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Großmann NL, Weihs A, Kühn L, Sauer S, Röh S, Wiechmann T, Rex-Haffner M, Völzke H, Völker U, Binder EB, Teumer A, Homuth G, Klinger-König J, Grabe HJ. Methylation Patterns of the FKBP5 Gene in Association with Childhood Maltreatment and Depressive Disorders. Int J Mol Sci 2024; 25:1485. [PMID: 38338761 PMCID: PMC10855893 DOI: 10.3390/ijms25031485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Childhood maltreatment is an important risk factor for adult depression and has been associated with changes in the hypothalamic pituitary adrenal (HPA) axis, including cortisol secretion and methylation of the FKBP5 gene. Furthermore, associations between depression and HPA changes have been reported. This study investigated the associations of whole-blood FKBP5 mRNA levels, serum cortisol levels, childhood maltreatment, and depressive symptoms with the whole-blood methylation status (assessed via target bisulfite sequencing) of 105 CpGs at the FKBP5 locus using data from the general population-based Study of Health in Pomerania (SHIP) (N = 203). Both direct and interaction effects with the rs1360780 single-nucleotide polymorphism were investigated. Nominally significant associations of main effects on methylation of a single CpG site were observed at intron 3, intron 7, and the 3'-end of the gene. Additionally, methylation at two clusters at the 3'-end and intron 7 were nominally associated with childhood maltreatment × rs1360780 and depressive symptoms × rs1360780, respectively. The results add to the understanding of molecular mechanisms underlying the emergence of depression and could aid the development of personalised depression therapy and drug development.
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Affiliation(s)
- Nora L Großmann
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489 Greifswald, Germany
| | - Luise Kühn
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Susann Sauer
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Simone Röh
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tobias Wiechmann
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Monika Rex-Haffner
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexander Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Johanna Klinger-König
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489 Greifswald, Germany
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2
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Penner-Goeke S, Bothe M, Rek N, Kreitmaier P, Pöhlchen D, Kühnel A, Glaser LV, Kaya E, Krontira AC, Röh S, Czamara D, Ködel M, Monteserin-Garcia J, Diener L, Wölfel B, Sauer S, Rummel C, Riesenberg S, Arloth-Knauer J, Ziller M, Labeur M, Meijsing S, Binder EB. High-throughput screening of glucocorticoid-induced enhancer activity reveals mechanisms of stress-related psychiatric disorders. Proc Natl Acad Sci U S A 2023; 120:e2305773120. [PMID: 38011552 DOI: 10.1073/pnas.2305773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/01/2023] [Indexed: 11/29/2023] Open
Abstract
Exposure to stressful life events increases the risk for psychiatric disorders. Mechanistic insight into the genetic factors moderating the impact of stress can increase our understanding of disease processes. Here, we test 3,662 single nucleotide polymorphisms (SNPs) from preselected expression quantitative trait loci in massively parallel reporter assays to identify genetic variants that modulate the activity of regulatory elements sensitive to glucocorticoids, important mediators of the stress response. Of the tested SNP sequences, 547 were located in glucocorticoid-responsive regulatory elements of which 233 showed allele-dependent activity. Transcripts regulated by these functional variants were enriched for those differentially expressed in psychiatric disorders in the postmortem brain. Phenome-wide Mendelian randomization analysis in 4,439 phenotypes revealed potentially causal associations specifically in neurobehavioral traits, including major depression and other psychiatric disorders. Finally, a functional gene score derived from these variants was significantly associated with differences in the physiological stress response, suggesting that these variants may alter disease risk by moderating the individual set point of the stress response.
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Affiliation(s)
- Signe Penner-Goeke
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Melissa Bothe
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Nils Rek
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Peter Kreitmaier
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg 85764, Germany
| | - Dorothee Pöhlchen
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Anne Kühnel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura V Glaser
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Ezgi Kaya
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Anthi C Krontira
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jose Monteserin-Garcia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura Diener
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Wölfel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Christine Rummel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Stephan Riesenberg
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janine Arloth-Knauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Michael Ziller
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Department of Psychiatry, University of Muenster, Muenster 48149, Germany
| | - Marta Labeur
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Sebastiaan Meijsing
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
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Yusupov N, van Doeselaar L, Röh S, Wiechmann T, Ködel M, Sauer S, Rex-Haffner M, Schmidt MV, Binder EB. Extensive evaluation of DNA methylation of functional elements in the murine Fkbp5 locus using high-accuracy DNA methylation measurement via targeted bisulfite sequencing. Eur J Neurosci 2023; 58:2662-2676. [PMID: 37414581 DOI: 10.1111/ejn.16078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023]
Abstract
FKBP5 is an important stress-regulatory gene implicated in stress-related psychiatric diseases. Single nucleotide polymorphisms of the FKBP5 gene were shown to interact with early life stress to alter the glucocorticoid-related stress response and moderate disease risk. Demethylation of cytosine-phosphate-guanine-dinucleotides (CpGs) in regulatory glucocorticoid-responsive elements was suggested to be the mediating epigenetic mechanism for long-term stress effects, but studies on Fkbp5 DNA methylation (DNAm) in rodents are so far limited. We evaluated the applicability of high-accuracy DNA methylation measurement via targeted bisulfite sequencing (HAM-TBS), a next-generation sequencing-based technology, to allow a more in-depth characterisation of the DNA methylation of the murine Fkbp5 locus in three different tissues (blood, frontal cortex and hippocampus). In this study, we not only increased the number of evaluated sites in previously described regulatory regions (in introns 1 and 5), but also extended the evaluation to novel, possibly relevant regulatory regions of the gene (in intron 8, the transcriptional start site, the proximal enhancer and CTCF-binding sites within the 5'UTR). We here describe the assessment of HAM-TBS assays for a panel of 157 CpGs with possible functional relevance in the murine Fkbp5 gene. DNAm profiles were tissue-specific, with lesser differences between the two brain regions than between the brain and blood. Moreover, we identified DNAm changes in the Fkbp5 locus after early life stress exposure in the frontal cortex and blood. Our findings indicate that HAM-TBS is a valuable tool for broader exploration of the DNAm of the murine Fkbp5 locus and its involvement in the stress response.
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Affiliation(s)
- Natan Yusupov
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Lotte van Doeselaar
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Tobias Wiechmann
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Mathias V Schmidt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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Kvist T, Sammallahti S, Lahti-Pulkkinen M, Cruceanu C, Czamara D, Dieckmann L, Tontsch A, Röh S, Rex-Haffner M, Wolford E, Reynolds R, Eriksson J, Suomalainen-König S, Laivuori H, Kajantie E, Lahdensuo E, Binder E, Räikkönen K. Cohort profile: InTraUterine sampling in early pregnancy (ITU), a prospective pregnancy cohort study in Finland: study design and baseline characteristics. BMJ Open 2022; 12:e049231. [PMID: 35105615 PMCID: PMC8804635 DOI: 10.1136/bmjopen-2021-049231] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE The InTraUterine sampling in early pregnancy (ITU) is a prospective pregnancy cohort study. The overarching aim of ITU is to unravel genomic, epigenomic, transcriptomic, endocrine, inflammatory and metabolic maternal-placental-fetal mechanisms involved in the programming of health and disease after exposure to prenatal environmental adversity, such as maternal malnutrition, cardiometabolic disorders, infections, medical interventions, mental disorders and psychosocial stress. This paper describes the study protocol, design and baseline characteristics of the cohort. PARTICIPANTS We included 944 pregnant Finnish women, their partners and children born alive between April 2012 and December 2017. The women were recruited through the national, voluntary trisomy 21 screening between 9+0 and 21+6 gestational weeks. Of the participating women, 543 were screen positive and underwent fetal chromosomal testing. Test result of these women suggested no fetal chromosomal abnormality. Further, we recruited 401 women who were screen negative and who did not undergo fetal chromosomal testing. FINDINGS TO DATE We have collected chorionic villi and amniotic fluid from the screen-positive women; blood, urine, buccal swabs and diurnal salivary samples from all women; blood and buccal swabs from all partners; and placenta, cord blood and buccal swabs from all newborns for analyses of the genome, epigenome, transcriptome, and endocrine, inflammatory and metabolic markers. These data are coupled with comprehensive phenotypes, including questions on demographic characteristics, health and well-being of the women and their partners during pregnancy and of the women and their children at the child's age of 1.7 and 3 years. Data also come from patient records and nationwide registers covering health, lifestyle and medication data. FUTURE PLANS Multiple layers of ITU data allow integrative data analyses, which translate to biomarker identification and allow risk stratification and understanding of the biological mechanisms involved in prenatal programming of health and disease.
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Affiliation(s)
- Tuomas Kvist
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Sara Sammallahti
- Department of Child and Adolescent Psychiatry and Psychology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Cristiana Cruceanu
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Linda Dieckmann
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Alina Tontsch
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Eiina Wolford
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Rebecca Reynolds
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Johan Eriksson
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Obstetrics and Gynaecology, National University of Singapore Yong Loo Lin School of Medicine, Singapore
| | - Sanna Suomalainen-König
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hannele Laivuori
- Medical and Clinical Genetics, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Science, Institute of Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Eero Kajantie
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
| | - Eija Lahdensuo
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
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5
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Czamara D, Dieckmann L, Röh S, Kraemer S, Rancourt RC, Sammallahti S, Kajantie E, Laivuori H, Eriksson JG, Räikkönen K, Henrich W, Plagemann A, Binder EB, Braun T, Entringer S. Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation. Clin Epigenetics 2021; 13:165. [PMID: 34446099 PMCID: PMC8393766 DOI: 10.1186/s13148-021-01153-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/12/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Glucocorticoids (GCs) play a pivotal role in fetal programming. Antenatal treatment with synthetic GCs (sGCs) in individuals in danger of preterm labor is common practice. Adverse short- and long-term effects of antenatal sGCs have been reported, but their effects on placental epigenetic characteristics have never been systematically studied in humans. RESULTS We tested the association between exposure to the sGC betamethasone (BET) and placental DNA methylation (DNAm) in 52 exposed cases and 84 gestational-age-matched controls. We fine-mapped associated loci using targeted bisulfite sequencing. The association of placental DNAm with gene expression and co-expression analysis on implicated genes was performed in an independent cohort including 494 placentas. Exposure to BET was significantly associated with lower placenta DNAm at an enhancer of FKBP5. FKBP5 (FK506-binding protein 51) is a co-chaperone that modulates glucocorticoid receptor activity. Lower DNAm at this enhancer site was associated with higher expression of FKBP5 and a co-expressed gene module. This module is enriched for genes associated with preeclampsia and involved in inflammation and immune response. CONCLUSIONS Our findings suggest that BET exposure during pregnancy associates with few but lasting changes in placental DNAm and may promote a gene expression profile associated with placental dysfunction and increased inflammation. This may represent a pathway mediating GC-associated negative long-term consequences and health outcomes in offspring.
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Affiliation(s)
- Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Linda Dieckmann
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- International Max Planck Research School for Translational Psychiatry, München, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
| | - Sarah Kraemer
- Institute of Medical Psychology, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Luisenstr. 57, 10117 Berlin, Germany
| | - Rebecca C. Rancourt
- Department of Experimental Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sara Sammallahti
- Department of Child and Adolescent Psychiatry, Erasmus MC, Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Faculty of Medicine, PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital and Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Johan G. Eriksson
- Department of General Practice and Primary Care, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Obstetrics and Gynaecology and Human Potential Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Wolfgang Henrich
- Department of Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andreas Plagemann
- Department of Experimental Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Department of Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Elisabeth B. Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329 USA
| | - Thorsten Braun
- Department of Experimental Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Department of Obstetrics, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sonja Entringer
- Institute of Medical Psychology, Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Luisenstr. 57, 10117 Berlin, Germany
- Development, Health, and Disease Research Program, University of California, Irvine, Orange, CA USA
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6
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Prestel M, Prell-Schicker C, Webb T, Malik R, Lindner B, Ziesch N, Rex-Haffner M, Röh S, Viturawong T, Lehm M, Mokry M, den Ruijter H, Haitjema S, Asare Y, Söllner F, Najafabadi MG, Aherrahrou R, Civelek M, Samani NJ, Mann M, Haffner C, Dichgans M. The Atherosclerosis Risk Variant rs2107595 Mediates Allele-Specific Transcriptional Regulation of HDAC9 via E2F3 and Rb1. Stroke 2019; 50:2651-2660. [PMID: 31500558 DOI: 10.1161/strokeaha.119.026112] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background and Purpose- Genome-wide association studies have identified the HDAC9 (histone deacetylase 9) gene region as a major risk locus for atherosclerotic stroke and coronary artery disease in humans. Previous results suggest a role of altered HDAC9 expression levels as the underlying disease mechanism. rs2107595, the lead single nucleotide polymorphism for stroke and coronary artery disease resides in noncoding DNA and colocalizes with histone modification marks suggestive of enhancer elements. Methods- To determine the mechanisms by which genetic variation at rs2107595 regulates HDAC9 expression and thus vascular risk we employed targeted resequencing, proteome-wide search for allele-specific nuclear binding partners, chromatin immunoprecipitation, genome-editing, reporter assays, circularized chromosome conformation capture, and gain- and loss-of-function experiments in cultured human cell lines and primary immune cells. Results- Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele. Gain- and loss-of-function studies showed a regulatory effect of E2F/Rb proteins on HDAC9 expression. Compared with the common allele, the rs2107595 risk allele exhibited higher transcriptional capacity in luciferase assays and was associated with higher HDAC9 mRNA levels in primary macrophages and genome-edited Jurkat cells. Circularized chromosome conformation capture revealed a genomic interaction of the rs2107595 region with the HDAC9 promoter, which was stronger for the common allele as was the in vivo interaction with E2F3 and Rb1 determined by chromatin immunoprecipitation. Gain-of-function experiments in isogenic Jurkat cells demonstrated a key role of E2F3 in mediating rs2107595-dependent transcriptional regulation of HDAC9. Conclusions- Collectively, our findings imply allele-specific transcriptional regulation of HDAC9 via E2F3 and Rb1 as a major mechanism mediating vascular risk at rs2107595.
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Affiliation(s)
- Matthias Prestel
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Caroline Prell-Schicker
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Tom Webb
- Department of Cardiovascular Sciences, University of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (T.W., M.G.N., N.J.S.)
| | - Rainer Malik
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Barbara Lindner
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Natalie Ziesch
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max-Planck-Institute for Psychiatry, Germany (M.R.H., S.R.)
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max-Planck-Institute for Psychiatry, Germany (M.R.H., S.R.)
| | - Thanatip Viturawong
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany (T.V., M.L., M. Mann)
| | - Manuel Lehm
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany (T.V., M.L., M. Mann)
- Abteilung für Diagnostische und Interventionelle Neuroradiologie, Klinikum rechts der Isar, Munich, Germany (M.L.)
| | - Michal Mokry
- Department of Pediatrics (M. Mokry), University Medical Center Utrecht, the Netherlands
| | - Hester den Ruijter
- Laboratory of Experimental Cardiology (H.d.R., S.H.), University Medical Center Utrecht, the Netherlands
| | - Saskia Haitjema
- Laboratory of Experimental Cardiology (H.d.R., S.H.), University Medical Center Utrecht, the Netherlands
| | - Yaw Asare
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Flavia Söllner
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
- Department of Physiological Chemistry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Germany (F.S.)
| | - Maryam Ghaderi Najafabadi
- Department of Cardiovascular Sciences, University of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (T.W., M.G.N., N.J.S.)
| | - Rédouane Aherrahrou
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, (R.A., M.C.)
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, (R.A., M.C.)
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester and National Institute for Health Research Leicester Biomedical Research Centre, Leicester, United Kingdom (T.W., M.G.N., N.J.S.)
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany (T.V., M.L., M. Mann)
| | - Christof Haffner
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
| | - Martin Dichgans
- From the Institute for Stroke and Dementia Research, Klinikum der Universität München, Germany (M.P., C.P.S., R.M., B.L., N.Z., M.L., Y.A., F.S., C.H., M.D.)
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany (M.D.)
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7
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Engel M, Eggert C, Kaplick PM, Eder M, Röh S, Tietze L, Namendorf C, Arloth J, Weber P, Rex-Haffner M, Geula S, Jakovcevski M, Hanna JH, Leshkowitz D, Uhr M, Wotjak CT, Schmidt MV, Deussing JM, Binder EB, Chen A. The Role of m 6A/m-RNA Methylation in Stress Response Regulation. Neuron 2019; 99:389-403.e9. [PMID: 30048615 PMCID: PMC6069762 DOI: 10.1016/j.neuron.2018.07.009] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/04/2018] [Accepted: 07/05/2018] [Indexed: 12/04/2022]
Abstract
N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m6A/m, in the stress response in the adult brain in vivo is currently unknown. Here, we provide a detailed analysis of the stress epitranscriptome using m6A/m-seq, global and gene-specific m6A/m measurements. We show that stress exposure and glucocorticoids region and time specifically alter m6A/m and its regulatory network. We demonstrate that deletion of the methyltransferase Mettl3 or the demethylase Fto in adult neurons alters the m6A/m epitranscriptome, increases fear memory, and changes the transcriptome response to fear and synaptic plasticity. Moreover, we report that regulation of m6A/m is impaired in major depressive disorder patients following glucocorticoid stimulation. Our findings indicate that brain m6A/m represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m6A/m response may contribute to the pathophysiology of stress-related psychiatric disorders. m6A/m mRNA methylation in the adult mouse brain is regulated by stress m6A/m mRNA regulation is brain region, time, and gene specific Mettl3 and Fto cKO alter m6A/m, fear memory, expression, and synaptic plasticity The m6A/m glucocorticoid response is impaired in major depressive disorder patients
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Affiliation(s)
- Mareen Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Carola Eggert
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Paul M Kaplick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Matthias Eder
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Lisa Tietze
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Christian Namendorf
- Clinical Laboratory, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Peter Weber
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Monika Rex-Haffner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Manfred Uhr
- Clinical Laboratory, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Carsten T Wotjak
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Mathias V Schmidt
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jan M Deussing
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
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8
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Wiechmann T, Röh S, Sauer S, Czamara D, Arloth J, Ködel M, Beintner M, Knop L, Menke A, Binder EB, Provençal N. Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus. Clin Epigenetics 2019; 11:83. [PMID: 31122292 PMCID: PMC6533766 DOI: 10.1186/s13148-019-0682-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/09/2019] [Indexed: 01/30/2023] Open
Abstract
Background Epigenetic mechanisms may play a major role in the biological embedding of early-life stress (ELS). One proposed mechanism is that glucocorticoid (GC) release following ELS exposure induces long-lasting alterations in DNA methylation (DNAm) of important regulatory genes of the stress response. Here, we investigate the dynamics of GC-dependent methylation changes in key regulatory regions of the FKBP5 locus in which ELS-associated DNAm changes have been reported. Results We repeatedly measured DNAm in human peripheral blood samples from 2 independent cohorts exposed to the GC agonist dexamethasone (DEX) using a targeted bisulfite sequencing approach, complemented by data from Illumina 450K arrays. We detected differentially methylated CpGs in enhancers co-localizing with GC receptor binding sites after acute DEX treatment (1 h, 3 h, 6 h), which returned to baseline levels within 23 h. These changes withstood correction for immune cell count differences. While we observed main effects of sex, age, body mass index, smoking, and depression symptoms on FKBP5 methylation levels, only the functional FKBP5 SNP (rs1360780) moderated the dynamic changes following DEX. This genotype effect was observed in both cohorts and included sites previously shown to be associated with ELS. Conclusion Our study highlights that DNAm levels within regulatory regions of the FKBP5 locus show dynamic changes following a GC challenge and suggest that factors influencing the dynamics of this regulation may contribute to the previously reported alterations in DNAm associated with current and past ELS exposure. Electronic supplementary material The online version of this article (10.1186/s13148-019-0682-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Wiechmann
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Madita Beintner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Lisanne Knop
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Andreas Menke
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Wuerzburg, Wuerzburg, Germany.,Comprehensive Heart Failure Center, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA.
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany. .,Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. .,BC Children's Hospital Research Institute, Vancouver, BC, Canada.
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9
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Schroeder M, Jakovcevski M, Polacheck T, Drori Y, Ben-Dor S, Röh S, Chen A. Sex dependent impact of gestational stress on predisposition to eating disorders and metabolic disease. Mol Metab 2018; 17:1-16. [PMID: 30174229 PMCID: PMC6197785 DOI: 10.1016/j.molmet.2018.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Vulnerability to eating disorders (EDs) is broadly assumed to be associated with early life stress. However, a careful examination of the literature shows that susceptibility to EDs may depend on the type, severity and timing of the stressor and the sex of the individual. We aimed at exploring the link between chronic prenatal stress and predisposition to EDs and metabolic disease. METHODS We used a chronic variable stress protocol during gestation to explore the metabolic response of male and female offspring to food restriction (FR), activity-based anorexia (ABA), binge eating (BE) and exposure to high fat (HF) diet. RESULTS Contrary to controls, prenatally stressed (PNS) female offspring showed resistance to ABA and BE and displayed a lower metabolic rate leading to hyperadiposity and obesity on HF diet. Male PNS offspring showed healthy responses to FR and ABA, increased propensity to binge and improved coping with HF compared to controls. We found that long-lasting abnormal responses to metabolic challenge are linked to fetal programming and adult hypothalamic dysregulation in PNS females, resulting from sexually dimorphic adaptations in placental methylation and gene expression. CONCLUSIONS Our results show that maternal stress may have variable and even opposing effects on ED risk, depending on the ED and the sex of the offspring.
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Affiliation(s)
- Mariana Schroeder
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Tamar Polacheck
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yonat Drori
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Biological Services, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
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10
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Zannas AS, Arloth J, Carrillo-Roa T, Iurato S, Röh S, Ressler KJ, Nemeroff CB, Smith AK, Bradley B, Heim C, Menke A, Lange JF, Brückl T, Ising M, Wray NR, Erhardt A, Binder EB, Mehta D. Correction to: Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. Genome Biol 2018; 19:61. [PMID: 29792225 PMCID: PMC5966922 DOI: 10.1186/s13059-018-1441-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Anthony S Zannas
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, USA.
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tania Carrillo-Roa
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Stella Iurato
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, USA.,Howard Hughes Medical Institute, Chevy Chase, USA.,Yerkes National Primate Research Center, Emory University, Atlanta, USA
| | - Charles B Nemeroff
- Department of Psychiatry and Behavioral Sciences and the Center on Aging, University of Miami Miller School of Medicine, Miami, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, USA
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, USA.,Atlanta Veterans Affairs Medical Center, Decatur, USA
| | - Christine Heim
- Institute of Medical Psychology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Biobehavioral Health, Pennsylvania State University, University Park, USA
| | - Andreas Menke
- Present Address: Department of Psychiatry, Psychosomatics, and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Jennifer F Lange
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Tanja Brückl
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Naomi R Wray
- The University of Queensland, Queensland Brain Institute, St Lucia, Australia
| | - Angelika Erhardt
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, USA.
| | - Divya Mehta
- The University of Queensland, Queensland Brain Institute, St Lucia, Australia
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11
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Zannas AS, Arloth J, Carrillo-Roa T, Iurato S, Röh S, Ressler KJ, Nemeroff CB, Smith AK, Bradley B, Heim C, Menke A, Lange JF, Brückl T, Ising M, Wray NR, Erhardt A, Binder EB, Mehta D. Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. Genome Biol 2015; 16:266. [PMID: 26673150 PMCID: PMC4699359 DOI: 10.1186/s13059-015-0828-5] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/10/2015] [Indexed: 12/22/2022] Open
Abstract
Background Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. Results We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood cell-type composition and lifestyle parameters, cumulative lifetime stress, but not childhood maltreatment or current stress alone, predicted accelerated epigenetic aging in an urban, African American cohort (n = 392). This effect was primarily driven by personal life stressors, was more pronounced with advancing age, and was blunted in individuals with higher childhood abuse exposure. Hypothesizing that these epigenetic effects could be mediated by glucocorticoid signaling, we found that a high number (n = 85) of epigenetic clock CpG sites were located within glucocorticoid response elements. We further examined the functional effects of glucocorticoids on epigenetic clock CpGs in an independent sample with genome-wide DNA methylation (n = 124) and gene expression data (n = 297) before and after exposure to the glucocorticoid receptor agonist dexamethasone. Dexamethasone induced dynamic changes in methylation in 31.2 % (110/353) of these CpGs and transcription in 81.7 % (139/170) of genes neighboring epigenetic clock CpGs. Disease enrichment analysis of these dexamethasone-regulated genes showed enriched association for aging-related diseases, including coronary artery disease, arteriosclerosis, and leukemias. Conclusions Cumulative lifetime stress may accelerate epigenetic aging, an effect that could be driven by glucocorticoid-induced epigenetic changes. These findings contribute to our understanding of mechanisms linking chronic stress with accelerated aging and heightened disease risk. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0828-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anthony S Zannas
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA.
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tania Carrillo-Roa
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Stella Iurato
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Charles B Nemeroff
- Department of Psychiatry and Behavioral Sciences and the Center on Aging, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA.,Atlanta Veterans Affairs Medical Center, Decatur, GA, USA
| | - Christine Heim
- Institute of Medical Psychology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Biobehavioral Health, Pennsylvania State University, University Park, PA, USA
| | - Andreas Menke
- Current Address: Department of Psychiatry, Psychosomatics, and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Jennifer F Lange
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Tanja Brückl
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Naomi R Wray
- The University of Queensland, Queensland Brain Institute, St Lucia, Qld 4072, Australia
| | - Angelika Erhardt
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA.
| | - Divya Mehta
- The University of Queensland, Queensland Brain Institute, St Lucia, Qld 4072, Australia
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12
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Abstract
Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.
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Affiliation(s)
- Janine Arloth
- Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2–10, 80804, Munich, Germany
- * E-mail:
| | - Daniel M. Bader
- Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2–10, 80804, Munich, Germany
- Gene Center Munich, Ludwig-Maximillians-Universität München, Feodor-Lynen Strasse 25, 81377, Munich, Germany
| | - Simone Röh
- Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2–10, 80804, Munich, Germany
| | - Andre Altmann
- Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, 780 Welch Road, CJ350 C38, CA-94304 Palo Alto, California, United States of America
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13
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Quast C, Cuboni S, Bader D, Altmann A, Weber P, Arloth J, Röh S, Brückl T, Ising M, Kopczak A, Erhardt A, Hausch F, Lucae S, Binder EB. Functional coding variants in SLC6A15, a possible risk gene for major depression. PLoS One 2013; 8:e68645. [PMID: 23874702 PMCID: PMC3712998 DOI: 10.1371/journal.pone.0068645] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
SLC6A15 is a neuron-specific neutral amino acid transporter that belongs to the solute carrier 6 gene family. This gene family is responsible for presynaptic re-uptake of the majority of neurotransmitters. Convergent data from human studies, animal models and pharmacological investigations suggest a possible role of SLC6A15 in major depressive disorder. In this work, we explored potential functional variants in this gene that could influence the activity of the amino acid transporter and thus downstream neuronal function and possibly the risk for stress-related psychiatric disorders. DNA from 400 depressed patients and 400 controls was screened for genetic variants using a pooled targeted re-sequencing approach. Results were verified by individual re-genotyping and validated non-synonymous coding variants were tested in an independent sample (N = 1934). Nine variants altering the amino acid sequence were then assessed for their functional effects by measuring SLC6A15 transporter activity in a cellular uptake assay. In total, we identified 405 genetic variants, including twelve non-synonymous variants. While none of the non-synonymous coding variants showed significant differences in case-control associations, two rare non-synonymous variants were associated with a significantly increased maximal (3)H proline uptake as compared to the wildtype sequence. Our data suggest that genetic variants in the SLC6A15 locus change the activity of the amino acid transporter and might thus influence its neuronal function and the risk for stress-related psychiatric disorders. As statistically significant association for rare variants might only be achieved in extremely large samples (N >70,000) functional exploration may shed light on putatively disease-relevant variants.
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Affiliation(s)
- Carina Quast
- Max Planck Institute of Psychiatry, Munich, Germany.
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14
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Jackstadt R, Röh S, Neumann J, Jung P, Hoffmann R, Horst D, Berens C, Bornkamm GW, Kirchner T, Menssen A, Hermeking H. AP4 is a mediator of epithelial-mesenchymal transition and metastasis in colorectal cancer. J Exp Med 2013; 210:1331-50. [PMID: 23752226 PMCID: PMC3698521 DOI: 10.1084/jem.20120812] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 05/20/2013] [Indexed: 12/14/2022] Open
Abstract
The basic helix-loop-helix transcription factor AP4/TFAP4/AP-4 is encoded by a c-MYC target gene and displays up-regulation concomitantly with c-MYC in colorectal cancer (CRC) and numerous other tumor types. Here a genome-wide characterization of AP4 DNA binding and mRNA expression was performed using a combination of microarray, genome-wide chromatin immunoprecipitation, next-generation sequencing, and bioinformatic analyses. Thereby, hundreds of induced and repressed AP4 target genes were identified. Besides many genes involved in the control of proliferation, the AP4 target genes included markers of stemness (LGR5 and CD44) and epithelial-mesenchymal transition (EMT) such as SNAIL, E-cadherin/CDH1, OCLN, VIM, FN1, and the Claudins 1, 4, and 7. Accordingly, activation of AP4 induced EMT and enhanced migration and invasion of CRC cells. Conversely, down-regulation of AP4 resulted in mesenchymal-epithelial transition and inhibited migration and invasion. In addition, AP4 induction was required for EMT, migration, and invasion caused by ectopic expression of c-MYC. Inhibition of AP4 in CRC cells resulted in decreased lung metastasis in mice. Elevated AP4 expression in primary CRC significantly correlated with liver metastasis and poor patient survival. These findings imply AP4 as a new regulator of EMT that contributes to metastatic processes in CRC and presumably other carcinomas.
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Affiliation(s)
- Rene Jackstadt
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
| | - Simone Röh
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
| | - Jens Neumann
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
| | - Peter Jung
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Reinhard Hoffmann
- Institute of Medical Microbiology, Immunology and Hygiene, Technical University of Munich, D-81675 Munich, Germany
| | - David Horst
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
| | - Christian Berens
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, D-91058 Erlangen, Germany
| | - Georg W. Bornkamm
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Center Munich, D-81377 Munich, Germany
| | - Thomas Kirchner
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Antje Menssen
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians University of Munich, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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Jackstadt R, Röh S, Neumann J, Jung P, Hoffmann R, Horst D, Berens C, Bornkamm GW, Kirchner T, Menssen A, Hermeking H. AP4 is a mediator of epithelial–mesenchymal transition and metastasis in colorectal cancer. J Biophys Biochem Cytol 2013. [DOI: 10.1083/jcb.2017oia33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Kaller M, Liffers ST, Oeljeklaus S, Kuhlmann K, Röh S, Hoffmann R, Warscheid B, Hermeking H. Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Mol Cell Proteomics 2011; 10:M111.010462. [PMID: 21566225 DOI: 10.1074/mcp.m111.010462] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gene encoding the miR-34a microRNA is a transcriptional target of the p53 tumor suppressor protein and subject to epigenetic inactivation in colorectal cancer and numerous other tumor types. Here, we combined pulsed SILAC (pSILAC) and microarray analyses to identify miR-34a-induced changes in protein and mRNA expression. pSILAC allowed to quantify the de novo protein synthesis of 1206 proteins after activation of a conditional miR-34a allele in a colorectal cancer cell line. ∼19% of the detected proteins were differentially regulated, with 113 proteins being down- and 115 up-regulated. The proteins with a miR-34a seed-matching-sequence in the 3'-untranslated region (UTR) of the corresponding mRNA showed a clear bias toward translational repression. Proteins involved in DNA replication, e.g. the MCM proteins, and cell proliferation, were over-represented among indirectly down-regulated proteins lacking a miR-34a seed-match. The decrease in de novo protein synthesis of direct miR-34a targets correlated with reduced levels of the corresponding mRNA in most cases, indicating an interdependence of both types of regulation. In addition, 43 mRNAs encoding proteins not detected by pSILAC were down-regulated after miR-34a expression and contained miR-34a seed-matches. The direct regulation of selected miR-34a target-mRNAs was confirmed using reporter assays. Via down-regulation of the proteins encoded by these mRNAs miR-34a presumably inhibits glycolysis (LDHA), WNT-signaling (LEF1), invasion/migration (AXL) and lipid metabolism (ACSL1, ACSL4). Furthermore, miR-34a may activate p53 by inhibiting its acetylation (MTA2, HDAC1) and degradation (YY1). In summary, miR-34a presumably participates in multiple tumor suppressive pathways by directly and indirectly suppressing the expression of numerous, critical proteins.
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Affiliation(s)
- Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Strasse 36, D-80337 Munich, Germany
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