301
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Hoffmann A, Ziller M, Spengler D. Focus on Causality in ESC/iPSC-Based Modeling of Psychiatric Disorders. Cells 2020; 9:E366. [PMID: 32033412 PMCID: PMC7072492 DOI: 10.3390/cells9020366] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified an increasing number of genetic variants that significantly associate with psychiatric disorders. Despite this wealth of information, our knowledge of which variants causally contribute to disease, how they interact, and even more so of the functions they regulate, is still poor. The availability of embryonic stem cells (ESCs) and the advent of patient-specific induced pluripotent stem cells (iPSCs) has opened new opportunities to investigate genetic risk variants in living disease-relevant cells. Here, we analyze how this progress has contributed to the analysis of causal relationships between genetic risk variants and neuronal phenotypes, especially in schizophrenia (SCZ) and bipolar disorder (BD). Studies on rare, highly penetrant risk variants have originally led the field, until more recently when the development of (epi-) genetic editing techniques spurred studies on cause-effect relationships between common low risk variants and their associated neuronal phenotypes. This reorientation not only offers new insights, but also raises issues on interpretability. Concluding, we consider potential caveats and upcoming developments in the field of ESC/iPSC-based modeling of causality in psychiatric disorders.
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Affiliation(s)
| | | | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany; (A.H.); (M.Z.)
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302
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Abstract
IMPORTANCE Schizophrenia is a common, severe mental illness that most clinicians will encounter regularly during their practice. This report provides an overview of the clinical characteristics, epidemiology, genetics, neuroscience, and psychopharmacology of schizophrenia to provide a basis to understand the disorder and its treatment. This educational review is integrated with a clinical case to highlight how recent research findings can inform clinical understanding. OBSERVATIONS The first theme considered is the role of early-life environmental and genetic risk factors in altering neurodevelopmental trajectories to predispose an individual to the disorder and leading to the development of prodromal symptoms. The second theme is the role of cortical excitatory-inhibitory imbalance in the development of the cognitive and negative symptoms of the disorder. The third theme considers the role of psychosocial stressors, psychological factors, and subcortical dopamine dysfunction in the onset of the positive symptoms of the disorder. The final theme considers the mechanisms underlying treatment for schizophrenia and common adverse effects of treatment. CONCLUSIONS AND RELEVANCE Schizophrenia has a complex presentation with a multifactorial cause. Nevertheless, advances in neuroscience have identified roles for key circuits, particularly involving frontal, temporal, and mesostriatal brain regions, in the development of positive, negative, and cognitive symptoms. Current pharmacological treatments operate using the same mechanism, blockade of dopamine D2 receptor, which contribute to their adverse effects. However, the circuit mechanisms discussed herein identify novel potential treatment targets that may be of particular benefit in symptom domains not well served by existing medications.
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Affiliation(s)
- Robert A McCutcheon
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, United Kingdom.,Psychiatric Imaging Group, Medical Research Council, London Institute of Medical Sciences, Hammersmith Hospital, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tiago Reis Marques
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, United Kingdom.,Psychiatric Imaging Group, Medical Research Council, London Institute of Medical Sciences, Hammersmith Hospital, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Oliver D Howes
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, United Kingdom.,Psychiatric Imaging Group, Medical Research Council, London Institute of Medical Sciences, Hammersmith Hospital, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
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303
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Huntley MA, Srinivasan K, Friedman BA, Wang TM, Yee AX, Wang Y, Kaminker JS, Sheng M, Hansen DV, Hanson JE. Genome-Wide Analysis of Differential Gene Expression and Splicing in Excitatory Neurons and Interneuron Subtypes. J Neurosci 2020; 40:958-973. [PMID: 31831521 PMCID: PMC6988999 DOI: 10.1523/jneurosci.1615-19.2019] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/17/2019] [Accepted: 12/03/2019] [Indexed: 11/21/2022] Open
Abstract
Cortical circuit activity is shaped by the parvalbumin (PV) and somatostatin (SST) interneurons that inhibit principal excitatory (EXC) neurons and the vasoactive intestinal peptide (VIP) interneurons that suppress activation of other interneurons. To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, we performed a genome wide assessment of both gene expression and splicing across EXC, PV, SST and VIP neurons from male and female mouse brains. These results reveal numerous examples where neuron subtype-specific gene expression, as well as splice-isoform usage, can explain functional differences between neuron subtypes, including in presynaptic plasticity, postsynaptic receptor function, and synaptic connectivity specification. We provide a searchable web resource for exploring differential mRNA expression and splice form usage between excitatory, PV, SST, and VIP neurons (http://research-pub.gene.com/NeuronSubtypeTranscriptomes). This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains.SIGNIFICANCE STATEMENT Understanding the basis of functional specialization of neuron subtypes and identifying drug targets for manipulating circuit function requires comprehensive information on cell-type-specific transcriptional profiles. We sorted excitatory neurons and key inhibitory neuron subtypes from mouse brains and assessed differential mRNA expression. We used a genome-wide analysis which not only examined differential gene expression levels but could also detect differences in splice isoform usage. This analysis reveals numerous examples of neuron subtype-specific isoform usage with functional importance, identifies potential drug targets, and provides insight into the neuron subtypes involved in psychiatric disease. We also apply our analysis to two other relevant datasets for comparison, and provide a searchable website for convenient access to the resource.
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Affiliation(s)
- Melanie A Huntley
- Departments of Bioinformatics and Computational Biology, and
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | | | - Brad A Friedman
- Departments of Bioinformatics and Computational Biology, and
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Tzu-Ming Wang
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Ada X Yee
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Yuanyuan Wang
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Josh S Kaminker
- Departments of Bioinformatics and Computational Biology, and
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Morgan Sheng
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - David V Hansen
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
| | - Jesse E Hanson
- Neuroscience, Genentech, Inc., South San Francisco, California 94080-4918
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304
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Muñoz-Manchado AB, Bengtsson Gonzales C, Zeisel A, Munguba H, Bekkouche B, Skene NG, Lönnerberg P, Ryge J, Harris KD, Linnarsson S, Hjerling-Leffler J. Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq. Cell Rep 2020; 24:2179-2190.e7. [PMID: 30134177 PMCID: PMC6117871 DOI: 10.1016/j.celrep.2018.07.053] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/03/2018] [Accepted: 07/16/2018] [Indexed: 11/02/2022] Open
Abstract
Striatal locally projecting neurons, or interneurons, act on nearby circuits and shape functional output to the rest of the basal ganglia. We performed single-cell RNA sequencing of striatal cells enriching for interneurons. We find seven discrete interneuron types, six of which are GABAergic. In addition to providing specific markers for the populations previously described, including those expressing Sst/Npy, Th, Npy without Sst, and Chat, we identify two small populations of cells expressing Cck with or without Vip. Surprisingly, the Pvalb-expressing cells do not constitute a discrete cluster but rather are part of a larger group of cells expressing Pthlh with a spatial gradient of Pvalb expression. Using PatchSeq, we show that Pthlh cells exhibit a continuum of electrophysiological properties correlated with expression of Pvalb. Furthermore, we find significant molecular differences that correlate with differences in electrophysiological properties between Pvalb-expressing cells of the striatum and those of the cortex.
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Affiliation(s)
- Ana B Muñoz-Manchado
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Carolina Bengtsson Gonzales
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Amit Zeisel
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hermany Munguba
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Bo Bekkouche
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Nathan G Skene
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Peter Lönnerberg
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jesper Ryge
- Brain Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Kenneth D Harris
- UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; UCL Department of Neuroscience, Physiology and Pharmacology, 21 University Street, London WC1E 6DE, UK
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.
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305
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Novel Approaches for Identifying the Molecular Background of Schizophrenia. Cells 2020; 9:cells9010246. [PMID: 31963710 PMCID: PMC7017322 DOI: 10.3390/cells9010246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advances in psychiatric genetics have led to the discovery of dozens of genomic loci associated with schizophrenia. However, a gap exists between the detection of genetic associations and understanding the underlying molecular mechanisms. This review describes the basic approaches used in the so-called post-GWAS studies to generate biological interpretation of the existing population genetic data, including both molecular (creation and analysis of knockout animals, exploration of the transcriptional effects of common variants in human brain cells) and computational (fine-mapping of causal variability, gene set enrichment analysis, partitioned heritability analysis) methods. The results of the crucial studies, in which these approaches were used to uncover the molecular and neurobiological basis of the disease, are also reported.
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306
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Maynard KR, Jaffe AE, Martinowich K. Spatial transcriptomics: putting genome-wide expression on the map. Neuropsychopharmacology 2020; 45:232-233. [PMID: 31444395 PMCID: PMC6879618 DOI: 10.1038/s41386-019-0484-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- K R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA.
| | - A E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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307
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Abstract
An essential part of the drug discovery and development process in the pharmaceutical industry is to provide a full characterization of cells expressing a given drug target and potential downstream markers in human tissues and in relevant preclinical animal species. This task is best solved by a combination of methods, including histological assessment of target protein and mRNA using immunohistochemistry (IHC) and in situ hybridization (ISH), respectively, as well as non-histology-based methods, such as fluorescence-activated cell sorting (FACS), and single-cell (SCS) or single-nuclei (SNS) sequencing. In reality, this work is often complicated by a combination of low target expression levels and a less than optimal availability of specific reagents for detection. In particular, the ability to specifically detect low-abundance receptor targets using IHC is notoriously difficult, due to a daunting lack of commercially available specific antibodies validated for use in IHC. In the absence of fully validated antibodies and protocols for IHC, the specific detection of target mRNA using ISH is often the only available histological method. A highly sensitive, nonradioactive, automated, and robust ISH method for use on formalin-fixed, paraffin-embedded (FFPE) tissue sections is presented for assessing histological localization of mRNA transcripts of lowly expressed genes.
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308
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Abstract
The genetic architecture of schizophrenia is complex and highly polygenic. This article discusses key findings from genetic studies of childhood-onset schizophrenia (COS) and the more common adult-onset schizophrenia (AOS), including studies of familial aggregation and common, rare, and copy number variants. Extant literature suggests that COS is a rare variant of AOS involving greater familial aggregation of schizophrenia spectrum disorders and a potentially higher occurrence of pathogenic copy number variants. The direct utility of genetics to clinical practice for COS is currently limited; however, identifying common pathways through which risk genes affect brain function offers promise for novel interventions.
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Affiliation(s)
- Jennifer K Forsyth
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Robert F Asarnow
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA; Department of Psychology, University of California, Los Angeles, 502 Portola Plaza Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA.
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309
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Seshadri S, Hoeppner DJ, Tajinda K. Calcium Imaging in Drug Discovery for Psychiatric Disorders. Front Psychiatry 2020; 11:713. [PMID: 32793004 PMCID: PMC7390878 DOI: 10.3389/fpsyt.2020.00713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/06/2020] [Indexed: 12/31/2022] Open
Abstract
The past 5 years have seen a sharp increase in the number of studies using calcium imaging in behaving rodents. These studies have helped identify important roles for individual cells, brain regions, and circuits in some of the core behavioral phenotypes of psychiatric disorders, such as schizophrenia and autism, and have characterized network dysfunction in well-established models of these disorders. Since rescuing clinically relevant behavioral deficits in disease model mice remains a foundation of preclinical CNS research, these studies have the potential to inform new therapeutic approaches targeting specific cell types or projections, or perhaps most importantly, the network-level context in which neurons function. In this mini-review, we will provide a brief overview of recent insights into psychiatric disease-associated mouse models and behavior paradigms, focusing on those achieved by cellular resolution imaging of calcium dynamics in neural populations. We will then discuss how these experiments can support efforts within the pharmaceutical industry, such as target identification, assay development, and candidate screening and validation. Calcium imaging is uniquely capable of bridging the gap between two of the key resources that currently enable CNS drug discovery: genomic and transcriptomic data from human patients, and translatable, population-resolution measures of brain activity (such as fMRI and EEG). Applying this knowledge could yield real value to patients in the near future.
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Affiliation(s)
- Saurav Seshadri
- Neuroscience, La Jolla Laboratory, Astellas Research Institute of America LLC, San Diego, CA, United States
| | - Daniel J Hoeppner
- Neuroscience, La Jolla Laboratory, Astellas Research Institute of America LLC, San Diego, CA, United States
| | - Katsunori Tajinda
- Neuroscience, La Jolla Laboratory, Astellas Research Institute of America LLC, San Diego, CA, United States
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310
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Mohammadi S, Davila-Velderrain J, Kellis M. Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution. Cell Syst 2019; 9:559-568.e4. [PMID: 31786210 PMCID: PMC6943823 DOI: 10.1016/j.cels.2019.10.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/13/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023]
Abstract
The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a computational framework that reconstructs an ensemble of cell-type-specific interactomes by integrating a global, context-independent reference interactome with a single-cell gene-expression profile. SCINET addresses technical challenges of single-cell data by robustly imputing, transforming, and normalizing the initially noisy and sparse expression of data. Inferred cell-level gene interaction probabilities and group-level interaction strengths define cell-type-specific interactomes. We use SCINET to reconstruct and analyze interactomes of the major human brain and immune cell types, revealing specificity and modularity of perturbations associated with neurodegenerative, neuropsychiatric, and autoimmune disorders. We report cell-type interactomes for brain and immune cell types, together with the SCINET package.
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Affiliation(s)
- Shahin Mohammadi
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jose Davila-Velderrain
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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311
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Hill WD, Davies NM, Ritchie SJ, Skene NG, Bryois J, Bell S, Di Angelantonio E, Roberts DJ, Xueyi S, Davies G, Liewald DCM, Porteous DJ, Hayward C, Butterworth AS, McIntosh AM, Gale CR, Deary IJ. Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income. Nat Commun 2019; 10:5741. [PMID: 31844048 PMCID: PMC6915786 DOI: 10.1038/s41467-019-13585-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/11/2019] [Indexed: 01/01/2023] Open
Abstract
Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30 (29 previously unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities.
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Affiliation(s)
- W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Stuart J Ritchie
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Nathan G Skene
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- UCL Institute of Neurology, Queen Square, London, UK
- Department of Medicine, Division of Brain Sciences, Imperial College, London, UK
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven Bell
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Emanuele Di Angelantonio
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- NHS Blood and Transplant, Cambridge, UK
| | - David J Roberts
- Cambridge Substantive Site, Health Data Research UK, Wellcome Genome Campus, Hinxton, UK
- BRC Haematology Theme and Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NHS Blood and Transplant - Oxford Centre, Oxford, UK
| | - Shen Xueyi
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Adam S Butterworth
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Catharine R Gale
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
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312
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Hill WD, Davies NM, Ritchie SJ, Skene NG, Bryois J, Bell S, Di Angelantonio E, Roberts DJ, Xueyi S, Davies G, Liewald DCM, Porteous DJ, Hayward C, Butterworth AS, McIntosh AM, Gale CR, Deary IJ. Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income. Nat Commun 2019; 10:5741. [PMID: 31844048 DOI: 10.1101/573691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/11/2019] [Indexed: 05/25/2023] Open
Abstract
Socioeconomic position (SEP) is a multi-dimensional construct reflecting (and influencing) multiple socio-cultural, physical, and environmental factors. In a sample of 286,301 participants from UK Biobank, we identify 30 (29 previously unreported) independent-loci associated with income. Using a method to meta-analyze data from genetically-correlated traits, we identify an additional 120 income-associated loci. These loci show clear evidence of functionality, with transcriptional differences identified across multiple cortical tissues, and links to GABAergic and serotonergic neurotransmission. By combining our genome wide association study on income with data from eQTL studies and chromatin interactions, 24 genes are prioritized for follow up, 18 of which were previously associated with intelligence. We identify intelligence as one of the likely causal, partly-heritable phenotypes that might bridge the gap between molecular genetic inheritance and phenotypic consequence in terms of income differences. These results indicate that, in modern era Great Britain, genetic effects contribute towards some of the observed socioeconomic inequalities.
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Affiliation(s)
- W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Stuart J Ritchie
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Nathan G Skene
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- UCL Institute of Neurology, Queen Square, London, UK
- Department of Medicine, Division of Brain Sciences, Imperial College, London, UK
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven Bell
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Emanuele Di Angelantonio
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- NHS Blood and Transplant, Cambridge, UK
| | - David J Roberts
- Cambridge Substantive Site, Health Data Research UK, Wellcome Genome Campus, Hinxton, UK
- BRC Haematology Theme and Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NHS Blood and Transplant - Oxford Centre, Oxford, UK
| | - Shen Xueyi
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Adam S Butterworth
- The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- UK Medical Research Council/British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Catharine R Gale
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
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313
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Guo L, Lin W, Zhang Y, Li W, Wang J. BEST: a web server for brain expression Spatio-temporal pattern analysis. BMC Bioinformatics 2019; 20:632. [PMID: 31805847 PMCID: PMC6896511 DOI: 10.1186/s12859-019-3222-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022] Open
Abstract
Background Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from genetics studies. By using reference data from brain expression studies, multiple types of comprehensive gene expression pattern analysis have been performed on psychiatric genetic results. These systems-level spatial-temporal expression pattern analyses provided evidence on specific brain regions, developmental stages and molecular pathways that are possibly involved in psychiatric pathophysiology. At present, there is no online tool for such systematic analysis, which hinders the applications of analysis by non-informatics researchers such as experimental biologists and clinical molecular biologists. Results We developed the BEST web server to support Brain Expression Spatio-Temporal pattern analysis. There are three highlighted features of BEST: 1) visualization: it generates user-friendly visual results that are easy to interpret, including heatmaps, Venn diagrams, gene co-expression networks and cluster-based Manhattan gene plots; these results illustrate the complex spatio-temporal expression patterns, including expression quantification and correlation between genes; 2) integration: it provides comprehensive human brain spatio-temporal expression patterns by integrating data from currently available databases; 3) multi-dimensionality: it analyses input genes as both a whole set and several subsets (clusters) which are enriched according to co-expression patterns, and it also presents the correlation between genetic and expression data. Conclusions To the best of our knowledge, BEST is the first data tool to support comprehensive human brain spatial-temporal expression pattern analysis. It helps to bridge disease-related genetic studies and mechanism studies, provides clues for key gene and molecular system identification, and supports the analysis of disease sensitive brain region and age stages. BEST is freely available at http://best.psych.ac.cn.
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Affiliation(s)
- Liyuan Guo
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China.,Department of Psycholog, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Lin
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China.,Department of Psycholog, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yidan Zhang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China.,Department of Psycholog, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenhan Li
- Oumeng V medical Laboratory, Hangzhou, 310013, Zhejiang, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Chaoyang District, Beijing, 100101, China. .,Department of Psycholog, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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314
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Reynolds RH, Hardy J, Ryten M, Gagliano Taliun SA. Informing disease modelling with brain-relevant functional genomic annotations. Brain 2019; 142:3694-3712. [PMID: 31603214 PMCID: PMC6885670 DOI: 10.1093/brain/awz295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
The past decade has seen a surge in the number of disease/trait-associated variants, largely because of the union of studies to share genetic data and the availability of electronic health records from large cohorts for research use. Variant discovery for neurological and neuropsychiatric genome-wide association studies, including schizophrenia, Parkinson's disease and Alzheimer's disease, has greatly benefitted; however, the translation of these genetic association results to interpretable biological mechanisms and models is lagging. Interpreting disease-associated variants requires knowledge of gene regulatory mechanisms and computational tools that permit integration of this knowledge with genome-wide association study results. Here, we summarize key conceptual advances in the generation of brain-relevant functional genomic annotations and amongst tools that allow integration of these annotations with association summary statistics, which together provide a new and exciting opportunity to identify disease-relevant genes, pathways and cell types in silico. We discuss the opportunities and challenges associated with these developments and conclude with our perspective on future advances in annotation generation, tool development and the union of the two.
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Affiliation(s)
- Regina H Reynolds
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
- UK Dementia Research Institute at University College London (UCL), London, UK
| | - Mina Ryten
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
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315
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Johnson MR, Kaminski RM. A systems-level framework for anti-epilepsy drug discovery. Neuropharmacology 2019; 170:107868. [PMID: 31785261 DOI: 10.1016/j.neuropharm.2019.107868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Modern anti-seizure drug development yielded benefits in terms of improved pharmacokinetics, safety and tolerability profiles, but offered no advances in efficacy compared to previous older generations of anti-seizure drugs. Despite significant advances in our understanding of the genetic bases to epilepsy, and a welcome renewed interest on the severe monogenic epilepsies, modern genetics has yet to directly inform more effective or disease-modifying anti-seizure drugs. Here, we describe a new approach to the identification of novel disease modifying anti-epilepsy drugs. The systems genetics approach aims to first identify pathophysiological mechanisms by integrating polygenic risk with cellular gene expression profiles and then to relate these molecular mechanisms to druggable targets using a gene regulatory (regulome) framework. The approach offers an exciting and flexible framework for future drug discovery in epilepsy, and is applicable to any disease for which appropriate cell-type and disease-context specific data exist. This article is part of the special issue entitled 'New Epilepsy Therapies for the 21st Century - From Antiseizure Drugs to Prevention, Modification and Cure of Epilepsy'.
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Affiliation(s)
- Michael R Johnson
- Department of Brain Sciences, Imperial College London, Room E419, Burlington Danes Building, Hammersmith Hospital Campus 160 Du Cane Road, London, W12 0NN, United Kingdom.
| | - Rafal M Kaminski
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse, 124 4070, Basel, Switzerland.
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316
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Raabe FJ, Slapakova L, Rossner MJ, Cantuti-Castelvetri L, Simons M, Falkai PG, Schmitt A. Oligodendrocytes as A New Therapeutic Target in Schizophrenia: From Histopathological Findings to Neuron-Oligodendrocyte Interaction. Cells 2019; 8:cells8121496. [PMID: 31771166 PMCID: PMC6952785 DOI: 10.3390/cells8121496] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022] Open
Abstract
Imaging and postmortem studies have revealed disturbed oligodendroglia-related processes in patients with schizophrenia and provided much evidence for disturbed myelination, irregular gene expression, and altered numbers of oligodendrocytes in the brains of schizophrenia patients. Oligodendrocyte deficits in schizophrenia might be a result of failed maturation and disturbed regeneration and may underlie the cognitive deficits of the disease, which are strongly associated with impaired long-term outcome. Cognition depends on the coordinated activity of neurons and interneurons and intact connectivity. Oligodendrocyte precursors form a synaptic network with parvalbuminergic interneurons, and disturbed crosstalk between these cells may be a cellular basis of pathology in schizophrenia. However, very little is known about the exact axon-glial cellular and molecular processes that may be disturbed in schizophrenia. Until now, investigations were restricted to peripheral tissues, such as blood, correlative imaging studies, genetics, and molecular and histological analyses of postmortem brain samples. The advent of human-induced pluripotent stem cells (hiPSCs) will enable functional analysis in patient-derived living cells and holds great potential for understanding the molecular mechanisms of disturbed oligodendroglial function in schizophrenia. Targeting such mechanisms may contribute to new treatment strategies for previously treatment-resistant cognitive symptoms.
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Affiliation(s)
- Florian J. Raabe
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany; (F.J.R.); (L.S.); (P.G.F.)
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Kraepelinstr, 2-10, 80804 Munich, Germany
- Molecular and Behavioural Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Lenka Slapakova
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany; (F.J.R.); (L.S.); (P.G.F.)
- International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Kraepelinstr, 2-10, 80804 Munich, Germany
| | - Moritz J. Rossner
- Molecular and Behavioural Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Ludovico Cantuti-Castelvetri
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany; (L.C.-C.); (M.S.)
| | - Mikael Simons
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany; (L.C.-C.); (M.S.)
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- Institute of Neuronal Cell Biology, Technical University Munich, 80805 Munich, Germany
| | - Peter G. Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany; (F.J.R.); (L.S.); (P.G.F.)
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany; (F.J.R.); (L.S.); (P.G.F.)
- Molecular and Behavioural Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany;
- Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of Sao Paulo, 05453-010 São Paulo, Brazil
- Correspondence: ; Tel.: +49-(0)89-4400-52761; Fax: +49-(0)89-4400-55530
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317
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Papiol S, Keeser D, Hasan A, Schneider-Axmann T, Raabe F, Degenhardt F, Rossner MJ, Bickeböller H, Cantuti-Castelvetri L, Simons M, Wobrock T, Schmitt A, Malchow B, Falkai P. Polygenic burden associated to oligodendrocyte precursor cells and radial glia influences the hippocampal volume changes induced by aerobic exercise in schizophrenia patients. Transl Psychiatry 2019; 9:284. [PMID: 31712617 PMCID: PMC6848123 DOI: 10.1038/s41398-019-0618-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/10/2019] [Accepted: 10/03/2019] [Indexed: 02/04/2023] Open
Abstract
Hippocampal volume decrease is a structural hallmark of schizophrenia (SCZ), and convergent evidence from postmortem and imaging studies suggests that it may be explained by changes in the cytoarchitecture of the cornu ammonis 4 (CA4) and dentate gyrus (DG) subfields. Increasing evidence indicates that aerobic exercise increases hippocampal volume in CA subfields and improves cognition in SCZ patients. Previous studies showed that the effects of exercise on the hippocampus might be connected to the polygenic burden of SCZ risk variants. However, little is known about cell type-specific genetic contributions to these structural changes. In this secondary analysis, we evaluated the modulatory role of cell type-specific SCZ polygenic risk scores (PRS) on volume changes in the CA1, CA2/3, and CA4/DG subfields over time. We studied 20 multi-episode SCZ patients and 23 healthy controls who performed aerobic exercise, and 21 multi-episode SCZ patients allocated to a control intervention (table soccer) for 3 months. Magnetic resonance imaging-based assessments were performed with FreeSurfer at baseline and after 3 months. The analyses showed that the polygenic burden associated with oligodendrocyte precursor cells (OPC) and radial glia (RG) significantly influenced the volume changes between baseline and 3 months in the CA4/DG subfield in SCZ patients performing aerobic exercise. A higher OPC- or RG-associated genetic risk burden was associated with a less pronounced volume increase or even a decrease in CA4/DG during the exercise intervention. We hypothesize that SCZ cell type-specific polygenic risk modulates the aerobic exercise-induced neuroplastic processes in the hippocampus.
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Affiliation(s)
- Sergi Papiol
- Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336, Munich, Germany. .,Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, Ludwig Maximilian University, Nussbaumstrasse 7, 80336, Munich, Germany.
| | - Daniel Keeser
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany ,0000 0004 1936 973Xgrid.5252.0Institute of Clinical Radiology, Ludwig Maximilian University Munich, Marchioninistrasse 15, 81377 Munich, Germany
| | - Alkomiet Hasan
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Thomas Schneider-Axmann
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Florian Raabe
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany ,International Max Planck Research School for Translational Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Franziska Degenhardt
- 0000 0001 2240 3300grid.10388.32Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Moritz J. Rossner
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-Universität Göttingen, Humboldtallee 32, 37073 Göttingen, Germany
| | - Ludovico Cantuti-Castelvetri
- 0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany
| | - Mikael Simons
- 0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany ,0000000123222966grid.6936.aInstitute of Neuronal Cell Biology, Technical University Munich, 80805 Munich, Germany
| | - Thomas Wobrock
- Department of Psychiatry and Psychotherapy, County Hospitals Darmstadt-Dieburg, Krankenhausstrasse 7, 64823 Groß-Umstadt, Germany
| | - Andrea Schmitt
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany ,0000 0004 1937 0722grid.11899.38Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of Sao Paulo, Rua Dr. Ovídio Pires de Campos 785, Sao Paulo-SP, 05403-903 Brazil
| | - Berend Malchow
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Peter Falkai
- 0000 0004 0477 2585grid.411095.8Department of Psychiatry, University Hospital, Nussbaumstrasse 7, 80336 Munich, Germany
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318
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Alexander Arguello P, Addington A, Borja S, Brady L, Dutka T, Gitik M, Koester S, Meinecke D, Merikangas K, McMahon FJ, Panchision D, Senthil G, Lehner T. From genetics to biology: advancing mental health research in the Genomics ERA. Mol Psychiatry 2019; 24:1576-1582. [PMID: 31164699 DOI: 10.1038/s41380-019-0445-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 11/09/2022]
Abstract
The Genomics Workgroup of the National Advisory Mental Health Council (NAMHC) recently issued a set of recommendations for advancing the NIMH psychiatric genetics research program and prioritizing subsequent follow-up studies. The report emphasized the primacy of rigorous statistical support from properly designed, well-powered studies for pursuing genetic variants robustly associated with disease. Here we discuss the major points NIMH program staff consider when assessing research applications based on common and rare variants, as well as genetic syndromes, associated with psychiatric disorders. These are broad guiding principles for investigators to consider prior to submission of their applications. NIMH staff weigh these points in the context of reviewer comments, the existing literature, and current investments in related projects. Following the recommendations of the NAMHC, statistical strength and robustness of the underlying genetic discovery weighs heavily in our funding considerations as does the suitability of the proposed experimental approach. We specifically address our evaluation of applications motivated in whole, or in part, by an association between human DNA sequence variation and a disease or trait relevant to the mission of the NIMH.
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Affiliation(s)
- P Alexander Arguello
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
| | - Anjené Addington
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Susan Borja
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Linda Brady
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Tara Dutka
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Miri Gitik
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Susan Koester
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Douglas Meinecke
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen Merikangas
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Francis J McMahon
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - David Panchision
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Geetha Senthil
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Lehner
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA.
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319
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Vgontzas A, Renthal W. Migraine-associated gene expression in cell types of the central and peripheral nervous system. Cephalalgia 2019; 40:517-523. [DOI: 10.1177/0333102419877834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Genome-wide association studies have implicated dozens of genes with migraine susceptibility, but it remains unclear in which nervous system cell types these genes are expressed. Methods Using single-cell RNA sequencing data from the central and peripheral nervous system, including the trigeminal ganglion, the expression of putative migraine-associated genes was compared across neuronal, glial and neurovascular cell types within these tissues. Results Fifty-four putative migraine-associated genes were expressed in the central nervous system, peripheral nervous system or neurovascular cell types analyzed. Six genes (11.1%) were selectively enriched in central nervous system cell types, three (5.5%) in neurovascular cell types, and two (3.7%) in peripheral nervous system cell types. The remaining genes were expressed in multiple cell types. Conclusions Single-cell RNA sequencing of the brain and peripheral nervous system localizes each migraine-associated gene to its respective nervous system tissue and the cell types in which it is expressed. While the majority of migraine-associated genes are broadly expressed, we identified several cell-type-specific migraine-associated genes in the central nervous system, peripheral nervous system, and neurovasculature. Trial registration: not applicable.
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Affiliation(s)
- Angeliki Vgontzas
- Department of Neurology, John R. Graham Headache Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - William Renthal
- Department of Neurology, John R. Graham Headache Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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320
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Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun 2019; 10:4902. [PMID: 31653841 PMCID: PMC6814749 DOI: 10.1038/s41467-019-12780-8] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified genetic variants associated with age-related macular degeneration (AMD), one of the leading causes of blindness in the elderly. However, it has been challenging to identify the cell types associated with AMD given the genetic complexity of the disease. Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the first single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. Heterogeneity is observed within macroglia, suggesting that human retinal glia are more diverse than previously thought. Finally, GWAS-based enrichment analysis identifies glia, vascular cells, and cone photoreceptors to be associated with the risk of AMD. These data provide a detailed analysis of the human retina, and show how scRNA-seq can provide insight into cell types involved in complex, inflammatory genetic diseases.
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Affiliation(s)
- Madhvi Menon
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Departments of Ophthalmology and Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA, 02115, USA
| | - Shahin Mohammadi
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA
| | - Brittany A Goods
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Tanina D Cadwell
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA, 02115, USA
| | - Yu Xing
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, 02142, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - John Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, 02142, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA, 02115, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA
| | - Brian P Hafler
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Departments of Ophthalmology and Neurology, Harvard Medical School, Boston, MA, 02115, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, 06510, USA.
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322
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Hoffmann A, Ziller M, Spengler D. Progress in iPSC-Based Modeling of Psychiatric Disorders. Int J Mol Sci 2019; 20:E4896. [PMID: 31581684 PMCID: PMC6801734 DOI: 10.3390/ijms20194896] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/19/2022] Open
Abstract
Progress in iPSC-based cellular systems provides new insights into human brain development and early neurodevelopmental deviations in psychiatric disorders. Among these, studies on schizophrenia (SCZ) take a prominent role owing to its high heritability and multifarious evidence that it evolves from a genetically induced vulnerability in brain development. Recent iPSC studies on patients with SCZ indicate that functional impairments of neural progenitor cells (NPCs) in monolayer culture extend to brain organoids by disrupting neocorticogenesis in an in vitro model. In addition, the formation of hippocampal circuit-like structures in vitro is impaired in patients with SCZ as is the case for glia development. Intriguingly, chimeric-mice experiments show altered oligodendrocyte and astrocyte development in vivo that highlights the importance of cell-cell interactions in the pathogenesis of early-onset SCZ. Likewise, cortical imbalances in excitatory-inhibitory signaling may result from a cell-autonomous defect in cortical interneuron (cIN) development. Overall, these findings indicate that genetic risk in SCZ impacts neocorticogenesis, hippocampal circuit formation, and the development of distinct glial and neuronal subtypes. In light of this remarkable progress, we discuss current limitations and further steps necessary to harvest the full potential of iPSC-based investigations on psychiatric disorders.
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Affiliation(s)
- Anke Hoffmann
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany.
| | - Michael Ziller
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany.
| | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany.
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323
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Schrode N, Ho SM, Yamamuro K, Dobbyn A, Huckins L, Matos MR, Cheng E, Deans PJM, Flaherty E, Barretto N, Topol A, Alganem K, Abadali S, Gregory J, Hoelzli E, Phatnani H, Singh V, Girish D, Aronow B, Mccullumsmith R, Hoffman GE, Stahl EA, Morishita H, Sklar P, Brennand KJ. Synergistic effects of common schizophrenia risk variants. Nat Genet 2019; 51:1475-1485. [PMID: 31548722 PMCID: PMC6778520 DOI: 10.1038/s41588-019-0497-5] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
The mechanisms by which common risk variants of small effect interact to contribute to complex genetic disorders are unclear. Here, we apply a genetic approach, using isogenic human induced pluripotent stem cells, to evaluate the effects of schizophrenia (SZ)-associated common variants predicted to function as SZ expression quantitative trait loci (eQTLs). By integrating CRISPR-mediated gene editing, activation and repression technologies to study one putative SZ eQTL (FURIN rs4702) and four top-ranked SZ eQTL genes (FURIN, SNAP91, TSNARE1 and CLCN3), our platform resolves pre- and postsynaptic neuronal deficits, recapitulates genotype-dependent gene expression differences and identifies convergence downstream of SZ eQTL gene perturbations. Our observations highlight the cell-type-specific effects of common variants and demonstrate a synergistic effect between SZ eQTL genes that converges on synaptic function. We propose that the links between rare and common variants implicated in psychiatric disease risk constitute a potentially generalizable phenomenon occurring more widely in complex genetic disorders.
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Affiliation(s)
- Nadine Schrode
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seok-Man Ho
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kazuhiko Yamamuro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Dobbyn
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P J Michael Deans
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Barretto
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khaled Alganem
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Sonya Abadali
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Gregory
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Emily Hoelzli
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Vineeta Singh
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Deeptha Girish
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Mccullumsmith
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela Sklar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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324
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Sanders SJ, Sahin M, Hostyk J, Thurm A, Jacquemont S, Avillach P, Douard E, Martin CL, Modi ME, Moreno-De-Luca A, Raznahan A, Anticevic A, Dolmetsch R, Feng G, Geschwind DH, Glahn DC, Goldstein DB, Ledbetter DH, Mulle JG, Pasca SP, Samaco R, Sebat J, Pariser A, Lehner T, Gur RE, Bearden CE. A framework for the investigation of rare genetic disorders in neuropsychiatry. Nat Med 2019; 25:1477-1487. [PMID: 31548702 PMCID: PMC8656349 DOI: 10.1038/s41591-019-0581-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/31/2019] [Indexed: 02/07/2023]
Abstract
De novo and inherited rare genetic disorders (RGDs) are a major cause of human morbidity, frequently involving neuropsychiatric symptoms. Recent advances in genomic technologies and data sharing have revolutionized the identification and diagnosis of RGDs, presenting an opportunity to elucidate the mechanisms underlying neuropsychiatric disorders by investigating the pathophysiology of high-penetrance genetic risk factors. Here we seek out the best path forward for achieving these goals. We think future research will require consistent approaches across multiple RGDs and developmental stages, involving both the characterization of shared neuropsychiatric dimensions in humans and the identification of neurobiological commonalities in model systems. A coordinated and concerted effort across patients, families, researchers, clinicians and institutions, including rapid and broad sharing of data, is now needed to translate these discoveries into urgently needed therapies.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Audrey Thurm
- National Institute of Mental Health, Bethesda, MD, USA
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Paul Avillach
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Elise Douard
- CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Christa L Martin
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Meera E Modi
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Alan Anticevic
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Ricardo Dolmetsch
- Department of Neuroscience, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior and Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - David H Ledbetter
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sergiu P Pasca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Rodney Samaco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
| | - Anne Pariser
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Thomas Lehner
- National Institute of Mental Health, Bethesda, MD, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, and the Lifespan Brain Institute, Perelman School of Medicine and Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA.
| | - Carrie E Bearden
- Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, Los Angeles, CA, USA.
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325
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Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH, Tao R, Ma L, Jia Y, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation. Genome Biol 2019; 20:196. [PMID: 31554518 PMCID: PMC6761727 DOI: 10.1186/s13059-019-1805-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/28/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we profile the DNAm landscape at single-base resolution across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compare them to non-neurons (primarily glia) and prenatal homogenate cortex. RESULTS We show that DNAm changes more dramatically during the first 5 years of postnatal life than during the entire remaining period. We further refine global patterns of increasingly divergent neuronal CpG and CpH methylation (mCpG and mCpH) into six developmental trajectories and find that in contrast to genome-wide patterns, neighboring mCpG and mCpH levels within these regions are highly correlated. We integrate paired RNA-seq data and identify putative regulation of hundreds of transcripts and their splicing events exclusively by mCpH levels, independently from mCpG levels, across this period. We finally explore the relationship between DNAm patterns and development of brain-related phenotypes and find enriched heritability for many phenotypes within identified DNAm features. CONCLUSIONS By profiling DNAm changes in NeuN-sorted neurons over the span of human cortical development, we identify novel, dynamic regions of DNAm that would be masked in homogenate DNAm data; expand on the relationship between CpG methylation, CpH methylation, and gene expression; and find enrichment particularly for neuropsychiatric diseases in genomic regions with cell type-specific, developmentally dynamic DNAm patterns.
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Affiliation(s)
- Amanda J Price
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nikolay A Ivanov
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Wei Xia
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Liang Ma
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Yankai Jia
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
- Department of Neurology, JHSOM, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD, 21205, USA
- Department of Neurology, JHSOM, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA
- Department of Neuroscience, JHSOM, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD, 21205, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA.
- Department of Neuroscience, JHSOM, Baltimore, MD, USA.
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health (JHBSPH), 615 N Wolfe St, Baltimore, MD, 21205, USA.
- Department of Biostatistics, JHBSPH, 615 N Wolfe St, Baltimore, MD, 21205, USA.
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326
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Gelernter J, Sun N, Polimanti R, Pietrzak R, Levey DF, Bryois J, Lu Q, Hu Y, Li B, Radhakrishnan K, Aslan M, Cheung KH, Li Y, Rajeevan N, Sayward F, Harrington K, Chen Q, Cho K, Pyarajan S, Sullivan PF, Quaden R, Shi Y, Hunter-Zinck H, Gaziano JM, Concato J, Zhao H, Stein MB. Genome-wide association study of post-traumatic stress disorder reexperiencing symptoms in >165,000 US veterans. Nat Neurosci 2019; 22:1394-1401. [PMID: 31358989 PMCID: PMC6953633 DOI: 10.1038/s41593-019-0447-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/11/2019] [Indexed: 12/20/2022]
Abstract
Post-traumatic stress disorder (PTSD) is a major problem among military veterans and civilians alike, yet its pathophysiology remains poorly understood. We performed a genome-wide association study and bioinformatic analyses, which included 146,660 European Americans and 19,983 African Americans in the US Million Veteran Program, to identify genetic risk factors relevant to intrusive reexperiencing of trauma, which is the most characteristic symptom cluster of PTSD. In European Americans, eight distinct significant regions were identified. Three regions had values of P < 5 × 10-10: CAMKV; chromosome 17 closest to KANSL1, but within a large high linkage disequilibrium region that also includes CRHR1; and TCF4. Associations were enriched with respect to the transcriptomic profiles of striatal medium spiny neurons. No significant associations were observed in the African American cohort of the sample. Results in European Americans were replicated in the UK Biobank data. These results provide new insights into the biology of PTSD in a well-powered genome-wide association study.
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Affiliation(s)
- Joel Gelernter
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA.
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
| | - Ning Sun
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Renato Polimanti
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Pietrzak
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel F Levey
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Qiongshi Lu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Yiming Hu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Krishnan Radhakrishnan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mihaela Aslan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kei-Hoi Cheung
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yuli Li
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Nallakkandi Rajeevan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Frederick Sayward
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Harrington
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Quan Chen
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Rachel Quaden
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Yunling Shi
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Haley Hunter-Zinck
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John Concato
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
- Departments of Psychiatry and of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
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327
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Feliciano P, Zhou X, Astrovskaya I, Turner TN, Wang T, Brueggeman L, Barnard R, Hsieh A, Snyder LG, Muzny DM, Sabo A, Gibbs RA, Eichler EE, O’Roak BJ, Michaelson JJ, Volfovsky N, Shen Y, Chung WK. Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ Genom Med 2019; 4:19. [PMID: 31452935 PMCID: PMC6707204 DOI: 10.1038/s41525-019-0093-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/11/2019] [Indexed: 12/30/2022] Open
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous condition, caused by a combination of rare de novo and inherited variants as well as common variants in at least several hundred genes. However, significantly larger sample sizes are needed to identify the complete set of genetic risk factors. We conducted a pilot study for SPARK (SPARKForAutism.org) of 457 families with ASD, all consented online. Whole exome sequencing (WES) and genotyping data were generated for each family using DNA from saliva. We identified variants in genes and loci that are clinically recognized causes or significant contributors to ASD in 10.4% of families without previous genetic findings. In addition, we identified variants that are possibly associated with ASD in an additional 3.4% of families. A meta-analysis using the TADA framework at a false discovery rate (FDR) of 0.1 provides statistical support for 26 ASD risk genes. While most of these genes are already known ASD risk genes, BRSK2 has the strongest statistical support and reaches genome-wide significance as a risk gene for ASD (p-value = 2.3e-06). Future studies leveraging the thousands of individuals with ASD who have enrolled in SPARK are likely to further clarify the genetic risk factors associated with ASD as well as allow accelerate ASD research that incorporates genetic etiology.
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Affiliation(s)
| | - Xueya Zhou
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | | | - Tychele N. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242 USA
| | - Rebecca Barnard
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Alexander Hsieh
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA
| | - Brian J. O’Roak
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242 USA
| | | | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY 10032 USA
| | - Wendy K. Chung
- Simons Foundation, New York, NY 10010 USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
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328
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Fjodorova M, Louessard M, Li Z, De La Fuente DC, Dyke E, Brooks SP, Perrier AL, Li M. CTIP2-Regulated Reduction in PKA-Dependent DARPP32 Phosphorylation in Human Medium Spiny Neurons: Implications for Huntington Disease. Stem Cell Reports 2019; 13:448-457. [PMID: 31447328 PMCID: PMC6739739 DOI: 10.1016/j.stemcr.2019.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/26/2022] Open
Abstract
The mechanisms underlying the selective degeneration of medium spiny neurons (MSNs) in Huntington disease (HD) remain largely unknown. CTIP2, a transcription factor expressed by all MSNs, is implicated in HD pathogenesis because of its interactions with mutant huntingtin. Here, we report a key role for CTIP2 in protein phosphorylation via governing protein kinase A (PKA) signaling in human striatal neurons. Transcriptomic analysis of CTIP2-deficient MSNs implicates CTIP2 target genes at the heart of cAMP-Ca2+ signal integration in the PKA pathway. These findings are further supported by experimental evidence of a substantial reduction in phosphorylation of DARPP32 and GLUR1, two PKA targets in CTIP2-deficient MSNs. Moreover, we show that CTIP2-dependent dysregulation of protein phosphorylation is shared by HD hPSC-derived MSNs and striatal tissues of two HD mouse models. This study therefore establishes an essential role for CTIP2 in human MSN homeostasis and provides mechanistic and potential therapeutic insight into striatal neurodegeneration.
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Affiliation(s)
- Marija Fjodorova
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.
| | - Morgane Louessard
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
| | - Zongze Li
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Daniel C De La Fuente
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Emma Dyke
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Simon P Brooks
- Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK
| | - Anselme L Perrier
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR861, I-Stem, AFM, 91100 Corbeil-Essonnes, France
| | - Meng Li
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK; Division of Neuroscience, School of Bioscience, Cardiff University, Cardiff CF10 3AX, UK.
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329
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Kameneva P, Adameyko I. Recent advances in our understanding of central and peripheral nervous system progenitors. Curr Opin Cell Biol 2019; 61:24-30. [PMID: 31369951 DOI: 10.1016/j.ceb.2019.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/25/2019] [Accepted: 07/02/2019] [Indexed: 10/26/2022]
Abstract
Several decades of intense research provided us with a grand framework describing the emergence of neurons in central (CNS) and peripheral (PNS) nervous systems. However, the specifics of molecular events and lineage control leading to a plethora of neuronal subtypes stayed largely unclear. Today, the advances in single cell omics, sample clearing and 3D-microscopy techniques, brain organoids, and synaptic connectivity tracing enabled systematic and unbiased understanding of neuronal diversity, development, circuitry and cell identity control. Novel technological advancements stimulated the transition from conceptual scheme of neuronal differentiation into precise maps of molecular events leading to the diversity of specific neuronal subtypes in relation to their locations and microenvironment. These high-resolution data opened a set of new questions including how transcriptional and epigenetics states control the proportionality of neuronal subpopulations or what are the evolutionary mechanisms of origin of different neuronal subtypes. In this review, we outline the most recent advancements in our understanding of how the neuronal diversity is generated in CNS and PNS and briefly address the challenges and questions arising in the field of neurogenesis.
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Affiliation(s)
- Polina Kameneva
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria.
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330
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Moslem M, Olive J, Falk A. Stem cell models of schizophrenia, what have we learned and what is the potential? Schizophr Res 2019; 210:3-12. [PMID: 30587427 DOI: 10.1016/j.schres.2018.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a complex disorder with clinical manifestations in early adulthood. However, it may start with disruption of brain development caused by genetic or environmental factors, or both. Early deteriorating effects of genetic/environmental factors on neural development might be key to described disease causing mechanisms. Establishing cellular models with cells from affected individual using the induced pluripotent stem cells (iPSC) technology could be used to mimic early neurodevelopment alterations caused by risk genes or environmental stressors. Indeed, cellular models have allowed identification and further study of risk factors and the biological pathways in which they are involved. New advancements in differentiation methods such as defined and robust monolayer protocols and cerebral 3D organoids have made it possible to faithfully mimic neural development and neuronal functionality while CRISPR-editing tools assist to engineer isogenic cell lines to precisely explore genetic variation in polygenic diseases such as schizophrenia. Here we review the current field of iPSC models of schizophrenia and how risk factors can be modelled as well as discussing the common biological pathways involved.
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Affiliation(s)
- Mohsen Moslem
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Jessica Olive
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Life Sciences, Imperial College London, United Kingdom.
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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331
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How genome-wide association studies (GWAS) made traditional candidate gene studies obsolete. Neuropsychopharmacology 2019; 44:1518-1523. [PMID: 30982060 PMCID: PMC6785091 DOI: 10.1038/s41386-019-0389-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
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332
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Mu Q, Chen Y, Wang J. Deciphering Brain Complexity Using Single-cell Sequencing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:344-366. [PMID: 31586689 PMCID: PMC6943771 DOI: 10.1016/j.gpb.2018.07.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 12/21/2022]
Abstract
The human brain contains billions of highly differentiated and interconnected cells that form intricate neural networks and collectively control the physical activities and high-level cognitive functions, such as memory, decision-making, and social behavior. Big data is required to decipher the complexity of cell types, as well as connectivity and functions of the brain. The newly developed single-cell sequencing technology, which provides a comprehensive landscape of brain cell type diversity by profiling the transcriptome, genome, and/or epigenome of individual cells, has contributed substantially to revealing the complexity and dynamics of the brain and providing new insights into brain development and brain-related disorders. In this review, we first introduce the progresses in both experimental and computational methods of single-cell sequencing technology. Applications of single-cell sequencing-based technologies in brain research, including cell type classification, brain development, and brain disease mechanisms, are then elucidated by representative studies. Lastly, we provided our perspectives into the challenges and future developments in the field of single-cell sequencing. In summary, this mini review aims to provide an overview of how big data generated from single-cell sequencing have empowered the advancements in neuroscience and shed light on the complex problems in understanding brain functions and diseases.
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Affiliation(s)
- Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Yiyun Chen
- Department of Chemical and Biological Engineering, Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
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333
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Grunwald LM, Stock R, Haag K, Buckenmaier S, Eberle MC, Wildgruber D, Storchak H, Kriebel M, Weißgraeber S, Mathew L, Singh Y, Loos M, Li KW, Kraushaar U, Fallgatter AJ, Volkmer H. Comparative characterization of human induced pluripotent stem cells (hiPSC) derived from patients with schizophrenia and autism. Transl Psychiatry 2019; 9:179. [PMID: 31358727 PMCID: PMC6663940 DOI: 10.1038/s41398-019-0517-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 06/01/2019] [Indexed: 12/12/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSC) provide an attractive tool to study disease mechanisms of neurodevelopmental disorders such as schizophrenia. A pertinent problem is the development of hiPSC-based assays to discriminate schizophrenia (SZ) from autism spectrum disorder (ASD) models. Healthy control individuals as well as patients with SZ and ASD were examined by a panel of diagnostic tests. Subsequently, skin biopsies were taken for the generation, differentiation, and testing of hiPSC-derived neurons from all individuals. SZ and ASD neurons share a reduced capacity for cortical differentiation as shown by quantitative analysis of the synaptic marker PSD95 and neurite outgrowth. By contrast, pattern analysis of calcium signals turned out to discriminate among healthy control, schizophrenia, and autism samples. Schizophrenia neurons displayed decreased peak frequency accompanied by increased peak areas, while autism neurons showed a slight decrease in peak amplitudes. For further analysis of the schizophrenia phenotype, transcriptome analyses revealed a clear discrimination among schizophrenia, autism, and healthy controls based on differentially expressed genes. However, considerable differences were still evident among schizophrenia patients under inspection. For one individual with schizophrenia, expression analysis revealed deregulation of genes associated with the major histocompatibility complex class II (MHC class II) presentation pathway. Interestingly, antipsychotic treatment of healthy control neurons also increased MHC class II expression. In conclusion, transcriptome analysis combined with pattern analysis of calcium signals appeared as a tool to discriminate between SZ and ASD phenotypes in vitro.
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Affiliation(s)
- Lena-Marie Grunwald
- 0000 0000 9457 1306grid.461765.7Department Molecular Biology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Ricarda Stock
- 0000 0000 9457 1306grid.461765.7Department Molecular Biology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Kathrina Haag
- 0000 0000 9457 1306grid.461765.7Department Molecular Biology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Sandra Buckenmaier
- 0000 0000 9457 1306grid.461765.7Department Cell Physiology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Mark-Christian Eberle
- 0000 0001 2190 1447grid.10392.39Department of Psychiatry, University of Tübingen, Osianderstrasse 24, 72076 Tübingen, Germany
| | - Dirk Wildgruber
- 0000 0001 2190 1447grid.10392.39Department of Psychiatry, University of Tübingen, Osianderstrasse 24, 72076 Tübingen, Germany
| | - Helena Storchak
- 0000 0001 2190 1447grid.10392.39Department of Psychiatry, University of Tübingen, Osianderstrasse 24, 72076 Tübingen, Germany
| | - Martin Kriebel
- 0000 0000 9457 1306grid.461765.7Department Molecular Biology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Stephanie Weißgraeber
- 0000 0004 6008 5552grid.498061.2CeGaT GmbH - Center for Genomics and Transcriptomics, Paul-Ehrlich-Str. 23, 72076 Tübingen, Germany
| | - Lisha Mathew
- 0000 0004 6008 5552grid.498061.2CeGaT GmbH - Center for Genomics and Transcriptomics, Paul-Ehrlich-Str. 23, 72076 Tübingen, Germany
| | - Yasmin Singh
- 0000 0004 6008 5552grid.498061.2CeGaT GmbH - Center for Genomics and Transcriptomics, Paul-Ehrlich-Str. 23, 72076 Tübingen, Germany
| | - Maarten Loos
- grid.426096.fSylics (Synaptologics BV), PO Box 71033, 1008 BA Amsterdam, The Netherlands
| | - Ka Wan Li
- grid.484519.5Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, The Netherlands
| | - Udo Kraushaar
- 0000 0000 9457 1306grid.461765.7Department Cell Physiology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Andreas J. Fallgatter
- 0000 0001 2190 1447grid.10392.39Department of Psychiatry, University of Tübingen, Osianderstrasse 24, 72076 Tübingen, Germany
| | - Hansjürgen Volkmer
- Department Molecular Biology, NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany.
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334
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Watanabe K, Umićević Mirkov M, de Leeuw CA, van den Heuvel MP, Posthuma D. Genetic mapping of cell type specificity for complex traits. Nat Commun 2019; 10:3222. [PMID: 31324783 PMCID: PMC6642112 DOI: 10.1038/s41467-019-11181-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/11/2019] [Indexed: 01/11/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) data allows to create cell type specific transcriptome profiles. Such profiles can be aligned with genome-wide association studies (GWASs) to implicate cell type specificity of the traits. Current methods typically rely only on a small subset of available scRNA-seq datasets, and integrating multiple datasets is hampered by complex batch effects. Here we collated 43 publicly available scRNA-seq datasets. We propose a 3-step workflow with conditional analyses within and between datasets, circumventing batch effects, to uncover associations of traits with cell types. Applying this method to 26 traits, we identify independent associations of multiple cell types. These results lead to starting points for follow-up functional studies aimed at gaining a mechanistic understanding of these traits. The proposed framework as well as the curated scRNA-seq datasets are made available via an online platform, FUMA, to facilitate rapid evaluation of cell type specificity by other researchers. Tissue- and cell type-specific information helps to interpret findings from genome-wide association studies. Here, the authors leverage multiple single cell expression datasets to infer cell type specificity of traits.
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Affiliation(s)
- Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Maša Umićević Mirkov
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Genetics, section Complex Trait Genetics, Neuroscience Campus Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands. .,Department of Clinical Genetics, section Complex Trait Genetics, Neuroscience Campus Amsterdam, VU Medical Center, Amsterdam, The Netherlands.
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335
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Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) has revolutionized biological sciences by revealing genome-wide gene expression levels within individual cells. However, a critical challenge faced by researchers is how to optimize the choices of sequencing platforms, sequencing depths and cell numbers in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information. RESULTS Here we present a flexible and robust simulator, scDesign, the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. In an evaluation based on 17 cell types and 6 different protocols, scDesign outperformed four state-of-the-art scRNA-seq simulation methods and led to rational experimental design. In addition, scDesign demonstrates reproducibility across biological replicates and independent studies. We also discuss the performance of multiple differential expression and dimension reduction methods based on the protocol-dependent scRNA-seq data generated by scDesign. scDesign is expected to be an effective bioinformatic tool that assists rational scRNA-seq experimental design and comparison of scRNA-seq computational methods based on specific research goals. AVAILABILITY AND IMPLEMENTATION We have implemented our method in the R package scDesign, which is freely available at https://github.com/Vivianstats/scDesign. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
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336
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Duarte RR, Bachtel ND, Côtel MC, Lee SH, Selvackadunco S, Watson IA, Hovsepian GA, Troakes C, Breen GD, Nixon DF, Murray RM, Bray NJ, Eleftherianos I, Vernon AC, Powell TR, Srivastava DP. The Psychiatric Risk Gene NT5C2 Regulates Adenosine Monophosphate-Activated Protein Kinase Signaling and Protein Translation in Human Neural Progenitor Cells. Biol Psychiatry 2019; 86:120-130. [PMID: 31097295 PMCID: PMC6614717 DOI: 10.1016/j.biopsych.2019.03.977] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 02/12/2019] [Accepted: 03/11/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND The 5'-nucleotidase, cytosolic II gene (NT5C2, cN-II) is associated with disorders characterized by psychiatric and psychomotor disturbances. Common psychiatric risk alleles at the NT5C2 locus reduce expression of this gene in the fetal and adult brain, but downstream biological risk mechanisms remain elusive. METHODS Distribution of the NT5C2 protein in the human dorsolateral prefrontal cortex and cortical human neural progenitor cells (hNPCs) was determined using immunostaining, publicly available expression data, and reverse transcriptase quantitative polymerase chain reaction. Phosphorylation quantification of adenosine monophosphate-activated protein kinase (AMPK) alpha (Thr172) and ribosomal protein S6 (Ser235/Ser236) was performed using Western blotting to infer the degree of activation of AMPK signaling and the rate of protein translation. Knockdowns were induced in hNPCs and Drosophila melanogaster using RNA interference. Transcriptomic profiling of hNPCs was performed using microarrays, and motility behavior was assessed in flies using the climbing assay. RESULTS Expression of NT5C2 was higher during neurodevelopment and was neuronally enriched in the adult human cortex. Knockdown in hNPCs affected AMPK signaling, a major nutrient-sensing mechanism involved in energy homeostasis, and protein translation. Transcriptional changes implicated in protein translation were observed in knockdown hNPCs, and expression changes to genes related to AMPK signaling and protein translation were confirmed using reverse transcriptase quantitative polymerase chain reaction. The knockdown in Drosophila was associated with drastic climbing impairment. CONCLUSIONS We provide an extensive neurobiological characterization of the psychiatric risk gene NT5C2, describing its previously unknown role in the regulation of AMPK signaling and protein translation in neural stem cells and its association with Drosophila melanogaster motility behavior.
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Affiliation(s)
- Rodrigo R.R. Duarte
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom,Department of Basic & Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Nathaniel D. Bachtel
- Department of Biological Sciences, Columbian College of Arts and Sciences, George Washington University, Washington, DC
| | - Marie-Caroline Côtel
- Department of Basic & Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom,Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Sang H. Lee
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Sashika Selvackadunco
- Medical Research Council London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Iain A. Watson
- Department of Basic & Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom,Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Gary A. Hovsepian
- Department of Biological Sciences, Columbian College of Arts and Sciences, George Washington University, Washington, DC
| | - Claire Troakes
- Medical Research Council London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Gerome D. Breen
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Douglas F. Nixon
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, New York
| | - Robin M. Murray
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Nicholas J. Bray
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ioannis Eleftherianos
- Department of Biological Sciences, Columbian College of Arts and Sciences, George Washington University, Washington, DC
| | - Anthony C. Vernon
- Department of Basic & Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom,Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Timothy R. Powell
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Deepak P. Srivastava
- Department of Basic & Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom,Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom,Address correspondence to Deepak P. Srivastava, Ph.D., Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, 5 Cutcombe Road, London SE5 9RX, United Kingdom.
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337
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Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron 2019; 103:785-801.e8. [PMID: 31303374 DOI: 10.1016/j.neuron.2019.06.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/20/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human subplate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase. By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.
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Affiliation(s)
- Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Luis de la Torre-Ubieta
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Andrew G Elkins
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason L Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Celine K Vuong
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Susanne Nichterwitz
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Gevorgian
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Biology, CSUN, Northridge, CA, USA
| | - Carli K Opland
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daning Lu
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William Connell
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Elizabeth K Ruzzo
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Tarik Hadzic
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Flora I Hinz
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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Pergola G, Di Carlo P, Jaffe AE, Papalino M, Chen Q, Hyde TM, Kleinman JE, Shin JH, Rampino A, Blasi G, Weinberger DR, Bertolino A. Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients. Biol Psychiatry 2019; 86:45-55. [PMID: 31126695 DOI: 10.1016/j.biopsych.2019.03.981] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Gene coexpression networks are relevant to functional and clinical translation of schizophrenia risk genes. We hypothesized that schizophrenia risk genes converge into coexpression pathways that may be associated with gene regulation mechanisms and with response to treatment in patients with schizophrenia. METHODS We identified gene coexpression networks in two prefrontal cortex postmortem RNA sequencing datasets (n = 688) and replicated them in four more datasets (n = 1295). We identified and replicated (p values < .001) a single module enriched for schizophrenia risk loci (13 risk genes in 10 loci). In silico screening of potential regulators of the schizophrenia risk module via bioinformatic analyses identified two transcription factors and three microRNAs associated with the risk module. To translate postmortem information into clinical phenotypes, we identified polymorphisms predicting coexpression and combined them to obtain an index approximating module coexpression (Polygenic Coexpression Index [PCI]). RESULTS The PCI-coexpression association was successfully replicated in two independent brain transcriptome datasets (n = 131; p values < .05). Finally, we tested the association between the PCI and short-term treatment response in two independent samples of patients with schizophrenia treated with olanzapine (n = 167). The PCI was associated with treatment response in the positive symptom domain in both clinical cohorts (p values < .05). CONCLUSIONS In summary, our findings in 1983 samples of human postmortem prefrontal cortex show that coexpression of a set of genes enriched for schizophrenia risk genes is relevant to treatment response. This coexpression pathway may be coregulated by transcription factors and microRNA associated with it.
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Affiliation(s)
- Giulio Pergola
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland.
| | - Pasquale Di Carlo
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland
| | - Marco Papalino
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Antonio Rampino
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Azienda Ospedaliero-Universitaria Consorziale Policlinico, Bari, Italy
| | - Giuseppe Blasi
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Azienda Ospedaliero-Universitaria Consorziale Policlinico, Bari, Italy
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alessandro Bertolino
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy; Azienda Ospedaliero-Universitaria Consorziale Policlinico, Bari, Italy.
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339
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Boutwell BB, White MA. Gene regulation and the architecture of complex human traits in the genomics era. Curr Opin Psychol 2019; 27:93-97. [PMID: 30933894 PMCID: PMC10868639 DOI: 10.1016/j.copsyc.2019.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
Abstract
Virtually all human psychological and behavioral traits are at least partially heritable. For nearly a century, classical genetic studies have sought to understand how genetic variation contributes to human variation in these traits. More recently, genome-wide association studies have identified large numbers of specific genetic variants linked with complex traits. Many of these variants fall outside of protein-coding genes, in putative gene regulatory elements. This suggests that some fraction of causal human genetic variation acts through gene regulation. New developments in the field of regulatory genomics offer resources and methods to understand how genetic variants that alter gene expression contribute to human psychology and risk for psychiatric disease.
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Affiliation(s)
- Brian B Boutwell
- Criminology and Criminal Justice, Saint Louis University, 3550 Lindell Blvd., St. Louis, MO 63013, United States.
| | - Michael A White
- Department of Genetics and Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Couch Biomedical Research Building, St. Louis, MO 63110, United States
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340
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Wu Y, Bi R, Zeng C, Ma C, Sun C, Li J, Xiao X, Li M, Zhang DF, Zheng P, Sheng N, Luo XJ, Yao YG. Identification of the primate-specific gene BTN3A2 as an additional schizophrenia risk gene in the MHC loci. EBioMedicine 2019; 44:530-541. [PMID: 31133542 PMCID: PMC6603853 DOI: 10.1016/j.ebiom.2019.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Schizophrenia is a complex mental disorder resulting in poor life quality and high social and economic burden. Despite the fact that genome-wide association studies (GWASs) have successfully identified a number of risk loci for schizophrenia, identifying the causal genes at the risk loci and elucidating their roles in disease pathogenesis remain major challenges. METHODS The summary data-based Mendelian randomization analysis (SMR) was used to integrate a large-scale GWAS of schizophrenia with brain expression quantitative trait loci (eQTL) data and brain methylation expression quantitative trait loci (meQTL) data, to identify novel risk gene(s) for schizophrenia. We then analyzed the mRNA expression and methylation statuses of the gene hit BTN3A2 during the early brain development. Electrophysiological analyses of CA1 pyramidal neurons were performed to evaluate the excitatory and inhibitory synaptic activity after overexpression of BTN3A2 in rat hippocampal slices. Cell surface binding assay was used to test the interaction of BTN3A2 and neurexins. FINDINGS We identified BTN3A2 as a potential risk gene for schizophrenia. The mRNA expression and methylation data showed that BTN3A2 expression in human brain is highest post-natally. Further electrophysiological analyses of rat hippocampal slices showed that BTN3A2 overexpression specifically suppressed the excitatory synaptic activity onto CA1 pyramidal neurons, most likely through its interaction with the presynaptic adhesion molecule neurexins. INTERPRETATION Increased expression of BTN3A2 might confer risk for schizophrenia by altering excitatory synaptic function. Our result constitutes a paradigm for distilling risk gene using an integrative analysis and functional characterization in the post-GWAS era. FUND: This study was supported by the Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB02020003 to Y-GY), the National Natural Science Foundation of China (31730037 to Y-GY), and the Bureau of Frontier Sciences and Education, Chinese Academy of Sciences (QYZDJ-SSW-SMC005 to Y-GY).
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Affiliation(s)
- Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Chunhua Zeng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Changguo Ma
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Chunli Sun
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jingzheng Li
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Ping Zheng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Nengyin Sheng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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Zhou J, Jiang X, He S, Jiang H, Feng F, Liu W, Qu W, Sun H. Rational Design of Multitarget-Directed Ligands: Strategies and Emerging Paradigms. J Med Chem 2019; 62:8881-8914. [PMID: 31082225 DOI: 10.1021/acs.jmedchem.9b00017] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to the complexity of multifactorial diseases, single-target drugs do not always exhibit satisfactory efficacy. Recently, increasing evidence indicates that simultaneous modulation of multiple targets may improve both therapeutic safety and efficacy, compared with single-target drugs. However, few multitarget drugs are on market or in clinical trials, despite the best efforts of medicinal chemists. This article discusses the systematic establishment of target combination, lead generation, and optimization of multitarget-directed ligands (MTDLs). Moreover, we analyze some MTDLs research cases for several complex diseases in recent years and the physicochemical properties of 117 clinical multitarget drugs, with the aim to reveal the trends and insights of the potential use of MTDLs.
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Affiliation(s)
- Junting Zhou
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Xueyang Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Siyu He
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
| | - Hongli Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China.,Jiangsu Food and Pharmaceutical Science College , Huaian 223003 , People's Republic of China
| | - Wenyuan Liu
- Department of Analytical Chemistry , China Pharmaceutical University , Nanjing 210009 , People's Republic of China
| | - Wei Qu
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Haopeng Sun
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
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342
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Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability. NPJ PARKINSONS DISEASE 2019; 5:6. [PMID: 31016231 PMCID: PMC6470136 DOI: 10.1038/s41531-019-0076-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/28/2019] [Indexed: 01/04/2023]
Abstract
Parkinson’s disease (PD), with its characteristic loss of nigrostriatal dopaminergic neurons and deposition of α-synuclein in neurons, is often considered a neuronal disorder. However, in recent years substantial evidence has emerged to implicate glial cell types, such as astrocytes and microglia. In this study, we used stratified LD score regression and expression-weighted cell-type enrichment together with several brain-related and cell-type-specific genomic annotations to connect human genomic PD findings to specific brain cell types. We found that PD heritability attributable to common variation does not enrich in global and regional brain annotations or brain-related cell-type-specific annotations. Likewise, we found no enrichment of PD susceptibility genes in brain-related cell types. In contrast, we demonstrated a significant enrichment of PD heritability in a curated lysosomal gene set highly expressed in astrocytic, microglial, and oligodendrocyte subtypes, and in LoF-intolerant genes, which were found highly expressed in almost all tested cellular subtypes. Our results suggest that PD risk loci do not lie in specific cell types or individual brain regions, but rather in global cellular processes detectable across several cell types.
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343
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McIntosh AM, Sullivan PF, Lewis CM. Uncovering the Genetic Architecture of Major Depression. Neuron 2019; 102:91-103. [PMID: 30946830 PMCID: PMC6482287 DOI: 10.1016/j.neuron.2019.03.022] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 12/21/2022]
Abstract
There have been several recent studies addressing the genetic architecture of depression. This review serves to take stock of what is known now about the genetics of depression, how it has increased our knowledge and understanding of its mechanisms, and how the information and knowledge can be leveraged to improve the care of people affected. We identify four priorities for how the field of MD genetics research may move forward in future years, namely by increasing the sample sizes available for genome-wide association studies (GWASs), greater inclusion of diverse ancestries and low-income countries, the closer integration of psychiatric genetics with electronic medical records, and the development of the neuroscience toolkit for polygenic disorders.
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Affiliation(s)
- Andrew M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK; Department of Medical and Molecular Genetics, King's College London, London UK
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344
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Ori APS, Bot MHM, Molenhuis RT, Olde Loohuis LM, Ophoff RA. A Longitudinal Model of Human Neuronal Differentiation for Functional Investigation of Schizophrenia Polygenic Risk. Biol Psychiatry 2019; 85:544-553. [PMID: 30340753 PMCID: PMC6401362 DOI: 10.1016/j.biopsych.2018.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/18/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Common psychiatric disorders are characterized by complex disease architectures with many small genetic effects that contribute and complicate biological understanding of their etiology. There is therefore a pressing need for in vitro experimental systems that allow for interrogation of polygenic psychiatric disease risk to study the underlying biological mechanisms. METHODS We have developed an analytical framework that integrates genome-wide disease risk from genome-wide association studies with longitudinal in vitro gene expression profiles of human neuronal differentiation. RESULTS We demonstrate that the cumulative impact of risk loci of specific psychiatric disorders is significantly associated with genes that are differentially expressed and upregulated during differentiation. We find the strongest evidence for schizophrenia, a finding that we replicate in an independent dataset. A longitudinal gene cluster involved in synaptic function primarily drives the association with schizophrenia risk. CONCLUSIONS These findings reveal that in vitro human neuronal differentiation can be used to translate the polygenic architecture of schizophrenia to biologically relevant pathways that can be modeled in an experimental system. Overall, this work emphasizes the use of longitudinal in vitro transcriptomic signatures as a cellular readout and the application to the genetics of complex traits.
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Affiliation(s)
- Anil P S Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Merel H M Bot
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Remco T Molenhuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
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345
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Brennand KJ. Leveraging Human Induced Pluripotent Stem Cell-Based Models Provides Biological Context to Genome-wide Association Study Findings. Biol Psychiatry 2019; 85:532-533. [PMID: 30871689 DOI: 10.1016/j.biopsych.2019.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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346
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Sullivan PF, Geschwind DH. Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders. Cell 2019; 177:162-183. [PMID: 30901538 PMCID: PMC6432948 DOI: 10.1016/j.cell.2019.01.015] [Citation(s) in RCA: 248] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 01/01/2023]
Abstract
Studies of the genetics of psychiatric disorders have become one of the most exciting and fast-moving areas in human genetics. A decade ago, there were few reproducible findings, and now there are hundreds. In this review, we focus on the findings that have illuminated the genetic architecture of psychiatric disorders and the challenges of using these findings to inform our understanding of pathophysiology. The evidence is now overwhelming that psychiatric disorders are "polygenic"-that many genetic loci contribute to risk. With the exception of a subset of those with ASD, few individuals with a psychiatric disorder have a single, deterministic genetic cause; rather, developing a psychiatric disorder is influenced by hundreds of different genetic variants, consistent with a polygenic model. As progressively larger studies have uncovered more about their genetic architecture, the need to elucidate additional architectures has become clear. Even if we were to have complete knowledge of the genetic architecture of a psychiatric disorder, full understanding requires deep knowledge of the functional genomic architecture-the implicated loci impact regulatory processes that influence gene expression and the functional coordination of genes that control biological processes. Following from this is cellular architecture: of all brain regions, cell types, and developmental stages, where and when are the functional architectures operative? Given that the genetic architectures of different psychiatric disorders often strongly overlap, we are challenged to re-evaluate and refine the diagnostic architectures of psychiatric disorders using fundamental genetic and neurobiological data.
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Affiliation(s)
- Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA.
| | - Daniel H Geschwind
- Departments of Neurology, Psychiatry, and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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347
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Xia H, Jahr FM, Kim NK, Xie L, Shabalin AA, Bryois J, Sweet DH, Kronfol MM, Palasuberniam P, McRae M, Riley BP, Sullivan PF, van den Oord EJ, McClay JL. Building a schizophrenia genetic network: transcription factor 4 regulates genes involved in neuronal development and schizophrenia risk. Hum Mol Genet 2019; 27:3246-3256. [PMID: 29905862 DOI: 10.1093/hmg/ddy222] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/04/2018] [Indexed: 01/05/2023] Open
Abstract
The transcription factor 4 (TCF4) locus is a robust association finding with schizophrenia (SCZ), but little is known about the genes regulated by the encoded transcription factor. Therefore, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) of TCF4 in neural-derived (SH-SY5Y) cells to identify genome-wide TCF4 binding sites, followed by data integration with SCZ association findings. We identified 11 322 TCF4 binding sites overlapping in two ChIP-seq experiments. These sites are significantly enriched for the TCF4 Ebox binding motif (>85% having ≥1 Ebox) and implicate a gene set enriched for genes downregulated in TCF4 small-interfering RNA (siRNA) knockdown experiments, indicating the validity of our findings. The TCF4 gene set was also enriched among (1) gene ontology categories such as axon/neuronal development, (2) genes preferentially expressed in brain, in particular pyramidal neurons of the somatosensory cortex and (3) genes downregulated in postmortem brain tissue from SCZ patients (odds ratio, OR = 2.8, permutation P < 4x10-5). Considering genomic alignments, TCF4 binding sites significantly overlapped those for neural DNA-binding proteins such as FOXP2 and the SCZ-associated EP300. TCF4 binding sites were modestly enriched among SCZ risk loci from the Psychiatric Genomic Consortium (OR = 1.56, P = 0.03). In total, 130 TCF4 binding sites occurred in 39 of the 108 regions published in 2014. Thirteen genes within the 108 loci had both a TCF4 binding site ±10kb and were differentially expressed in siRNA knockdown experiments of TCF4, suggesting direct TCF4 regulation. These findings confirm TCF4 as an important regulator of neural genes and point toward functional interactions with potential relevance for SCZ.
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Affiliation(s)
- Hanzhang Xia
- Center for Biomarker Research and Precision Medicine
| | - Fay M Jahr
- Department of Pharmacotherapy and Outcomes Science
| | - Nak-Kyeong Kim
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Linying Xie
- Center for Biomarker Research and Precision Medicine
| | - Andrey A Shabalin
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Douglas H Sweet
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA, USA
| | | | | | | | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.,Departments of Genetics and Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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Ayhan F, Konopka G. Regulatory genes and pathways disrupted in autism spectrum disorders. Prog Neuropsychopharmacol Biol Psychiatry 2019; 89:57-64. [PMID: 30165121 PMCID: PMC6249101 DOI: 10.1016/j.pnpbp.2018.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/01/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a highly prevalent and complex genetic disorder. The complex genetic make-up of ASD has been extensively studied and both common and rare genetic variants in up to 1000 genes have been linked to increased ASD risk. While these studies highlight the genetic complexity and begin to provide a window for delineating pathways at risk in ASD, the pathogenicity and specific contribution of many mutations to the disorder are poorly understood. Defining the convergent pathways disrupted by this large number of ASD-associated genetic variants will help to understand disease pathogenesis and direct future therapeutic efforts for the groups of patients with distinct etiologies. Here, we review some of the common regulatory pathways including chromatin remodeling, transcription, and alternative splicing that have emerged as common features from genetic and transcriptomic profiling of ASD. For each category, we focus on one gene (CHD8, FOXP1, and RBFOX1) that is significantly linked to ASD and functionally characterized in recent years. Finally, we discuss genetic and transcriptomic overlap between ASD and other neurodevelopmental disorders.
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Affiliation(s)
- Fatma Ayhan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas 75390-9111, USA.
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349
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Schulmann A, Ryu E, Goncalves V, Rollins B, Christiansen M, Frye MA, Biernacka J, Vawter MP. Novel Complex Interactions between Mitochondrial and Nuclear DNA in Schizophrenia and Bipolar Disorder. MOLECULAR NEUROPSYCHIATRY 2019; 5:13-27. [PMID: 31019915 PMCID: PMC6465701 DOI: 10.1159/000495658] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022]
Abstract
Mitochondrial dysfunction has been associated with schizophrenia (SZ) and bipolar disorder (BD). This review examines recent publications and novel associations between mitochondrial genes and SZ and BD. Associations of nuclear-encoded mitochondrial variants with SZ were found using gene- and pathway-based approaches. Two control region mitochondrial DNA (mtDNA) SNPs, T16519C and T195C, both showed an association with SZ and BD. A review of 4 studies of A15218G located in the cytochrome B oxidase gene (CYTB, SZ = 11,311, control = 35,735) shows a moderate association with SZ (p = 2.15E-03). Another mtDNA allele A12308G was nominally associated with psychosis in BD type I subjects and SZ. The first published study testing the epistatic interaction between nuclear-encoded and mitochondria-encoded genes demonstrated evidence for potential interactions between mtDNA and the nuclear genome for BD. A similar analysis for the risk of SZ revealed significant joint effects (34 nuclear-mitochondria SNP pairs with joint effect p ≤ 5E-07) and significant enrichment of projection neurons. The mitochondria-encoded gene CYTB was found in both the epistatic interactions for SZ and BD and the single SNP association of SZ. Future efforts considering population stratification and polygenic risk scores will test the role of mitochondrial variants in psychiatric disorders.
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Affiliation(s)
- Anton Schulmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Vanessa Goncalves
- Molecular Brain Science Department, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Brandi Rollins
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, California, USA
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joanna Biernacka
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marquis P. Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, California, USA
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350
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Howard DM, Adams MJ, Clarke TK, Hafferty JD, Gibson J, Shirali M, Coleman JRI, Hagenaars SP, Ward J, Wigmore EM, Alloza C, Shen X, Barbu MC, Xu EY, Whalley HC, Marioni RE, Porteous DJ, Davies G, Deary IJ, Hemani G, Berger K, Teismann H, Rawal R, Arolt V, Baune BT, Dannlowski U, Domschke K, Tian C, Hinds DA, Trzaskowski M, Byrne EM, Ripke S, Smith DJ, Sullivan PF, Wray NR, Breen G, Lewis CM, McIntosh AM. Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions. Nat Neurosci 2019; 22:343-352. [PMID: 30718901 PMCID: PMC6522363 DOI: 10.1038/s41593-018-0326-7] [Citation(s) in RCA: 1304] [Impact Index Per Article: 260.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022]
Abstract
Major depression is a debilitating psychiatric illness that is typically associated with low mood and anhedonia. Depression has a heritable component that has remained difficult to elucidate with current sample sizes due to the polygenic nature of the disorder. To maximize sample size, we meta-analyzed data on 807,553 individuals (246,363 cases and 561,190 controls) from the three largest genome-wide association studies of depression. We identified 102 independent variants, 269 genes, and 15 genesets associated with depression, including both genes and gene pathways associated with synaptic structure and neurotransmission. An enrichment analysis provided further evidence of the importance of prefrontal brain regions. In an independent replication sample of 1,306,354 individuals (414,055 cases and 892,299 controls), 87 of the 102 associated variants were significant after multiple testing correction. These findings advance our understanding of the complex genetic architecture of depression and provide several future avenues for understanding etiology and developing new treatment approaches.
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Affiliation(s)
- David M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Jonathan D Hafferty
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Jude Gibson
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Masoud Shirali
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Jonathan R I Coleman
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - Saskia P Hagenaars
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - Joey Ward
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Eleanor M Wigmore
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Clara Alloza
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Eileen Y Xu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Gibran Hemani
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health, Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Klaus Berger
- Institute of Epidemiology & Social Medicine, University of Münster, Münster, Germany
| | - Henning Teismann
- Institute of Epidemiology & Social Medicine, University of Münster, Münster, Germany
| | - Rajesh Rawal
- Institute of Epidemiology & Social Medicine, University of Münster, Münster, Germany
| | - Volker Arolt
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Bernhard T Baune
- Department of Psychiatry, University of Melbourne, Victoria, Australia
| | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Chao Tian
- 23andMe, Inc, Mountain View, CA, USA
| | | | - Maciej Trzaskowski
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Stephan Ripke
- Department of Psychiatry, Charite Universitatsmedizin Berlin Campus Benjamin Franklin, Berlin, Germany
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel J Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Gerome Breen
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - Cathryn M Lewis
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
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