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Chung IH, Huang YS, Fang TH, Chen CH. Whole Genome Sequencing Revealed Inherited Rare Oligogenic Variants Contributing to Schizophrenia and Major Depressive Disorder in Two Families. Int J Mol Sci 2023; 24:11777. [PMID: 37511534 PMCID: PMC10380944 DOI: 10.3390/ijms241411777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Schizophrenia and affective disorder are two major complex mental disorders with high heritability. Evidence shows that rare variants with significant clinical impacts contribute to the genetic liability of these two disorders. Also, rare variants associated with schizophrenia and affective disorders are highly personalized; each patient may carry different variants. We used whole genome sequencing analysis to study the genetic basis of two families with schizophrenia and major depressive disorder. We did not detect de novo, autosomal dominant, or recessive pathogenic or likely pathogenic variants associated with psychiatric disorders in these two families. Nevertheless, we identified multiple rare inherited variants with unknown significance in the probands. In family 1, with singleton schizophrenia, we detected four rare variants in genes implicated in schizophrenia, including p.Arg1627Trp of LAMA2, p.Pro1338Ser of CSMD1, p.Arg691Gly of TLR4, and Arg182X of AGTR2. The p.Arg691Gly of TLR4 was inherited from the father, while the other three were inherited from the mother. In family 2, with two affected sisters diagnosed with major depressive disorder, we detected three rare variants shared by the two sisters in three genes implicated in affective disorders, including p.Ala4551Gly of FAT1, p.Val231Leu of HOMER3, and p.Ile185Met of GPM6B. These three rare variants were assumed to be inherited from their parents. Prompted by these findings, we suggest that these rare inherited variants may interact with each other and lead to psychiatric conditions in these two families. Our observations support the conclusion that inherited rare variants may contribute to the heritability of psychiatric disorders.
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Affiliation(s)
- I-Hang Chung
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
- Department of Psychiatry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Ting-Hsuan Fang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
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2
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Van der Auwera S, Peyrot WJ, Milaneschi Y, Hertel J, Baune B, Breen G, Byrne E, Dunn EC, Fisher H, Homuth G, Levinson D, Lewis C, Mills N, Mullins N, Nauck M, Pistis G, Preisig M, Rietschel M, Ripke S, Sullivan P, Teumer A, Völzke H, Boomsma DI, Wray NR, Penninx B, Grabe H. Genome-wide gene-environment interaction in depression: A systematic evaluation of candidate genes: The childhood trauma working-group of PGC-MDD. Am J Med Genet B Neuropsychiatr Genet 2018; 177:40-49. [PMID: 29159863 PMCID: PMC5726923 DOI: 10.1002/ajmg.b.32593] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/16/2022]
Abstract
Gene by environment (GxE) interaction studies have investigated the influence of a number of candidate genes and variants for major depressive disorder (MDD) on the association between childhood trauma and MDD. Most of these studies are hypothesis driven and investigate only a limited number of SNPs in relevant pathways using differing methodological approaches. Here (1) we identified 27 genes and 268 SNPs previously associated with MDD or with GxE interaction in MDD and (2) analyzed their impact on GxE in MDD using a common approach in 3944 subjects of European ancestry from the Psychiatric Genomics Consortium who had completed the Childhood Trauma Questionnaire. (3) We subsequently used the genome-wide SNP data for a genome-wide case-control GxE model and GxE case-only analyses testing for an enrichment of associated SNPs. No genome-wide significant hits and no consistency among the signals of the different analytic approaches could be observed. This is the largest study for systematic GxE interaction analysis in MDD in subjects of European ancestry to date. Most of the known candidate genes/variants could not be supported. Thus, their impact on GxE interaction in MDD may be questionable. Our results underscore the need for larger samples, more extensive assessment of environmental exposures, and greater efforts to investigate new methodological approaches in GxE models for MDD.
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Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Wouter J Peyrot
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ in Geest, Amsterdam, The Netherlands
| | - Yuri Milaneschi
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ in Geest, Amsterdam, The Netherlands
| | - Johannes Hertel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Bernhard Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, Australia
| | - Gerome Breen
- Institute of Psychiatry, Psychology and Neuroscience, MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, Great Britain
- NIHR BRC for Mental Health, King's College London, London, Great Britain
| | - Enda Byrne
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Erin C Dunn
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, Massachusetts
| | - Helen Fisher
- Institute of Psychiatry, Psychology and Neuroscience, MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, Great Britain
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Douglas Levinson
- Psychiatry and Behavioral Sciences, Stanford University, Stanford, California
| | - Cathryn Lewis
- Institute of Psychiatry, Psychology and Neuroscience, MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, Great Britain
- Department of Medical and& Molecular Genetics, King's College London, London, Great Britain
| | - Natalie Mills
- Discipline of Psychiatry, University of Adelaide, Adelaide, Australia
| | - Niamh Mullins
- Institute of Psychiatry, Psychology and Neuroscience, MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, Great Britain
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Giorgio Pistis
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Martin Preisig
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Stephan Ripke
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Psychiatry and Psychotherapy, University medicine Berlin Campus Charité Mitte, Berlin, Germany
| | - Patrick Sullivan
- Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Dorret I Boomsma
- Department of Biological Psychology & EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brenda Penninx
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ in Geest, Amsterdam, The Netherlands
| | - Hans Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
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Configuring a robust nervous system with Fat cadherins. Semin Cell Dev Biol 2017; 69:91-101. [PMID: 28603077 DOI: 10.1016/j.semcdb.2017.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/26/2017] [Accepted: 06/07/2017] [Indexed: 01/14/2023]
Abstract
Atypical Fat cadherins represent a small but versatile group of signaling molecules that influence proliferation and tissue polarity. With huge extracellular domains and intracellular domains harboring many independent protein interaction sites, Fat cadherins are poised to translate local cell adhesion events into a variety of cell behaviors. The need for such global coordination is particularly prominent in the nervous system, where millions of morphologically diverse neurons are organized into functional networks. As we learn more about their biological functions and molecular properties, increasing evidence suggests that Fat cadherins mediate contact-induced changes that ultimately impose a structure to developing neuronal circuits.
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Schraut KG, Jakob SB, Weidner MT, Schmitt AG, Scholz CJ, Strekalova T, El Hajj N, Eijssen LMT, Domschke K, Reif A, Haaf T, Ortega G, Steinbusch HWM, Lesch KP, Van den Hove DL. Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice. Transl Psychiatry 2014; 4:e473. [PMID: 25335169 PMCID: PMC4350514 DOI: 10.1038/tp.2014.107] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
The serotonin transporter gene (5-HTT/SLC6A4)-linked polymorphic region has been suggested to have a modulatory role in mediating effects of early-life stress exposure on psychopathology rendering carriers of the low-expression short (s)-variant more vulnerable to environmental adversity in later life. The underlying molecular mechanisms of this gene-by-environment interaction are not well understood, but epigenetic regulation including differential DNA methylation has been postulated to have a critical role. Recently, we used a maternal restraint stress paradigm of prenatal stress (PS) in 5-HTT-deficient mice and showed that the effects on behavior and gene expression were particularly marked in the hippocampus of female 5-Htt+/- offspring. Here, we examined to which extent these effects are mediated by differential methylation of DNA. For this purpose, we performed a genome-wide hippocampal DNA methylation screening using methylated-DNA immunoprecipitation (MeDIP) on Affymetrix GeneChip Mouse Promoter 1.0 R arrays. Using hippocampal DNA from the same mice as assessed before enabled us to correlate gene-specific DNA methylation, mRNA expression and behavior. We found that 5-Htt genotype, PS and their interaction differentially affected the DNA methylation signature of numerous genes, a subset of which showed overlap with the expression profiles of the corresponding transcripts. For example, a differentially methylated region in the gene encoding myelin basic protein (Mbp) was associated with its expression in a 5-Htt-, PS- and 5-Htt × PS-dependent manner. Subsequent fine-mapping of this Mbp locus linked the methylation status of two specific CpG sites to Mbp expression and anxiety-related behavior. In conclusion, hippocampal DNA methylation patterns and expression profiles of female prenatally stressed 5-Htt+/- mice suggest that distinct molecular mechanisms, some of which are promoter methylation-dependent, contribute to the behavioral effects of the 5-Htt genotype, PS exposure and their interaction.
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Affiliation(s)
- K G Schraut
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany
| | - S B Jakob
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany
| | - M T Weidner
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - A G Schmitt
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Wuerzburg, Wuerzburg, Germany
| | - C J Scholz
- Laboratory for Microarray Applications, Interdisciplinary Center for Clinical Research, University of Wuerzburg, Wuerzburg, Germany
| | - T Strekalova
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands,Institute for Hygiene and Tropical Medicine, New University of Lisbon, Lisbon, Portugal
| | - N El Hajj
- Institute of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - L M T Eijssen
- Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - K Domschke
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Wuerzburg, Wuerzburg, Germany
| | - A Reif
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Wuerzburg, Wuerzburg, Germany
| | - T Haaf
- Institute of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
| | - G Ortega
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany
| | - H W M Steinbusch
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - K P Lesch
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands,Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Department of Psychiatry, University of Wuerzburg, 97080 Wuerzburg, Germany. E-mail:
| | - D L Van den Hove
- Division of Molecular Psychiatry, Laboratory of Translational Neuroscience, Center of Mental Health, Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
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Sundararajan L, Norris ML, Schöneich S, Ackley BD, Lundquist EA. The fat-like cadherin CDH-4 acts cell-non-autonomously in anterior-posterior neuroblast migration. Dev Biol 2014; 392:141-52. [PMID: 24954154 DOI: 10.1016/j.ydbio.2014.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/04/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
Directed migration of neurons is critical in the normal and pathological development of the brain and central nervous system. In Caenorhabditis elegans, the bilateral Q neuroblasts, QR on the right and QL on the left, migrate anteriorly and posteriorly, respectively. Initial protrusion and migration of the Q neuroblasts is autonomously controlled by the transmembrane proteins UNC-40/DCC, PTP-3/LAR, and MIG-21. As QL migrates posteriorly, it encounters and EGL-20/Wnt signal that induces MAB-5/Hox expression that drives QL descendant posterior migration. QR migrates anteriorly away from EGL-20/Wnt and does not activate MAB-5/Hox, resulting in anterior QR descendant migration. A forward genetic screen for new mutations affecting initial Q migrations identified alleles of cdh-4, which caused defects in both QL and QR directional migration similar to unc-40, ptp-3, and mig-21. Previous studies showed that in QL, PTP-3/LAR and MIG-21 act in a pathway in parallel to UNC-40/DCC to drive posterior QL migration. Here we show genetic evidence that CDH-4 acts in the PTP-3/MIG-21 pathway in parallel to UNC-40/DCC to direct posterior QL migration. In QR, the PTP-3/MIG-21 and UNC-40/DCC pathways mutually inhibit each other, allowing anterior QR migration. We report here that CDH-4 acts in both the PTP-3/MIG-21 and UNC-40/DCC pathways in mutual inhibition in QR, and that CDH-4 acts cell-non-autonomously. Interaction of CDH-4 with UNC-40/DCC in QR but not QL represents an inherent left-right asymmetry in the Q cells, the nature of which is not understood. We conclude that CDH-4 might act as a permissive signal for each Q neuroblast to respond differently to anterior-posterior guidance information based upon inherent left-right asymmetries in the Q neuroblasts.
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Affiliation(s)
- Lakshmi Sundararajan
- Programs in Genetics and Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States
| | - Megan L Norris
- Programs in Genetics and Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States
| | - Sebastian Schöneich
- Programs in Genetics and Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States
| | - Brian D Ackley
- Programs in Genetics and Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States
| | - Erik A Lundquist
- Programs in Genetics and Molecular, Cellular, and Developmental Biology, Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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