - Valentina Escott‐Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffUnited Kingdom
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9
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Leonenko G, Richards AL, Walters JT, Pocklington A, Chambert K, Al Eissa MM, Sharp SI, O'Brien NL, Curtis D, Bass NJ, McQuillin A, Hultman C, Moran JL, McCarroll SA, Sklar P, Neale BM, Holmans PA, Owen MJ, Sullivan PF, O'Donovan MC. Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2017; 174:724-731. [PMID: 28719003 PMCID: PMC5669020 DOI: 10.1002/ajmg.b.32560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/19/2017] [Indexed: 12/24/2022]
Abstract
Risk of schizophrenia is conferred by alleles occurring across the full spectrum of frequencies from common SNPs of weak effect through to ultra rare alleles, some of which may be moderately to highly penetrant. Previous studies have suggested that some of the risk of schizophrenia is attributable to uncommon alleles represented on Illumina exome arrays. Here, we present the largest study of exomic variation in schizophrenia to date, using samples from the United Kingdom and Sweden (10,011 schizophrenia cases and 13,791 controls). Single variants, genes, and gene sets were analyzed for association with schizophrenia. No single variant or gene reached genome-wide significance. Among candidate gene sets, we found significant enrichment for rare alleles (minor allele frequency [MAF] < 0.001) in genes intolerant of loss-of-function (LoF) variation and in genes whose messenger RNAs bind to fragile X mental retardation protein (FMRP). We further delineate the genetic architecture of schizophrenia by excluding a role for uncommon exomic variants (0.01 ≤ MAF ≥ 0.001) that confer a relatively large effect (odds ratio [OR] > 4). We also show risk alleles within this frequency range exist, but confer smaller effects and should be identified by larger studies.
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Affiliation(s)
- Ganna Leonenko
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Alexander L. Richards
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - James T. Walters
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Andrew Pocklington
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Kimberly Chambert
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
| | - Mariam M. Al Eissa
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Sally I. Sharp
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Niamh L. O'Brien
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | | | - Nicholas J. Bass
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Andrew McQuillin
- Division of Psychiatry, Molecular Psychiatry LaboratoryUniversity College LondonLondonUK
| | - Christina Hultman
- Department of Medical Epidemiology and BiostatisticsKarolinska InstituteStockholmSweden
| | - Jennifer L. Moran
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
| | - Steven A. McCarroll
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
- Program in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMassachusetts
- Department of GeneticsHarvard Medical SchoolBostonMassachusetts
| | - Pamela Sklar
- Icahn School of Medicine at Mount SinaiNew YorkNew York
| | - Benjamin M. Neale
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusetts
- Analytical and Translational Genetics UnitMassachusetts General HospitalBostonMassachusetts
| | - Peter A. Holmans
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Michael J. Owen
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and BiostatisticsKarolinska InstituteStockholmSweden
- Departments of Genetics and PsychiatryUniversity of North CarolinaChapel HillNorth Carolina
| | - Michael C. O'Donovan
- Division of Psychological Medicine and Clinical NeurosciencesMRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of MedicineCardiffUK
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10
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Rees E, Kendall K, Pardiñas AF, Legge SE, Pocklington A, Escott-Price V, MacCabe JH, Collier DA, Holmans P, O’Donovan MC, Owen MJ, Walters JTR, Kirov G. Analysis of Intellectual Disability Copy Number Variants for Association With Schizophrenia. JAMA Psychiatry 2016; 73:963-969. [PMID: 27602560 PMCID: PMC5014093 DOI: 10.1001/jamapsychiatry.2016.1831] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE At least 11 rare copy number variants (CNVs) have been shown to be major risk factors for schizophrenia (SZ). These CNVs also increase the risk for other neurodevelopmental disorders, such as intellectual disability. It is possible that additional intellectual disability-associated CNVs increase the risk for SZ but have not yet been implicated in SZ because of previous studies being underpowered. OBJECTIVE To examine whether additional CNVs implicated in intellectual disability represent novel SZ risk loci. DESIGN, SETTING, AND PARTICIPANTS We used single-nucleotide polymorphism (SNP) array data to evaluate a set of 51 CNVs implicated in intellectual disability (excluding the known SZ loci) in a large data set of patients with SZ and healthy persons serving as controls recruited in a variety of settings. We analyzed a new sample of 6934 individuals with SZ and 8751 controls and combined those data with previously published large data sets for a total of 20 403 cases of SZ and 26 628 controls. MAIN OUTCOMES AND MEASURES Burden analysis of CNVs implicated in intellectual disability (excluding known SZ CNVs) for association with SZ. Association of individual intellectual disability CNV loci with SZ. RESULTS Of data on the 20 403 cases (6151 [30.15%] female) and 26 628 controls (14 252 [53.52%] female), 51 intellectual disability CNVs were analyzed. Collectively, intellectual disability CNVs were significantly enriched for SZ (P = 1.0 × 10-6; odds ratio [OR], 1.9 [95% CI, 1.46-2.49]). Of the 51 CNVs tested, 19 (37%) were more common in SZ cases; only 4 (8%) were more common in controls (no observations were made for the remaining 28 [55%] loci). One novel locus, deletion at 16p12.1, was significantly associated with SZ after correction for multiple testing (rate in SZ, 33 [0.16%]; rate in controls, 12 [0.05%]; corrected P = .017; OR, 3.3; 95% CI, 1.61-7.05), and 2 loci reached nominal levels of significance (deletions at 2q11.2: 6 [0.03%] vs 1 [0.004%]; OR, 9.3; 95% CI, 1.03-447.76; corrected P > .99; and duplications at 10q11.21q11.23: 5 [0.2%] vs 0 [0.03%]; OR, infinity; 95% CI, 1.26-infinity; corrected P = .71). Our new data set also provided independent support for the 11 SZ risk loci previously reported to be associated with the disorder and for the protective effect of 22q11.2 duplication. CONCLUSIONS AND RELEVANCE A large proportion of CNV loci implicated in intellectual disability are risk factors for SZ, but the available sample size precludes statistical confirmation for additional individual loci.
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Affiliation(s)
- Elliott Rees
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Kimberley Kendall
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Antonio F. Pardiñas
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Sophie E. Legge
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Andrew Pocklington
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - James H. MacCabe
- Department of Psychosis Studies, Institute of Psychiatry Psychology
and Neuroscience, King’s College London, London, England
| | - David A. Collier
- SGDP Centre, Institute of Psychiatry, Psychology and Neuroscience,
King's College London, London, England; Discovery Neuroscience
Research, Eli Lilly and Company Ltd, Lilly Research Laboratories, Surrey,
England
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Michael C. O’Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales; Division of Psychological
Medicine and Clinical Neurosciences, Cardiff University, Cardiff,
Wales
| | - James T. R. Walters
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and
Genomics, Cardiff University, Cardiff, Wales
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11
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Martin J, Cooper M, Hamshere ML, Pocklington A, Scherer SW, Kent L, Gill M, Owen MJ, Williams N, O'Donovan MC, Thapar A, Holmans P. Biological overlap of attention-deficit/hyperactivity disorder and autism spectrum disorder: evidence from copy number variants. J Am Acad Child Adolesc Psychiatry 2014; 53:761-70.e26. [PMID: 24954825 PMCID: PMC4074351 DOI: 10.1016/j.jaac.2014.03.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/24/2014] [Accepted: 04/11/2014] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) often co-occur and share genetic risks. The aim of this analysis was to determine more broadly whether ADHD and ASD share biological underpinnings. METHOD We compared copy number variant (CNV) data from 727 children with ADHD and 5,081 population controls to data from 996 individuals with ASD and an independent set of 1,287 controls. Using pathway analyses, we investigated whether CNVs observed in individuals with ADHD have an impact on genes in the same biological pathways as on those observed in individuals with ASD. RESULTS The results suggest that the biological pathways affected by CNVs in ADHD overlap with those affected by CNVs in ASD more than would be expected by chance. Moreover, this was true even when specific CNV regions common to both disorders were excluded from the analysis. After correction for multiple testing, genes involved in 3 biological processes (nicotinic acetylcholine receptor signalling pathway, cell division, and response to drug) showed significant enrichment for case CNV hits in the combined ADHD and ASD sample. CONCLUSION The results of this study indicate the presence of significant overlap of shared biological processes disrupted by large rare CNVs in children with these 2 neurodevelopmental conditions.
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Affiliation(s)
- Joanna Martin
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK.
| | - Miriam Cooper
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Marian L Hamshere
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Andrew Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Stephen W Scherer
- Hospital for Sick Children and University of Toronto, Ontario, Canada
| | - Lindsey Kent
- Bute Medical School, University of St. Andrews, Fife, Scotland
| | - Michael Gill
- Trinity Centre for Health Sciences, Dublin, Ireland
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Nigel Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Anita Thapar
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, UK
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12
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Erk S, Meyer-Lindenberg A, Linden DE, Lancaster T, Mohnke S, Grimm O, Degenhardt F, Holmans P, Pocklington A, Schmierer P, Haddad L, Mühleisen TW, Mattheisen M, Witt SH, Romanczuk-Seiferth N, Tost H, Schott BH, Cichon S, Nöthen MM, Rietschel M, Heinz A, Walter H. Replication of brain function effects of a genome-wide supported psychiatric risk variant in the CACNA1C gene and new multi-locus effects. Neuroimage 2014; 94:147-154. [DOI: 10.1016/j.neuroimage.2014.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/09/2014] [Accepted: 03/09/2014] [Indexed: 12/12/2022] Open
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13
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Jones L, Holmans PA, Hamshere ML, Harold D, Moskvina V, Ivanov D, Pocklington A, Abraham R, Hollingworth P, Sims R, Gerrish A, Pahwa JS, Jones N, Stretton A, Morgan AR, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Morgan K, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Holmes C, Mann D, Smith AD, Love S, Kehoe PG, Mead S, Fox N, Rossor M, Collinge J, Maier W, Jessen F, Schürmann B, van den Bussche H, Heuser I, Peters O, Kornhuber J, Wiltfang J, Dichgans M, Frölich L, Hampel H, Hüll M, Rujescu D, Goate AM, Kauwe JSK, Cruchaga C, Nowotny P, Morris JC, Mayo K, Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Al-Chalabi A, Shaw CE, Singleton AB, Guerreiro R, Mühleisen TW, Nöthen MM, Moebus S, Jöckel KH, Klopp N, Wichmann HE, Rüther E, Carrasquillo MM, Pankratz VS, Younkin SG, Hardy J, O'Donovan MC, Owen MJ, Williams J. Genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer's disease. PLoS One 2010; 5:e13950. [PMID: 21085570 PMCID: PMC2981526 DOI: 10.1371/journal.pone.0013950] [Citation(s) in RCA: 299] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 10/06/2010] [Indexed: 12/04/2022] Open
Abstract
Background Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches.
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Affiliation(s)
- Lesley Jones
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Peter A. Holmans
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Marian L. Hamshere
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Denise Harold
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Valentina Moskvina
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Dobril Ivanov
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Andrew Pocklington
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Richard Abraham
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Paul Hollingworth
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Rebecca Sims
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Amy Gerrish
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jaspreet Singh Pahwa
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicola Jones
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Alexandra Stretton
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Angharad R. Morgan
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Simon Lovestone
- National Institute for Health Research Biomedical Research Centre for Mental Health at the South London and Maudsley National Health Service Foundation Trust and Institute of Psychiatry, Kings College, London, United Kingdom
| | - John Powell
- Department of Neuroscience, Institute of Psychiatry, Kings College, London, United Kingdom
| | - Petroula Proitsi
- Department of Neuroscience, Institute of Psychiatry, Kings College, London, United Kingdom
| | - Michelle K. Lupton
- Department of Neuroscience, Institute of Psychiatry, Kings College, London, United Kingdom
| | - Carol Brayne
- Institute of Public Health, University of Cambridge, Cambridge, United Kingdom
| | - David C. Rubinsztein
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Michael Gill
- Mercer's Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Brian Lawlor
- Mercer's Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Aoibhinn Lynch
- Mercer's Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Kevin Morgan
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Kristelle S. Brown
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Peter A. Passmore
- Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - David Craig
- Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Bernadette McGuinness
- Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen Todd
- Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Clive Holmes
- Division of Clinical Neurosciences, School of Medicine, University of Southampton, Southampton, United Kingdom
| | - David Mann
- Clinical Neuroscience Research Group, Greater Manchester Neurosciences Centre, University of Manchester, Salford, United Kingdom
| | - A. David Smith
- Oxford Project to Investigate Memory and Ageing, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Seth Love
- Dementia Research Group, University of Bristol Institute of Clinical Neurosciences, Frenchay Hospital, Bristol, United Kingdom
| | - Patrick G. Kehoe
- Dementia Research Group, University of Bristol Institute of Clinical Neurosciences, Frenchay Hospital, Bristol, United Kingdom
| | - Simon Mead
- MRC Prion Unit, Department of Neurodegenerative Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Nick Fox
- Dementia Research Centre, Department of Neurodegenerative Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Martin Rossor
- Dementia Research Centre, Department of Neurodegenerative Diseases, UCL Institute of Neurology, London, United Kingdom
| | - John Collinge
- MRC Prion Unit, Department of Neurodegenerative Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Frank Jessen
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | | | | | - Isabella Heuser
- Institute of Primary Medical Care, University Medical Center Hamburg-Eppendorf, Germany
| | - Oliver Peters
- Institute of Primary Medical Care, University Medical Center Hamburg-Eppendorf, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jens Wiltfang
- Landschaftsverband Rheinland-Hospital Essen, Department of Psychiatry and Psychotherapy, University Duisburg-Essen, Essen, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Munich, Germany
- Department of Neurology, Klinikum der Universität München, Munich, Germany
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Harald Hampel
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Laboratory of Neuroimaging and Biomarker Research, Trinity College, University of Dublin, Dublin, Ireland
- Alzheimer Memorial Center and Geriatric Psychiatry Branch, Department of Psychiatry, Ludwig-Maximilian University, Munich, Germany
| | - Michael Hüll
- Centre for Geriatric Medicine and Section of Gerontopsychiatry and Neuropsychology, Medical School, University of Freiburg, Freiburg, Germany
| | - Dan Rujescu
- Alzheimer Memorial Center and Geriatric Psychiatry Branch, Department of Psychiatry, Ludwig-Maximilian University, Munich, Germany
| | - Alison M. Goate
- Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Carlos Cruchaga
- Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Petra Nowotny
- Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John C. Morris
- Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin Mayo
- Departments of Psychiatry, Neurology and Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gill Livingston
- Department of Mental Health Sciences, UCL, London, United Kingdom
| | - Nicholas J. Bass
- Department of Mental Health Sciences, UCL, London, United Kingdom
| | - Hugh Gurling
- Department of Mental Health Sciences, UCL, London, United Kingdom
| | - Andrew McQuillin
- Department of Mental Health Sciences, UCL, London, United Kingdom
| | - Rhian Gwilliam
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Panos Deloukas
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Ammar Al-Chalabi
- MRC Centre for Neurodegeneration Research, Department of Clinical Neuroscience, King's College London, Institute of Psychiatry, London, United Kingdom
| | - Christopher E. Shaw
- MRC Centre for Neurodegeneration Research, Department of Clinical Neuroscience, King's College London, Institute of Psychiatry, London, United Kingdom
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rita Guerreiro
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas W. Mühleisen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Norman Klopp
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - Eckhard Rüther
- Department of Psychiatry, University of Gottingen, Gottingen, Germany
| | - Minerva M. Carrasquillo
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida, United States of America
| | - V. Shane Pankratz
- Division of Biomedical Statistics and Informatics, Mayo Clinic and Mayo Foundation, Rochester, Minnesota, United States of America
| | - Steven G. Younkin
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida, United States of America
| | - John Hardy
- Department of Molecular Neuroscience and Reta Lilla Weston Laboratories, Institute of Neurology, London, United Kingdom
| | - Michael C. O'Donovan
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael J. Owen
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail: (JW); (MJO)
| | - Julie Williams
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
- * E-mail: (JW); (MJO)
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