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Banasik K, Møller PL, Techlo TR, Holm PC, Walters GB, Ingason A, Rosengren A, Rohde PD, Kogelman LJA, Westergaard D, Siggaard T, Chmura PJ, Chalmer MA, Magnússon ÓÞ, Þórisson GÁ, Stefánsson H, Guðbjartsson DF, Stefánsson K, Olesen J, Winther S, Bøttcher M, Brunak S, Werge T, Nyegaard M, Hansen TF. DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals. BMC Genom Data 2023; 24:30. [PMID: 37244984 DOI: 10.1186/s12863-023-01132-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 05/18/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega. DATASET EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation. DATA DESCRIPTION Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.
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Affiliation(s)
- Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark.
| | - Peter L Møller
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, DK-8000, Aarhus C, Denmark
| | - Tanya R Techlo
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Valdemar Hansensvej 1-13, DK-2600, Glostrup, Denmark
| | - Peter C Holm
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | | | - Andrés Ingason
- Institute for Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Boeserup vej 2, DK-4000, Roskilde, Denmark
| | - Anders Rosengren
- Institute for Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Boeserup vej 2, DK-4000, Roskilde, Denmark
| | - Palle D Rohde
- Department of Health Science and Technology, Genomic Medicine Group, Aalborg University, Selma Lagerløfs Vej 249, DK-9260, Gistrup, Denmark
| | - Lisette J A Kogelman
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Valdemar Hansensvej 1-13, DK-2600, Glostrup, Denmark
| | - David Westergaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Troels Siggaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Piotr J Chmura
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Mona A Chalmer
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Valdemar Hansensvej 1-13, DK-2600, Glostrup, Denmark
| | | | | | | | | | | | - Jes Olesen
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Valdemar Hansensvej 1-13, DK-2600, Glostrup, Denmark
| | - Simon Winther
- Department of Cardiology, University Clinic for Cardiovascular Research, Gødstrup Hospital, Hospitalsvej 15, DK-7400, Herning, Denmark
| | - Morten Bøttcher
- Department of Cardiology, University Clinic for Cardiovascular Research, Gødstrup Hospital, Hospitalsvej 15, DK-7400, Herning, Denmark
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Thomas Werge
- Institute for Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Boeserup vej 2, DK-4000, Roskilde, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, DK-8000, Aarhus C, Denmark
- Department of Health Science and Technology, Genomic Medicine Group, Aalborg University, Selma Lagerløfs Vej 249, DK-9260, Gistrup, Denmark
| | - Thomas F Hansen
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
- Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Valdemar Hansensvej 1-13, DK-2600, Glostrup, Denmark
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Kim H, Kim D, Cho Y, Kim K, Roh JD, Kim Y, Yang E, Kim SS, Ahn S, Kim H, Kang H, Bae Y, Kim E. Early postnatal serotonin modulation prevents adult-stage deficits in Arid1b-deficient mice through synaptic transcriptional reprogramming. Nat Commun 2022; 13:5051. [PMID: 36030255 PMCID: PMC9420115 DOI: 10.1038/s41467-022-32748-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Autism spectrum disorder is characterized by early postnatal symptoms, although little is known about the mechanistic deviations that produce them and whether correcting them has long-lasting preventive effects on adult-stage deficits. ARID1B, a chromatin remodeler implicated in neurodevelopmental disorders, including autism spectrum disorder, exhibits strong embryonic- and early postnatal-stage expression. We report here that Arid1b-happloinsufficient (Arid1b+/-) mice display autistic-like behaviors at juvenile and adult stages accompanied by persistent decreases in excitatory synaptic density and transmission. Chronic treatment of Arid1b+/- mice with fluoxetine, a selective serotonin-reuptake inhibitor, during the first three postnatal weeks prevents synaptic and behavioral deficits in adults. Mechanistically, these rescues accompany transcriptomic changes, including upregulation of FMRP targets and normalization of HDAC4/MEF2A-related transcriptional regulation of the synaptic proteins, SynGAP1 and Arc. These results suggest that chronic modulation of serotonergic receptors during critical early postnatal periods prevents synaptic and behavioral deficits in adult Arid1b+/- mice through transcriptional reprogramming.
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Affiliation(s)
- Hyosang Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Doyoun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Yisul Cho
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea
| | - Kyungdeok Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Junyeop Daniel Roh
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Yangsik Kim
- Graduate School of Biomedical Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Esther Yang
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Seong Soon Kim
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Korea
| | - Sunjoo Ahn
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Korea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Hyojin Kang
- Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Korea
| | - Yongchul Bae
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea.
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea.
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Liu B, Ou WC, Fang L, Tian CW, Xiong Y. Myocyte Enhancer Factor 2A Plays a Central Role in the Regulatory Networks of Cellular Physiopathology. Aging Dis 2022; 14:331-349. [PMID: 37008050 PMCID: PMC10017154 DOI: 10.14336/ad.2022.0825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Cell regulatory networks are the determinants of cellular homeostasis. Any alteration to these networks results in the disturbance of cellular homeostasis and induces cells towards different fates. Myocyte enhancer factor 2A (MEF2A) is one of four members of the MEF2 family of transcription factors (MEF2A-D). MEF2A is highly expressed in all tissues and is involved in many cell regulatory networks including growth, differentiation, survival and death. It is also necessary for heart development, myogenesis, neuronal development and differentiation. In addition, many other important functions of MEF2A have been reported. Recent studies have shown that MEF2A can regulate different, and sometimes even mutually exclusive cellular events. How MEF2A regulates opposing cellular life processes is an interesting topic and worthy of further exploration. Here, we reviewed almost all MEF2A research papers published in English and summarized them into three main sections: 1) the association of genetic variants in MEF2A with cardiovascular disease, 2) the physiopathological functions of MEF2A, and 3) the regulation of MEF2A activity and its regulatory targets. In summary, multiple regulatory patterns for MEF2A activity and a variety of co-factors cause its transcriptional activity to switch to different target genes, thereby regulating opposing cell life processes. The association of MEF2A with numerous signaling molecules establishes a central role for MEF2A in the regulatory network of cellular physiopathology.
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Affiliation(s)
- Benrong Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
- Correspondence should be addressed to: Dr. Benrong Liu, the Second Affiliated Hospital, Guangzhou Medical University, Guangdong, China. E-mail: ; or Yujuan Xiong, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangdong, China. .
| | - Wen-Chao Ou
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Lei Fang
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Chao-Wei Tian
- General Practice, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Yujuan Xiong
- Department of Laboratory Medicine, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
- Correspondence should be addressed to: Dr. Benrong Liu, the Second Affiliated Hospital, Guangzhou Medical University, Guangdong, China. E-mail: ; or Yujuan Xiong, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangdong, China. .
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Calati R, Nemeroff CB, Lopez-Castroman J, Cohen LJ, Galynker I. Candidate Biomarkers of Suicide Crisis Syndrome: What to Test Next? A Concept Paper. Int J Neuropsychopharmacol 2019; 23:192-205. [PMID: 31781761 PMCID: PMC7171927 DOI: 10.1093/ijnp/pyz063] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND There has been increasing interest in both suicide-specific diagnoses within the psychiatric nomenclature and related biomarkers. Because the Suicide Crisis Syndrome-an emotional crescendo of several interrelated symptoms-seems to be promising for the identification of individuals at risk of suicide, the aim of the present paper is to review the putative biological underpinnings of the Suicide Crisis Syndrome symptoms (entrapment, affective disturbance, loss of cognitive control, hyperarousal, social withdrawal). METHODS A PubMed literature search was performed to identify studies reporting a link between each of the 5 Suicide Crisis Syndrome symptoms and biomarkers previously reported to be associated with suicidal outcomes. RESULTS Disturbances in the hypothalamic-pituitary-adrenal axis, with dysregulated corticotropin-releasing hormone and cortisol levels, may be linked to a sense of entrapment. Affective disturbance is likely mediated by alterations in dopaminergic circuits involved in reward and antireward systems as well as endogenous opioids. Loss of cognitive control is linked to altered neurocognitive function in the areas of executive function, attention, and decision-making. Hyperarousal is linked to autonomic dysregulation, which may be characterized by a reduction in both heart rate variability and electrodermal activity. Social withdrawal has been associated with oxytocin availability. There is also evidence that inflammatory processes may contribute to individual Suicide Crisis Syndrome symptoms. CONCLUSION The Suicide Crisis Syndrome is a complex syndrome that is likely the consequence of distinct changes in interconnected neural, neuroendocrine, and autonomic systems. Available clinical and research data allow for development of empirically testable hypotheses and experimental paradigms to scrutinize the biological substrates of the Suicide Crisis Syndrome.
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Affiliation(s)
- Raffaella Calati
- Department of Psychiatry, Mount Sinai Beth Israel, New York, New York,Icahn School of Medicine at Mount Sinai, New York, New York,Department of Psychology, University of Milan-Bicocca, Milan, Italy,Department of Adult Psychiatry, Nîmes University Hospital, Nîmes, France,Correspondence: Raffaella Calati, PsyD, PhD, Department of Psychology, University of Milan-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126, Milan, Italy ()
| | - Charles B Nemeroff
- Department of Psychiatry, University of Texas Dell Medical School, Austin, Texas
| | - Jorge Lopez-Castroman
- Department of Adult Psychiatry, Nîmes University Hospital, Nîmes, France,INSERM, University of Montpellier, Neuropsychiatry: Epidemiological and Clinical Research, Montpellier, France
| | - Lisa J Cohen
- Department of Psychiatry, Mount Sinai Beth Israel, New York, New York,Icahn School of Medicine at Mount Sinai, New York, New York
| | - Igor Galynker
- Department of Psychiatry, Mount Sinai Beth Israel, New York, New York,Icahn School of Medicine at Mount Sinai, New York, New York
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MEF-2 isoforms' (A-D) roles in development and tumorigenesis. Oncotarget 2019; 10:2755-2787. [PMID: 31105874 PMCID: PMC6505634 DOI: 10.18632/oncotarget.26763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/01/2019] [Indexed: 12/29/2022] Open
Abstract
Myocyte enhancer factor (MEF)-2 plays a critical role in proliferation, differentiation, and development of various cell types in a tissue specific manner. Four isoforms of MEF-2 (A-D) differentially participate in controlling the cell fate during the developmental phases of cardiac, muscle, vascular, immune and skeletal systems. Through their associations with various cellular factors MEF-2 isoforms can trigger alterations in complex protein networks and modulate various stages of cellular differentiation, proliferation, survival and apoptosis. The role of the MEF-2 family of transcription factors in the development has been investigated in various cell types, and the evolving alterations in this family of transcription factors have resulted in a diverse and wide spectrum of disease phenotypes, ranging from cancer to infection. This review provides a comprehensive account on MEF-2 isoforms (A-D) from their respective localization, signaling, role in development and tumorigenesis as well as their association with histone deacetylases (HDACs), which can be exploited for therapeutic intervention.
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Rediscovering the value of families for psychiatric genetics research. Mol Psychiatry 2019; 24:523-535. [PMID: 29955165 PMCID: PMC7028329 DOI: 10.1038/s41380-018-0073-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
As it is likely that both common and rare genetic variation are important for complex disease risk, studies that examine the full range of the allelic frequency distribution should be utilized to dissect the genetic influences on mental illness. The rate limiting factor for inferring an association between a variant and a phenotype is inevitably the total number of copies of the minor allele captured in the studied sample. For rare variation, with minor allele frequencies of 0.5% or less, very large samples of unrelated individuals are necessary to unambiguously associate a locus with an illness. Unfortunately, such large samples are often cost prohibitive. However, by using alternative analytic strategies and studying related individuals, particularly those from large multiplex families, it is possible to reduce the required sample size while maintaining statistical power. We contend that using whole genome sequence (WGS) in extended pedigrees provides a cost-effective strategy for psychiatric gene mapping that complements common variant approaches and WGS in unrelated individuals. This was our impetus for forming the "Pedigree-Based Whole Genome Sequencing of Affective and Psychotic Disorders" consortium. In this review, we provide a rationale for the use of WGS with pedigrees in modern psychiatric genetics research. We begin with a focused review of the current literature, followed by a short history of family-based research in psychiatry. Next, we describe several advantages of pedigrees for WGS research, including power estimates, methods for studying the environment, and endophenotypes. We conclude with a brief description of our consortium and its goals.
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Crawford B, Craig Z, Mansell G, White I, Smith A, Spaull S, Imm J, Hannon E, Wood A, Yaghootkar H, Ji Y, Mullins N, Lewis CM, Mill J, Murphy TM. DNA methylation and inflammation marker profiles associated with a history of depression. Hum Mol Genet 2018; 27:2840-2850. [PMID: 29790996 PMCID: PMC6680088 DOI: 10.1093/hmg/ddy199] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.
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Affiliation(s)
- Bethany Crawford
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Zoe Craig
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Isobel White
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Adam Smith
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Steve Spaull
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Jennifer Imm
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Andrew Wood
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Hanieh Yaghootkar
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Yingjie Ji
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | | | - Niamh Mullins
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Division of Genetics and Molecular Medicine, King’s College London, London SE1 9RT, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Therese M Murphy
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
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Hansen RD, Christensen AF, Olesen J. Family studies to find rare high risk variants in migraine. J Headache Pain 2017; 18:32. [PMID: 28255817 PMCID: PMC5334193 DOI: 10.1186/s10194-017-0729-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. METHOD PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific variants (less than five), while other studies found several possible variants. Not all of them were genome wide significant. Four studies performed follow-up analyses in unrelated cases and controls and calculated odds ratios that supported an association between detected variants and risk of disease. Studies of 11 diseases identified rare variants that segregated fully or to a large degree with the disease in the pedigrees. CONCLUSION It is possible to find rare high risk variants for common complex diseases through a family-based approach. One study using a family approach and NGS to find rare variants in migraine has already been published but with strong limitations. More studies are under way.
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Affiliation(s)
- Rikke Dyhr Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
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Roche E, Lyne J, O'Donoghue B, Segurado R, Behan C, Renwick L, Fanning F, Madigan K, Clarke M. The prognostic value of formal thought disorder following first episode psychosis. Schizophr Res 2016; 178:29-34. [PMID: 27639419 DOI: 10.1016/j.schres.2016.09.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/09/2016] [Accepted: 09/09/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Formal thought disorder (FTD) is associated with poor outcome in established psychotic illnesses and it can be assessed as a categorical or dimensional variable. However, its influence on functional outcome and hospitalisation patterns in early psychosis has not been investigated. We evaluated the relationship between FTD and these outcomes in a first episode psychosis (FEP) sample. MATERIALS AND METHODS A mixed diagnostic FEP cohort was recruited through an Early Intervention in Psychosis Service in Ireland. Participants were assessed at initial presentation and one year later with the MIRECC GAF to evaluate social and occupational functioning domains. Disorganisation (disFTD), verbosity (verFTD) and poverty (povFTD) dimensions of FTD were examined at both time points, as well as a unitary FTD construct. Analyses were controlled for demographic, clinical and treatment variables. RESULTS DisFTD was the only FTD dimension associated with functional outcome, specifically social functioning, on multivariate analysis (beta=0.13, P<0.05). The unitary FTD construct was not associated with functional outcome. DisFTD at FEP presentation predicted a greater number of hospitalisations (adjusted beta=0.24, P<0.001) and prolonged inpatient admission (adjusted OR=1.08, 95% CI 1.02-1.15, P<0.05) following FEP. CONCLUSIONS Longitudinal and dimensional evaluation of FTD has a clinical utility that is distinct from a cross-sectional or unitary assessment. Dimensions of FTD may map onto different domains of functioning. These findings are supportive of some of the changes in DSM-V with an emphasis on longitudinal and dimensional appraisal of psychopathology. Communication disorders may be considered a potential target for intervention in psychotic disorders.
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Affiliation(s)
- Eric Roche
- DETECT Early Intervention in Psychosis Service, Blackrock Business Park, Blackrock, Dublin, Ireland.
| | - John Lyne
- Royal College of Surgeons in Ireland and North Dublin Mental Health Services, Ashlin Centre, Beaumont Road, Dublin 9, Ireland
| | - Brian O'Donoghue
- Orygen, National Centre for Excellence in Youth Mental Health, Melbourne, Australia
| | - Ricardo Segurado
- Centre for Support and Training in Analysis and Research, University College Dublin, Ireland
| | - Caragh Behan
- DETECT Early Intervention in Psychosis Service, Blackrock Business Park, Blackrock, Dublin, Ireland
| | - Laoise Renwick
- School of Nursing, Midwifery and Social Work, University of Manchester, UK
| | - Felicity Fanning
- DETECT Early Intervention in Psychosis Service, Blackrock Business Park, Blackrock, Dublin, Ireland
| | - Kevin Madigan
- DETECT Early Intervention in Psychosis Service, Blackrock Business Park, Blackrock, Dublin, Ireland
| | - Mary Clarke
- DETECT Early Intervention in Psychosis Service, Blackrock Business Park, Blackrock, Dublin, Ireland
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Ayer A, Yalınçetin B, Aydınlı E, Sevilmiş Ş, Ulaş H, Binbay T, Akdede BB, Alptekin K. Formal thought disorder in first-episode psychosis. Compr Psychiatry 2016; 70:209-15. [PMID: 27565775 DOI: 10.1016/j.comppsych.2016.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 08/01/2016] [Accepted: 08/05/2016] [Indexed: 12/25/2022] Open
Abstract
Formal thought disorder (FTD) is one of the fundamental symptom clusters of schizophrenia and it was found to be the strongest predictor determining conversion from first-episode acute transient psychotic disorder to schizophrenia. Our goal in the present study was to compare a first-episode psychosis (FEP) sample to a healthy control group in relation to subtypes of FTD. Fifty six patients aged between 15 and 45years with FEP and forty five control subjects were included in the study. All the patients were under medication for less than six weeks or drug-naive. FTD was assessed using the Thought and Language Index (TLI), which is composed of impoverishment of thought and disorganization of thought subscales. FEP patients showed significantly higher scores on the items of poverty of speech, weakening of goal, perseveration, looseness, peculiar word use, peculiar sentence construction and peculiar logic compared to controls. Poverty of speech, perseveration and peculiar word use were the significant factors differentiating FEP patients from controls when controlling for years of education, family history of psychosis and drug abuse.
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Affiliation(s)
- Ahmet Ayer
- Manisa Psychiatric Hospital, Manisa, Turkey
| | - Berna Yalınçetin
- Department of Neuroscience, Dokuz Eylul University, Izmir, Turkey
| | - Esra Aydınlı
- Department of Neuroscience, Dokuz Eylul University, Izmir, Turkey
| | - Şilay Sevilmiş
- Department of Neuroscience, Dokuz Eylul University, Izmir, Turkey
| | - Halis Ulaş
- Department of Psychiatry, Medical School of Dokuz Eylul University, Izmir, Turkey
| | - Tolga Binbay
- Department of Psychiatry, Medical School of Dokuz Eylul University, Izmir, Turkey
| | - Berna Binnur Akdede
- Department of Neuroscience, Dokuz Eylul University, Izmir, Turkey; Department of Psychiatry, Medical School of Dokuz Eylul University, Izmir, Turkey
| | - Köksal Alptekin
- Department of Neuroscience, Dokuz Eylul University, Izmir, Turkey; Department of Psychiatry, Medical School of Dokuz Eylul University, Izmir, Turkey.
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Murphy E, Benítez-Burraco A. Bridging the Gap between Genes and Language Deficits in Schizophrenia: An Oscillopathic Approach. Front Hum Neurosci 2016; 10:422. [PMID: 27601987 PMCID: PMC4993770 DOI: 10.3389/fnhum.2016.00422] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 08/08/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia is characterized by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the etiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London London, UK
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