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Moon YM, Park SE, Smith-Hicks C, Hauptman A. Resolution of severe neurobehavioral difficulties in an individual with Primrose syndrome with sertraline. Am J Med Genet A 2024; 194:e63610. [PMID: 38517161 DOI: 10.1002/ajmg.a.63610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/23/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Primrose syndrome (PS) is a rare genetic disease characterized by developmental delay, intellectual disability, sensorineural hearing loss, and dysmorphic features. PS is caused by de novo pathogenic variants in the ZBTB20 gene, which encodes a transcription factor modulating neurogenesis. We describe resolution with sertraline of neurobehavioral difficulties in a 17-year-old Hispanic male with PS with de novo heterozygous c.1916G > A (p.C639Y) variant of ZBTB20. Neurobehavioral difficulties included aggression towards self and others, irritability, tearfulness, and mood liability that did not respond to behavioral interventions or aripiprazole. Treatment with sertraline, a medication indicated for psychiatric disorders including anxiety and depression, led to the resolution of neurobehavioral difficulties after 2 weeks of initiation of medication. The treatment course suggests that selective serotonin reuptake inhibitors, such as sertraline, may be a useful tool for neurobehavioral difficulties in PS over antipsychotics that are accompanied by complex side effect profiles, and suggest that anxiety is the primary cause of the neurobehavioral difficulties in this patient.
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Affiliation(s)
- Young Min Moon
- Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sa Eun Park
- Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Constance Smith-Hicks
- Department of Neurology, School of Medicine, Johns Hopkins Univerisity, Baltimore, Maryland, USA
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Aaron Hauptman
- Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland, USA
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2
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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3
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Dang T, Russel WA, Saad T, Dhawka L, Ay A, Ingram KK. Risk for Seasonal Affective Disorder (SAD) Linked to Circadian Clock Gene Variants. BIOLOGY 2023; 12:1532. [PMID: 38132358 PMCID: PMC10741218 DOI: 10.3390/biology12121532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Molecular pathways affecting mood are associated with circadian clock gene variants and are influenced, in part, by the circadian clock, but the molecular mechanisms underlying this link are poorly understood. We use machine learning and statistical analyses to determine the circadian gene variants and clinical features most highly associated with symptoms of seasonality and seasonal affective disorder (SAD) in a deeply phenotyped population sample. We report sex-specific clock gene effects on seasonality and SAD symptoms; genotypic combinations of CLOCK3111/ZBTB20 and PER2/PER3B were significant genetic risk factors for males, and CRY2/PER3C and CRY2/PER3-VNTR were significant risk factors for females. Anxiety, eveningness, and increasing age were significant clinical risk factors for seasonality and SAD for females. Protective factors for SAD symptoms (in females only) included single gene variants: CRY1-GG and PER3-VNTR-4,5. Clock gene effects were partially or fully mediated by diurnal preference or chronotype, suggesting multiple indirect effects of clock genes on seasonality symptoms. Interestingly, protective effects of CRY1-GG, PER3-VNTR-4,5, and ZBTB20 genotypes on seasonality and depression were not mediated by chronotype, suggesting some clock variants have direct effects on depressive symptoms related to SAD. Our results support previous links between CRY2, PER2, and ZBTB20 genes and identify novel links for CLOCK and PER3 with symptoms of seasonality and SAD. Our findings reinforce the sex-specific nature of circadian clock influences on seasonality and SAD and underscore the multiple pathways by which clock variants affect downstream mood pathways via direct and indirect mechanisms.
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Affiliation(s)
- Thanh Dang
- Department of Computer Science, Colgate University, Hamilton, NY 13346, USA; (T.D.); (T.S.)
| | - William A. Russel
- Department of Biology, Colgate University, Hamilton, NY 13346, USA; (W.A.R.); (A.A.)
| | - Tazmilur Saad
- Department of Computer Science, Colgate University, Hamilton, NY 13346, USA; (T.D.); (T.S.)
- Department of Mathematics, Colgate University, Hamilton, NY 13346, USA
| | - Luvna Dhawka
- Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ahmet Ay
- Department of Biology, Colgate University, Hamilton, NY 13346, USA; (W.A.R.); (A.A.)
- Department of Mathematics, Colgate University, Hamilton, NY 13346, USA
| | - Krista K. Ingram
- Department of Biology, Colgate University, Hamilton, NY 13346, USA; (W.A.R.); (A.A.)
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4
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Ventresca C, Mohamed W, Russel WA, Ay A, Ingram KK. Machine learning analyses reveal circadian clock features predictive of anxiety among UK biobank participants. Sci Rep 2023; 13:22304. [PMID: 38102312 PMCID: PMC10724169 DOI: 10.1038/s41598-023-49644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Mood disorders, including depression and anxiety, affect almost one-fifth of the world's adult population and are becoming increasingly prevalent. Mutations in circadian clock genes have previously been associated with mood disorders both directly and indirectly through alterations in circadian phase, suggesting that the circadian clock influences multiple molecular pathways involved in mood. By targeting previously identified single nucleotide polymorphisms (SNPs) that have been implicated in anxiety and depressive disorders, we use a combination of statistical and machine learning techniques to investigate associations with the generalized anxiety disorder assessment (GAD-7) scores in a UK Biobank sample of 90,882 individuals. As in previous studies, we observed that females exhibited higher GAD-7 scores than males regardless of genotype. Interestingly, we found no significant effects on anxiety from individual circadian gene variants; only circadian genotypes with multiple SNP variants showed significant associations with anxiety. For both sexes, severe anxiety is associated with a 120-fold increase in odds for individuals with CRY2_AG(rs1083852)/ZBTB20_TT(rs1394593) genotypes and is associated with a near 40-fold reduction in odds for individuals with PER3-A_CG(rs228697)/ZBTB20_TT(rs1394593) genotypes. We also report several sex-specific associations with anxiety. In females, the CRY2/ZBTB20 genotype combination showed a > 200-fold increase in odds of anxiety and PER3/ZBTB20 and CRY1 /PER3-A genotype combinations also appeared as female risk factors. In males, CRY1/PER3-A and PER3-B/ZBTB20 genotype combinations were associated with anxiety risk. Mediation analysis revealed direct associations of CRY2/ZBTB20 variant genotypes with moderate anxiety in females and CRY1/PER3-A variant genotypes with severe anxiety in males. The association of CRY1/PER3-A variant genotypes with severe anxiety in females was partially mediated by extreme evening chronotype. Our results reinforce existing findings that females exhibit stronger anxiety outcomes than males, and provide evidence for circadian gene associations with anxiety, particularly in females. Our analyses only identified significant associations using two-gene combinations, underscoring the importance of combined gene effects on anxiety risk. We describe novel, robust associations between gene combinations involving the ZBTB20 SNP (rs1394593) and risk of anxiety symptoms in a large population sample. Our findings also support previous findings that the ZBTB20 SNP is an important factor in mood disorders, including seasonal affective disorder. Our results suggest that reduced expression of this gene significantly modulates the risk of anxiety symptoms through direct influences on mood-related pathways. Together, these observations provide novel links between the circadian clockwork and anxiety symptoms and identify potential molecular pathways through which clock genes may influence anxiety risk.
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Affiliation(s)
- Cole Ventresca
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Wael Mohamed
- Department of Computer Science, Colgate University, Hamilton, NY, USA
- Department of Psychological and Brain Sciences, Colgate University, Hamilton, NY, USA
| | | | - Ahmet Ay
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Biology, Colgate University, Hamilton, NY, USA
| | - Krista K Ingram
- Department of Biology, Colgate University, Hamilton, NY, USA.
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Mohan K, Gasparoni G, Salhab A, Orlich MM, Geffers R, Hoffmann S, Adams RH, Walter J, Nordheim A. Age-Associated Changes in Endothelial Transcriptome and Epigenetic Landscapes Correlate With Elevated Risk of Cerebral Microbleeds. J Am Heart Assoc 2023; 12:e031044. [PMID: 37609982 PMCID: PMC10547332 DOI: 10.1161/jaha.123.031044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/24/2023] [Indexed: 08/24/2023]
Abstract
Background Stroke is a leading global cause of human death and disability, with advanced aging associated with elevated incidences of stroke. Despite high mortality and morbidity of stroke, the mechanisms leading to blood-brain barrier dysfunction and development of stroke with age are poorly understood. In the vasculature of brain, endothelial cells (ECs) constitute the core component of the blood-brain barrier and provide a physical barrier composed of tight junctions, adherens junctions, and basement membrane. Methods and Results We show, in mice, the incidents of intracerebral bleeding increases with age. After isolating an enriched population of cerebral ECs from murine brains at 2, 6, 12, 18, and 24 months, we studied age-associated changes in gene expression. The study reveals age-dependent dysregulation of 1388 genes, including many involved in the maintenance of the blood-brain barrier and vascular integrity. We also investigated age-dependent changes on the levels of CpG methylation and accessible chromatin in cerebral ECs. Our study reveals correlations between age-dependent changes in chromatin structure and gene expression, whereas the dynamics of DNA methylation changes are different. Conclusions We find significant age-dependent downregulation of the Aplnr gene along with age-dependent reduction in chromatin accessibility of promoter region of the Aplnr gene in cerebral ECs. Aplnr is associated with positive regulation of vasodilation and is implicated in vascular health. Altogether, our data suggest a potential role of the apelinergic axis involving the ligand apelin and its receptor to be critical in maintenance of the blood-brain barrier and vascular integrity.
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Affiliation(s)
- Kshitij Mohan
- Interfaculty Institute of Cell BiologyUniversity of TübingenTübingenGermany
- International Max Planck Research School “From Molecules to Organisms”TübingenGermany
| | | | | | - Michael M. Orlich
- Interfaculty Institute of Cell BiologyUniversity of TübingenTübingenGermany
- International Max Planck Research School “From Molecules to Organisms”TübingenGermany
| | - Robert Geffers
- Genome AnalyticsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Steve Hoffmann
- Leibniz Institute on AgingFritz Lipmann InstituteJenaGermany
| | - Ralf H. Adams
- Department of Tissue MorphogenesisMax Planck Institute for Molecular BiomedicineMünsterGermany
- Faculty of MedicineUniversity of MünsterMünsterGermany
| | - Jörn Walter
- Department of GeneticsUniversity of SaarlandSaarbrückenGermany
| | - Alfred Nordheim
- Interfaculty Institute of Cell BiologyUniversity of TübingenTübingenGermany
- Leibniz Institute on AgingFritz Lipmann InstituteJenaGermany
- International Max Planck Research School “From Molecules to Organisms”TübingenGermany
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6
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Strekalova T, Moskvin O, Jain AY, Gorbunov N, Gorlova A, Sadovnik D, Umriukhin A, Cespuglio R, Yu WS, Tse ACK, Kalueff AV, Lesch KP, Lim LW. Molecular signature of excessive female aggression: study of stressed mice with genetic inactivation of neuronal serotonin synthesis. J Neural Transm (Vienna) 2023; 130:1113-1132. [PMID: 37542675 PMCID: PMC10460733 DOI: 10.1007/s00702-023-02677-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023]
Abstract
Aggression is a complex social behavior, critically involving brain serotonin (5-HT) function. The neurobiology of female aggression remains elusive, while the incidence of its manifestations has been increasing. Yet, animal models of female aggression are scarce. We previously proposed a paradigm of female aggression in the context of gene x environment interaction where mice with partial genetic inactivation of tryptophan hydroxylase-2 (Tph2+/- mice), a key enzyme of neuronal 5-HT synthesis, are subjected to predation stress resulting in pathological aggression. Using deep sequencing and the EBSeq method, we studied the transcriptomic signature of excessive aggression in the prefrontal cortex of female Tph2+/- mice subjected to rat exposure stress and food deprivation. Challenged mutants, but not other groups, displayed marked aggressive behaviors. We found 26 genes with altered expression in the opposite direction between stressed groups of both Tph2 genotypes. We identified several molecular markers, including Dgkh, Arfgef3, Kcnh7, Grin2a, Tenm1 and Epha6, implicated in neurodevelopmental deficits and psychiatric conditions featuring impaired cognition and emotional dysregulation. Moreover, while 17 regulons, including several relevant to neural plasticity and function, were significantly altered in stressed mutants, no alteration in regulons was detected in stressed wildtype mice. An interplay of the uncovered pathways likely mediates partial Tph2 inactivation in interaction with severe stress experience, thus resulting in excessive female aggression.
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Affiliation(s)
- Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Oleg Moskvin
- Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Singapore Medical School, BluMaiden Biosciences, Singapore, Singapore
| | - Aayushi Y Jain
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Nikita Gorbunov
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Anna Gorlova
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Daria Sadovnik
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Aleksei Umriukhin
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
| | - Raymond Cespuglio
- Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine and Department of Normal Physiology, Sechenov Moscow State Medical University, Moscow, Russia
- Neuroscience Research Center of Lyon, Beliv Plateau, Claude-Bernard Lyon-1 University, Bron, France
| | - Wing Shan Yu
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anna Chung Kwan Tse
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Allan V Kalueff
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany.
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.
| | - Lee Wei Lim
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China.
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7
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Scala JJ, Ganz AB, Snyder MP. Precision Medicine Approaches to Mental Health Care. Physiology (Bethesda) 2023; 38:0. [PMID: 36099270 PMCID: PMC9870582 DOI: 10.1152/physiol.00013.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023] Open
Abstract
Developing a more comprehensive understanding of the physiological underpinnings of mental illness, precision medicine has the potential to revolutionize psychiatric care. With recent breakthroughs in next-generation multi-omics technologies and data analytics, it is becoming more feasible to leverage multimodal biomarkers, from genetic variants to neuroimaging biomarkers, to objectify diagnostics and treatment decisions in psychiatry and improve patient outcomes. Ongoing work in precision psychiatry will parallel progress in precision oncology and cardiology to develop an expanded suite of blood- and neuroimaging-based diagnostic tests, empower monitoring of treatment efficacy over time, and reduce patient exposure to ineffective treatments. The emerging model of precision psychiatry has the potential to mitigate some of psychiatry's most pressing issues, including improving disease classification, lengthy treatment duration, and suboptimal treatment outcomes. This narrative-style review summarizes some of the emerging breakthroughs and recurring challenges in the application of precision medicine approaches to mental health care.
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Affiliation(s)
- Jack J Scala
- Department of Genetics, Stanford University, Stanford, California
| | - Ariel B Ganz
- Department of Genetics, Stanford University, Stanford, California
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California
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8
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Paoli C, Misztak P, Mazzini G, Musazzi L. DNA Methylation in Depression and Depressive-Like Phenotype: Biomarker or Target of Pharmacological Intervention? Curr Neuropharmacol 2022; 20:2267-2291. [PMID: 35105292 PMCID: PMC9890294 DOI: 10.2174/1570159x20666220201084536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 12/29/2022] Open
Abstract
Major depressive disorder (MDD) is a debilitating psychiatric disorder, the third leading global cause of disability. Regarding aetiopathogenetic mechanisms involved in the onset of depressive disorders, the interaction between genetic vulnerability traits and environmental factors is believed to play a major role. Although much is still to be elucidated about the mechanisms through which the environment can interact with genetic background shaping the disease risk, there is a general agreement about a key role of epigenetic marking. In this narrative review, we focused on the association between changes in DNA methylation patterns and MDD or depressive-like phenotype in animal models, as well as mechanisms of response to antidepressant drugs. We discussed studies presenting DNA methylation changes at specific genes of interest and profiling analyses in both patients and animal models of depression. Overall, we collected evidence showing that DNA methylation could not only be considered as a promising epigenetic biomarker of pathology but could also help in predicting antidepressant treatment efficacy. Finally, we discussed the hypothesis that specific changes in DNA methylation signature could play a role in aetiopathogenetic processes as well as in the induction of antidepressant effect.
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Affiliation(s)
- Caterina Paoli
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- School of Pharmacy, Pharmacy Unit, University of Camerino, 62032 Camerino, Italy
| | - Paulina Misztak
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Giulia Mazzini
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Laura Musazzi
- Department of Medicine and Surgery, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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9
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Haas-Neill S, Iwashita E, Dvorkin-Gheva A, Forsythe P. Effects of Two Distinct Psychoactive Microbes, Lacticaseibacillus rhamnosus JB-1 and Limosilactobacillus reuteri 6475, on Circulating and Hippocampal mRNA in Male Mice. Int J Mol Sci 2022; 23:ijms23179653. [PMID: 36077051 PMCID: PMC9456087 DOI: 10.3390/ijms23179653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Discovery of the microbiota-gut–brain axis has led to proposed microbe-based therapeutic strategies in mental health, including the use of mood-altering bacterial species, termed psychobiotics. However, we still have limited understanding of the key signaling pathways engaged by specific organisms in modulating brain function, and evidence suggests that bacteria with broadly similar neuroactive and immunomodulatory actions can drive different behavioral outcomes. We sought to identify pathways distinguishing two psychoactive bacterial strains that seemingly engage similar gut–brain signaling pathways but have distinct effects on behaviour. We used RNAseq to identify mRNAs differentially expressed in the blood and hippocampus of mice following Lacticaseibacillus rhamnosus JB-1, and Limosilactobacillus reuteri 6475 treatment and performed Gene Set Enrichment Analysis (GSEA) to identify enrichment in pathway activity. L. rhamnosus, but not L. reuteri treatment altered several pathways in the blood and hippocampus, and the rhamnosus could be clearly distinguished based on mRNA profile. In particular, L. rhamnosus treatment modulated the activity of interferon signaling, JAK/STAT, and TNF-alpha via NF-KB pathways. Our results highlight that psychobiotics can induce complex changes in host gene expression, andin understanding these changes, we may help fine-tune selection of psychobiotics for treating mood disorders.
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Affiliation(s)
- Sandor Haas-Neill
- The Brain Body Institute, St. Joseph’s Hospital, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Eiko Iwashita
- The Brain Body Institute, St. Joseph’s Hospital, McMaster University, Hamilton, ON L8N 4A6, Canada
| | - Anna Dvorkin-Gheva
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Paul Forsythe
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, 569 Heritage Medical Research Center, Edmonton, AB T6G 2S2, Canada
- Alberta Respiratory Centre, University of Alberta, Edmonton, AB T6G 1H9, Canada
- Correspondence:
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10
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Elevated BICD2 DNA methylation in blood of major depressive disorder patients and reduction of depressive-like behaviors in hippocampal Bicd2-knockdown mice. Proc Natl Acad Sci U S A 2022; 119:e2201967119. [PMID: 35858435 PMCID: PMC9335189 DOI: 10.1073/pnas.2201967119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Major depressive disorder (MDD) is a prevalent and devastating mental illness. To date, the diagnosis of MDD is largely dependent on clinical interviews and questionnaires and still lacks a reliable biomarker. DNA methylation has a stable and reversible nature and is likely associated with the course and therapeutic efficacy of complex diseases, which may play an important role in the etiology of a disease. Here, we identified and validated a DNA methylation biomarker for MDD from four independent cohorts of the Chinese Han population. First, we integrated the analysis of the DNA methylation microarray (n = 80) and RNA expression microarray data (n = 40) and identified BICD2 as the top-ranked gene. In the replication phase, we employed the Sequenom MassARRAY method to confirm the DNA hypermethylation change in a large sample size (n = 1,346) and used the methylation-sensitive restriction enzymes and a quantitative PCR approach (MSE-qPCR) and qPCR method to confirm the correlation between DNA hypermethylation and mRNA down-regulation of BICD2 (n = 60). The results were replicated in the peripheral blood of mice with depressive-like behaviors, while in the hippocampus of mice, Bicd2 showed DNA hypomethylation and mRNA/protein up-regulation. Hippocampal Bicd2 knockdown demonstrates antidepressant action in the chronic unpredictable mild stress (CUMS) mouse model of depression, which may be mediated by increased BDNF expression. Our study identified a potential DNA methylation biomarker and investigated its functional implications, which could be exploited to improve the diagnosis and treatment of MDD.
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Abstract
Epigenetic mechanisms such as DNA methylation (DNAm) have been associated with stress responses and increased vulnerability to depression. Abnormal DNAm is observed in stressed animals and depressed individuals. Antidepressant treatment modulates DNAm levels and regulates gene expression in diverse tissues, including the brain and the blood. Therefore, DNAm could be a potential therapeutic target in depression. Here, we reviewed the current knowledge about the involvement of DNAm in the behavioural and molecular changes associated with stress exposure and depression. We also evaluated the possible use of DNAm changes as biomarkers of depression. Finally, we discussed current knowledge limitations and future perspectives.
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12
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Medeiros de Araújo JA, Barão S, Mateos-White I, Espinosa A, Costa MR, Gil-Sanz C, Müller U. ZBTB20 is crucial for the specification of a subset of callosal projection neurons and astrocytes in the mammalian neocortex. Development 2021; 148:271200. [PMID: 34351428 DOI: 10.1242/dev.196642] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 07/17/2021] [Indexed: 12/25/2022]
Abstract
Neocortical progenitor cells generate subtypes of excitatory projection neurons in sequential order followed by the generation of astrocytes. The transcription factor zinc finger and BTB domain-containing protein 20 (ZBTB20) has been implicated in regulation of cell specification during neocortical development. Here, we show that ZBTB20 instructs the generation of a subset of callosal projections neurons in cortical layers II/III in mouse. Conditional deletion of Zbtb20 in cortical progenitors, and to a lesser degree in differentiating neurons, leads to an increase in the number of layer IV neurons at the expense of layer II/III neurons. Astrogliogenesis is also affected in the mutants with an increase in the number of a specific subset of astrocytes expressing GFAP. Astrogliogenesis is more severely disrupted by a ZBTB20 protein containing dominant mutations linked to Primrose syndrome, suggesting that ZBTB20 acts in concert with other ZBTB proteins that were also affected by the dominant-negative protein to instruct astrogliogenesis. Overall, our data suggest that ZBTB20 acts both in progenitors and in postmitotic cells to regulate cell fate specification in the mammalian neocortex.
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Affiliation(s)
- Jéssica Alves Medeiros de Araújo
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59056-450, Brazil
| | - Soraia Barão
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Isabel Mateos-White
- BIOTECMED Institute, Universidad de Valencia, Burjassot, Valencia 46100, Spain
| | - Ana Espinosa
- AntalGenics, Quorum Building III, Scientific Park - UMH. Avda. de la Universidad, s/n. 03202 Elche (Alicante), Spain
| | - Marcos Romualdo Costa
- Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59056-450, Brazil.,Unité INSERM 1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, University of Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille Cedex 59019, France
| | - Cristina Gil-Sanz
- BIOTECMED Institute, Universidad de Valencia, Burjassot, Valencia 46100, Spain
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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13
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Abstract
Epigenetics has enriched human disease studies by adding new interpretations to disease features that cannot be explained by genetic and environmental factors. However, identifying causal mechanisms of epigenetic origin has been challenging. New opportunities have risen from recent findings in intra-individual and cyclical epigenetic variation, which includes circadian epigenetic oscillations. Cytosine modifications display deterministic temporal rhythms, which may drive ageing and complex disease. Temporality in the epigenome, or the 'chrono' dimension, may help the integration of epigenetic, environmental and genetic disease studies, and reconcile several disparities stemming from the arbitrarily delimited research fields. The ultimate goal of chrono-epigenetics is to predict disease risk, age of onset and disease dynamics from within individual-specific temporal dynamics of epigenomes.
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14
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Distinct epigenetic signatures between adult-onset and late-onset depression. Sci Rep 2021; 11:2296. [PMID: 33504850 PMCID: PMC7840753 DOI: 10.1038/s41598-021-81758-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
The heterogeneity of major depressive disorder (MDD) is attributed to the fact that diagnostic criteria (e.g., DSM-5) are only based on clinical symptoms. The discovery of blood biomarkers has the potential to change the diagnosis of MDD. The purpose of this study was to identify blood biomarkers of DNA methylation by strategically subtyping patients with MDD by onset age. We analyzed genome-wide DNA methylation of patients with adult-onset depression (AOD; age ≥ 50 years, age at depression onset < 50 years; N = 10) and late-onset depression (LOD; age ≥ 50 years, age at depression onset ≥ 50 years; N = 25) in comparison to that of 30 healthy subjects. The methylation profile of the AOD group was not only different from that of the LOD group but also more homogenous. Six identified methylation CpG sites were validated by pyrosequencing and amplicon bisulfite sequencing as potential markers for AOD in a second set of independent patients with AOD and healthy control subjects (N = 11). The combination of three specific methylation markers achieved the highest accuracy (sensitivity, 64%; specificity, 91%; accuracy, 77%). Taken together, our findings suggest that DNA methylation markers are more suitable for AOD than for LOD patients.
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15
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Yin L, Zhu X, Novák P, Zhou L, Gao L, Yang M, Zhao G, Yin K. The epitranscriptome of long noncoding RNAs in metabolic diseases. Clin Chim Acta 2021; 515:80-89. [PMID: 33422492 DOI: 10.1016/j.cca.2021.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have abundant content and extensive functions that regulate the expression of genes at multiple levels. Recently, transcriptome-wide analysis confirmed that RNA can undergo various chemical modifications in response to stimulation by the environment that further determine the action mechanisms of RNAs and expand the diversity of the transcriptome. Modifications that occur in lncRNAs can affect their expression and the regulation of downstream molecules by changing the secondary structure, splicing, degradation or molecular stability of lncRNAs. During the development of metabolic diseases, reversible RNA modifications show a complex transcriptional landscape. Although a wide quantity and variety of lncRNA modifications have been identified, the knowledge regarding their underlying actions in alcohol use disorders (AUDs), osteoporosis, obesity, and cardiovascular disease (CVD) is still in its infancy. Herein, we will focus on the epitranscriptomic modifications that occur on lncRNAs and the crosstalk between them that affect metabolic diseases.
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Affiliation(s)
- Linjie Yin
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Xiao Zhu
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Petr Novák
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Le Zhou
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Ling Gao
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China
| | - Min Yang
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - GuoJun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People's Hospital, Qingyuan 511518, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China.
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16
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Ward J, Tunbridge EM, Sandor C, Lyall LM, Ferguson A, Strawbridge RJ, Lyall DM, Cullen B, Graham N, Johnston KJA, Webber C, Escott-Price V, O'Donovan M, Pell JP, Bailey MES, Harrison PJ, Smith DJ. The genomic basis of mood instability: identification of 46 loci in 363,705 UK Biobank participants, genetic correlation with psychiatric disorders, and association with gene expression and function. Mol Psychiatry 2020; 25:3091-3099. [PMID: 31168069 PMCID: PMC7116257 DOI: 10.1038/s41380-019-0439-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/03/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023]
Abstract
Genome-wide association studies (GWAS) of psychiatric phenotypes have tended to focus on categorical diagnoses, but to understand the biology of mental illness it may be more useful to study traits which cut across traditional boundaries. Here, we report the results of a GWAS of mood instability as a trait in a large population cohort (UK Biobank, n = 363,705). We also assess the clinical and biological relevance of the findings, including whether genetic associations show enrichment for nervous system pathways. Forty six unique loci associated with mood instability were identified with a SNP heritability estimate of 9%. Linkage Disequilibrium Score Regression (LDSR) analyses identified genetic correlations with Major Depressive Disorder (MDD), Bipolar Disorder (BD), Schizophrenia, anxiety, and Post Traumatic Stress Disorder (PTSD). Gene-level and gene set analyses identified 244 significant genes and 6 enriched gene sets. Tissue expression analysis of the SNP-level data found enrichment in multiple brain regions, and eQTL analyses highlighted an inversion on chromosome 17 plus two brain-specific eQTLs. In addition, we used a Phenotype Linkage Network (PLN) analysis and community analysis to assess for enrichment of nervous system gene sets using mouse orthologue databases. The PLN analysis found enrichment in nervous system PLNs for a community containing serotonin and melatonin receptors. In summary, this work has identified novel loci, tissues and gene sets contributing to mood instability. These findings may be relevant for the identification of novel trans-diagnostic drug targets and could help to inform future stratified medicine innovations in mental health.
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Affiliation(s)
- Joey Ward
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Cynthia Sandor
- UK Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Laura M Lyall
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Amy Ferguson
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Donald M Lyall
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Breda Cullen
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Nicholas Graham
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | | | - Caleb Webber
- UK Dementia Research Institute, Cardiff University, Cardiff, UK
- Department of Physiology, Anatomy and Genetics, Oxford, UK
| | | | | | - Jill P Pell
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Mark E S Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Daniel J Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK.
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17
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Aberg KA, Dean B, Shabalin AA, Chan RF, Han LK, Zhao M, van Grootheest G, Xie LY, Milaneschi Y, Clark SL, Turecki G, Penninx BW, van den Oord EJ. Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples. Mol Psychiatry 2020; 25:1344-1354. [PMID: 30242228 PMCID: PMC6428621 DOI: 10.1038/s41380-018-0247-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/26/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
We present the first large-scale methylome-wide association studies (MWAS) for major depressive disorder (MDD) to identify sites of potential importance for MDD etiology. Using a sequencing-based approach that provides near-complete coverage of all 28 million common CpGs in the human genome, we assay methylation in MDD cases and controls from both blood (N = 1132) and postmortem brain tissues (N = 61 samples from Brodmann Area 10, BA10). The MWAS for blood identified several loci with P ranging from 1.91 × 10-8 to 4.39 × 10-8 and a resampling approach showed that the cumulative association was significant (P = 4.03 × 10-10) with the signal coming from the top 25,000 MWAS markers. Furthermore, a permutation-based analysis showed significant overlap (P = 5.4 × 10-3) between the MWAS findings in blood and brain (BA10). This overlap was significantly enriched for a number of features including being in eQTLs in blood and the frontal cortex, CpG islands and shores, and exons. The overlapping sites were also enriched for active chromatin states in brain including genic enhancers and active transcription start sites. Furthermore, three loci located in GABBR2, RUFY3, and in an intergenic region on chromosome 2 replicated with the same direction of effect in the second brain tissue (BA25, N = 60) from the same individuals and in two independent brain collections (BA10, N = 81 and 64). GABBR2 inhibits neuronal activity through G protein-coupled second-messenger systems and RUFY3 is implicated in the establishment of neuronal polarity and axon elongation. In conclusion, we identified and replicated methylated loci associated with MDD that are involved in biological functions of likely importance to MDD etiology.
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Affiliation(s)
- Karolina A. Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA,Correspondence should be addressed to: Karolina A. Aberg, P.O. Box 980533, Richmond, VA 23298, Phone: (804) 628-3023, Fax: (804) 628-3991,
| | - Brian Dean
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia,Centre for Mental Health, Swinburne University, Hawthorn, Victoria, Australia
| | - Andrey A. Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Robin F. Chan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Laura K.M. Han
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Gerard van Grootheest
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Lin Y. Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Shaunna L. Clark
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Gustavo Turecki
- Douglas Mental Health University Institute and McGill University, Montréal, Québec, Canada
| | - Brenda W.J.H. Penninx
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Edwin J.C.G. van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
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18
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Policicchio S, Washer S, Viana J, Iatrou A, Burrage J, Hannon E, Turecki G, Kaminsky Z, Mill J, Dempster EL, Murphy TM. Genome-wide DNA methylation meta-analysis in the brains of suicide completers. Transl Psychiatry 2020; 10:69. [PMID: 32075955 PMCID: PMC7031296 DOI: 10.1038/s41398-020-0752-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
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Affiliation(s)
- Stefania Policicchio
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Sam Washer
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana Viana
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Artemis Iatrou
- grid.240684.c0000 0001 0705 3621Rush Alzheimer’s Neurodisease Center, Rush University Medical Center, 600 South Paulina Street, Chicago, IL 60612 USA
| | - Joe Burrage
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gustavo Turecki
- grid.14709.3b0000 0004 1936 8649Douglas Institute, Department of Psychiatry, McGill University, Verdun, QC H4H 1R3 Canada
| | - Zachary Kaminsky
- grid.21107.350000 0001 2171 9311Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L. Dempster
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Therese M. Murphy
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK ,grid.497880.aSchool of Biological and Health Sciences, Technological University Dublin, City Campus, Dublin, 2 Ireland
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19
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Twin study designs as a tool to identify new candidate genes for depression: A systematic review of DNA methylation studies. Neurosci Biobehav Rev 2020; 112:345-352. [PMID: 32068032 DOI: 10.1016/j.neubiorev.2020.02.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Monozygotic (MZ) twin studies constitute a key resource for the dissection of environmental and biological risk factors for human complex disorders. Given that epigenetic differences accumulate throughout the lifespan, the assessment of MZ twin pairs discordant for depression offers a genetically informative design to explore DNA methylation while accounting for the typical confounders of the field, shared by co-twins of a pair. In this review, we systematically evaluate all twin studies published to date assessing DNA methylation in association with depressive phenotypes. However, difficulty to recruit large numbers of MZ twin pairs fails to provide enough sample size to develop genome-wide approaches. Alternatively, region and pathway analysis revealed an enrichment for nervous system related functions; likewise, evidence supports an accumulation of methylation variability in affected subjects when compared to their co-twins. Nevertheless, longitudinal studies incorporating known risk factors for depression such as childhood trauma are required for understanding the role that DNA methylation plays in the etiology of depression.
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20
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Tenorio J, Nevado J, González-Meneses A, Arias P, Dapía I, Venegas-Vega CA, Calvente M, Hernández A, Landera L, Ramos S, Cigudosa JC, Pérez-Jurado LA, Lapunzina P. Further definition of the proximal 19p13.3 microdeletion/microduplication syndrome and implication of PIAS4 as the major contributor. Clin Genet 2020; 97:467-476. [PMID: 31972898 DOI: 10.1111/cge.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 12/15/2022]
Abstract
The proximal 19p13.3 microdeletion/microduplication (prox19p13.3del/dup) syndrome is a recently described disorder with common clinical features including developmental delay, intellectual disability, speech delay, facial dysmorphic features with ear defects, anomalies of the hands and feet, umbilical hernia and hypotonia. While deletions are associated with macrocephaly, patients with duplications have microcephaly. The smallest region of overlap in multiple patients (113.5 kb) included three genes and one pseudogene, with a suggested major role of PIAS4 in determination of the phenotype and head size in these patients. Here, we refine the prox19p13.3del/dup with four additional patients: two with microdeletions, one with microduplication and one family with single-nucleotide nonsense variant in PIAS4. The patient with the PIAS4 loss of function variant displayed a phenotype quite similar to deletion patients -including the macrocephaly and many other core features of the syndrome. Patient's SNV was inherited from her mother who is similarly affected. Thus, our data indicate that PIAS4 is a major contributor to the proximal 19p13.3del/dup syndrome phenotype. In summary, we report the first patient with a pathogenic variant in PIAS4- and three additional rearrangements at the proximal 19p13.3 locus. These observations add further evidence about the molecular basis of this microdeletion/microduplication syndrome.
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Affiliation(s)
- Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Antonio González-Meneses
- Dysmorphology and Metabolism unit, Hospital Universitario Virgen del Rocío, Av. Manuel Siurot, Sevilla, Spain
| | - Pedro Arias
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Irene Dapía
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Carlos A Venegas-Vega
- Unidadde Genética, Hospital General de México, México City, Mexico, Facultad deMedicina, Universidad Nacional Autónoma de México, México City, Mexico
| | - María Calvente
- NIMGENETICS, c/ Faraday, 7 Parque Científico de Madrid, Madrid, Spain
| | - Alicia Hernández
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Leandro Landera
- Congenital Malformations Laboratory, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho, Rio deJaneiro, Brazil
| | - Sergio Ramos
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | -
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | | | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra, and IMIM-Hospital del Mar, Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI), The University of Adelaide, Adelaide, Australia
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
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21
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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22
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Bhak Y, Jeong HO, Cho YS, Jeon S, Cho J, Gim JA, Jeon Y, Blazyte A, Park SG, Kim HM, Shin ES, Paik JW, Lee HW, Kang W, Kim A, Kim Y, Kim BC, Ham BJ, Bhak J, Lee S. Depression and suicide risk prediction models using blood-derived multi-omics data. Transl Psychiatry 2019; 9:262. [PMID: 31624227 PMCID: PMC6797735 DOI: 10.1038/s41398-019-0595-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
More than 300 million people worldwide experience depression; annually, ~800,000 people die by suicide. Unfortunately, conventional interview-based diagnosis is insufficient to accurately predict a psychiatric status. We developed machine learning models to predict depression and suicide risk using blood methylome and transcriptome data from 56 suicide attempters (SAs), 39 patients with major depressive disorder (MDD), and 87 healthy controls. Our random forest classifiers showed accuracies of 92.6% in distinguishing SAs from MDD patients, 87.3% in distinguishing MDD patients from controls, and 86.7% in distinguishing SAs from controls. We also developed regression models for predicting psychiatric scales with R2 values of 0.961 and 0.943 for Hamilton Rating Scale for Depression-17 and Scale for Suicide Ideation, respectively. Multi-omics data were used to construct psychiatric status prediction models for improved mental health treatment.
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Affiliation(s)
- Youngjune Bhak
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea ,Clinomics Inc., Ulsan, 44919 Republic of Korea
| | - Hyoung-oh Jeong
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | | | - Sungwon Jeon
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Juok Cho
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Jeong-An Gim
- 0000 0004 0470 5905grid.31501.36Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, 16229 Republic of Korea
| | - Yeonsu Jeon
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea
| | - Asta Blazyte
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Seung Gu Park
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Hak-Min Kim
- 0000 0004 0381 814Xgrid.42687.3fKorean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea ,0000 0004 0381 814Xgrid.42687.3fDepartment of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919 Republic of Korea ,Clinomics Inc., Ulsan, 44919 Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan, Republic of Korea
| | - Jong-Woo Paik
- 0000 0001 2171 7818grid.289247.2Department of Neuropsychiatry, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hae-Woo Lee
- 0000 0004 0642 340Xgrid.415520.7Department of Psychiatry, Seoul Medical Center, Seoul, Republic of Korea
| | - Wooyoung Kang
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aram Kim
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Yumi Kim
- Clinomics Inc., Ulsan, 44919 Republic of Korea
| | | | - Byung-Joo Ham
- 0000 0001 0840 2678grid.222754.4Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea ,0000 0004 0474 0479grid.411134.2Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea ,0000 0004 0474 0479grid.411134.2Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Jong Bhak
- Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919, Republic of Korea. .,Clinomics Inc., Ulsan, 44919, Republic of Korea. .,Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea.
| | - Semin Lee
- Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea. .,Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan, 44919, Republic of Korea.
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Abstract
AbstractTwinsUK is the largest cohort of community-dwelling adult twins in the UK. The registry comprises over 14,000 volunteer twins (14,838 including mixed, single and triplets); it is predominantly female (82%) and middle-aged (mean age 59). In addition, over 1800 parents and siblings of twins are registered volunteers. During the last 27 years, TwinsUK has collected numerous questionnaire responses, physical/cognitive measures and biological measures on over 8500 subjects. Data were collected alongside four comprehensive phenotyping clinical visits to the Department of Twin Research and Genetic Epidemiology, King’s College London. Such collection methods have resulted in very detailed longitudinal clinical, biochemical, behavioral, dietary and socioeconomic cohort characterization; it provides a multidisciplinary platform for the study of complex disease during the adult life course, including the process of healthy aging. The major strength of TwinsUK is the availability of several ‘omic’ technologies for a range of sample types from participants, which includes genomewide scans of single-nucleotide variants, next-generation sequencing, metabolomic profiles, microbiomics, exome sequencing, epigenetic markers, gene expression arrays, RNA sequencing and telomere length measures. TwinsUK facilitates and actively encourages sharing the ‘TwinsUK’ resource with the scientific community — interested researchers may request data via the TwinsUK website (http://twinsuk.ac.uk/resources-for-researchers/access-our-data/) for their own use or future collaboration with the study team. In addition, further cohort data collection is planned via the Wellcome Open Research gateway (https://wellcomeopenresearch.org/gateways). The current article presents an up-to-date report on the application of technological advances, new study procedures in the cohort and future direction of TwinsUK.
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24
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The epigenome of twins as a perfect laboratory for studying behavioural traits. Neurosci Biobehav Rev 2019; 107:192-195. [PMID: 31536737 DOI: 10.1016/j.neubiorev.2019.09.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 01/04/2023]
Abstract
The debate upon the relative importance of nature vs nurture in the development of human behaviour can be traced back to ancient times. Traditional epidemiology and genetic epidemiology have confirmed the association of environmental and genetic factors with behavioural traits. Current genomic studies are identifying genetic variants associated with various behavioural traits. However, exploring the relationship of abundant environmental factors with the complex epigenome that mediates human behaviour is just at its beginning. Identical twins can serve as perfect experiments for studying the environmental impact on behavioural epigenetics advantaged by enriched power in association analysis due to controlling of their genetic make-ups. Recent development in causal inference using twin-based models adds more values in twins. This review briefly introduces the various approaches in making use of twins in studying behavioural epigenetics from experiment design to practical applications. Exploring the epigenome of twins using the powerful twin-based study designs and analytical approaches will help identifying causal epigenetic markers mediating environmental exposures and behavioural traits enabling both pharmaceutical intervention and effective prevention.
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25
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Zhu Y, Strachan E, Fowler E, Bacus T, Roy-Byrne P, Zhao J. Genome-wide profiling of DNA methylome and transcriptome in peripheral blood monocytes for major depression: A Monozygotic Discordant Twin Study. Transl Psychiatry 2019; 9:215. [PMID: 31477685 PMCID: PMC6718674 DOI: 10.1038/s41398-019-0550-2] [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: 10/05/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
DNA methylation plays an important role in major depressive disorder (MDD), but the specific genes and genomic regions associated with MDD remain largely unknown. Here we conducted genome-wide profiling of DNA methylation (Infinium MethylationEPIC BeadChip) and gene expression (RNA-seq) in peripheral blood monocytes from 79 monozygotic twin pairs (mean age 38.2 ± 15.6 years) discordant on lifetime history of MDD to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with MDD, followed by replication in brain tissue samples. Integrative DNA methylome and transcriptome analysis and network analysis was performed to identify potential functional epigenetic determinants for MDD. We identified 39 DMRs and 30 DEGs associated with lifetime history of MDD. Some genes were replicated in postmortem brain tissue. Integrative DNA methylome and transcriptome analysis revealed both negative and positive correlations between DNA methylation and gene expression, but the correlation pattern varies greatly by genomic locations. Network analysis revealed distinct gene modules enriched in signaling pathways related to stress responses, neuron apoptosis, insulin receptor signaling, mTOR signaling, and nerve growth factor receptor signaling, suggesting potential functional relevance to MDD. These results demonstrated that altered DNA methylation and gene expression in peripheral blood monocytes are associated with MDD. Our results highlight the utility of using peripheral blood epigenetic markers and demonstrate that a monozygotic discordant co-twin control design can aid in the discovery of novel genes associated with MDD. If validated, the newly identified genes may serve as novel biomarkers or druggable targets for MDD and related disorders.
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Affiliation(s)
- Yun Zhu
- 0000 0004 1936 8091grid.15276.37Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL USA
| | - Eric Strachan
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Emily Fowler
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Tamara Bacus
- 0000000122986657grid.34477.33Department of Pediatrics, University of Washington, Seattle, WA USA
| | - Peter Roy-Byrne
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA.
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26
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Friedenson B. A Genome Model to Explain Major Features of Neurodevelopmental Disorders in Newborns. BIOMEDICAL INFORMATICS INSIGHTS 2019; 11:1178222619863369. [PMID: 31391780 PMCID: PMC6669855 DOI: 10.1177/1178222619863369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]
Abstract
The purpose of this study was to test the hypothesis that infections are linked to chromosomal anomalies that cause neurodevelopmental disorders. In children with disorders in the development of their nervous systems, chromosome anomalies known to cause these disorders were compared with foreign DNAs, including known teratogens. Genes essential for neurons, lymphatic drainage, immunity, circulation, angiogenesis, cell barriers, structure, epigenetic and chromatin modifications were all found close together in polyfunctional clusters that were deleted or rearranged in neurodevelopmental disorders. In some patients, epigenetic driver mutations also changed access to large chromosome segments. These changes account for immune, circulatory, and structural deficits that accompany neurologic deficits. Specific and repetitive human DNA encompassing large deletions matched infections and passed rigorous artifact tests. Deletions of up to millions of bases accompanied infection-matching sequences and caused massive changes in human homologies to foreign DNAs. In data from 3 independent studies of private, familial, and recurrent chromosomal rearrangements, massive changes in homologous microbiomes were found and may drive rearrangements and encourage pathogens. At least 1 chromosomal anomaly was found to consist of human DNA fragments with a gap that corresponded to a piece of integrated foreign DNA. Microbial DNAs that match repetitive or specific human DNA segments are thus proposed to interfere with the epigenome and highly active recombination during meiosis, driven by massive changes in human DNA-foreign DNA homologies. Abnormal recombination in gametes produces zygotes containing rare chromosome anomalies that cause neurologic disorders and nonneurologic signs. Neurodevelopmental disorders may be examples of assault on the human genome by foreign DNAs at a critical stage. Some infections may be more likely tolerated because they resemble human DNA segments. Even rare developmental disorders can be screened for homology to infections within altered epigenomes and chromatin structures. Considering effects of foreign DNAs can assist prenatal and genetic counseling, diagnosis, prevention, and early intervention.
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Affiliation(s)
- Bernard Friedenson
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, IL, USA
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27
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Braun PR, Tanaka-Sahker M, Chan AC, Jellison SS, Klisares MJ, Hing BW, Shabbir Y, Gaul LN, Nagahama Y, Robles J, Heinzman JT, Sabbagh S, Cramer EM, Duncan GN, Yuki K, Close LN, Dlouhy BJ, Howard MA, Kawasaki H, Stein KM, Potash JB, Shinozaki G. Genome-wide DNA methylation investigation of glucocorticoid exposure within buccal samples. Psychiatry Clin Neurosci 2019; 73:323-330. [PMID: 30821055 PMCID: PMC6561812 DOI: 10.1111/pcn.12835] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/20/2019] [Accepted: 02/26/2019] [Indexed: 12/19/2022]
Abstract
AIM Glucocorticoids play a major role in regulating the stress response, and an imbalance of glucocorticoids has been implicated in stress-related disorders. Within mouse models, CpGs across the genome have been shown to be differentially methylated in response to glucocorticoid treatment, and using the Infinium 27K array, it was shown that humans given synthetic glucocorticoids had DNA methylation (DNAm) changes in blood. However, further investigation of the extent to which glucocorticoids affect DNAm across a larger proportion of the genome is needed. METHODS Buccal samples were collected before and after synthetic glucocorticoid treatment in the context of a dental procedure. This included 30 tooth extraction surgery patients who received 10 mg of dexamethasone. Genome-wide DNAm was assessed with the Infinium HumanMethylationEPIC array. RESULTS Five CpGs showed genome-wide significant DNAm changes that were >10%. These differentially methylated CpGs were in or nearest the following genes: ZNF438, KLHDC10, miR-544 or CRABP1, DPH5, and WDFY2. Using previously published datasets of human blood gene expression changes following dexamethasone exposure, a significant proportion of genes with false-discovery-rate-adjusted significant CpGs were also differentially expressed. A pathway analysis of the genes with false-discovery-rate-adjusted significant CpGs revealed significant enrichment of olfactory transduction, pentose and glucuronate interconversions, ascorbate and aldarate metabolism, and steroid hormone biosynthesis pathways. CONCLUSION High-dose synthetic glucocorticoid administration in the setting of a dental procedure was significantly associated with DNAm changes within buccal samples. These findings are consistent with prior findings of an influence of glucocorticoids on DNAm in humans.
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Affiliation(s)
- Patricia R Braun
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA.,Department of Psychiatry and Behavioral Science, School of Medicine, Johns Hopkins University, Baltimore, USA
| | - Mai Tanaka-Sahker
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Aubrey C Chan
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Sydney S Jellison
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mason J Klisares
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Benjamin W Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Yaseen Shabbir
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Lindsey N Gaul
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Yasunori Nagahama
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Julian Robles
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Jonathan T Heinzman
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Sayeh Sabbagh
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Ellyn M Cramer
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Gabrielle N Duncan
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Kumi Yuki
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Liesl N Close
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Brian J Dlouhy
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Matthew A Howard
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Kyle M Stein
- Department of Oral and Maxillofacial Surgery, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - James B Potash
- Department of Psychiatry and Behavioral Science, School of Medicine, Johns Hopkins University, Baltimore, USA
| | - Gen Shinozaki
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, USA.,Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, USA.,Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, USA.,Interdisciplinary Graduate Program for Neuroscience, Carver College of Medicine, University of Iowa, Iowa City, USA
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28
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What do DNA methylation studies tell us about depression? A systematic review. Transl Psychiatry 2019; 9:68. [PMID: 30718449 PMCID: PMC6362194 DOI: 10.1038/s41398-019-0412-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 11/09/2022] Open
Abstract
There has been a limited number of systematic reviews conducted to summarize the overview of the relationship between DNA methylation and depression, and to critically appraise the roles of major study characteristics in the accuracy of study findings. This systematic review aims to critically appraise the impact of study characteristics on the association between DNA methylation and depression, and summarize the overview of this association. Electronic databases and gray literatures until December 2017 were searched for English-language studies with standard diagnostic criteria of depression. A total of 67 studies were included in this review along with a summary of their study characteristics. We grouped the findings into etiological and treatment studies. Majority of these selected studies were recently published and from developed countries. Whole blood samples were the most studied common tissues. Bisulfite conversion, along with pyrosequencing, was widely used to test the DNA methylation level across all the studies. High heterogeneity existed among the studies in terms of experimental and statistical methodologies and study designs. As recommended by the Cochrane guideline, a systematic review without meta-analysis should be undertaken. This review has, in general, found that DNA methylation modifications were associated with depression. Subgroup analyses showed that most studies found BDNF and SLC6A4 hypermethylations to be associated with MDD or depression in general. In contrast, studies on NR3C1, OXTR, and other genes, which were tested by only few studies, reported mixed findings. More longitudinal studies using standardized experimental and laboratory methodologies are needed in future studies to enable more systematical comparisons and quantitative synthesis.
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29
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Genetic loci for alcohol-related life events and substance-induced affective symptoms: indexing the "dark side" of addiction. Transl Psychiatry 2019; 9:71. [PMID: 30718457 PMCID: PMC6362044 DOI: 10.1038/s41398-019-0397-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/17/2019] [Indexed: 12/24/2022] Open
Abstract
A limited number of genetic variants have been identified in traditional GWAS as risk or protective factors for alcohol use disorders (AUD) and related phenotypes. We herein report whole-genome association and rare-variant analyses on AUD traits in American Indians (AI) and European Americans (EA). We evaluated 742 AIs and 1711 EAs using low-coverage whole-genome sequencing. Phenotypes included: (1) a metric based on the occurrence of 36 alcohol-related life events that reflect AUD severity; (2) two alcohol-induced affective symptoms that accompany severe AUDs. We identified two new loci for alcohol-related life events with converging evidence from both cohorts: rare variants of K2P channel gene KCNK2, and rare missense and splice-site variants in pro-inflammatory mediator gene PDE4C. A NAF1-FSTL5 intergenic variant and an FSTL5 variant were respectively associated with alcohol-related life events in AI and EA. PRKG2 of serine/threonine protein kinase family, and rare variants in interleukin subunit gene EBI3 (IL-27B) were uniquely associated with alcohol-induced affective symptoms in AI. LncRNA LINC02347 on 12q24.32 was uniquely associated with alcohol-induced depression in EA. The top GWAS findings were primarily rare/low-frequency variants in AI, and common variants in EA. Adrenal gland was the most enriched in tissue-specific gene expression analysis for alcohol-related life events, and nucleus accumbens was the most enriched for alcohol-induced affective states in AI. Prefrontal cortex was the most enriched in EA for both traits. These studies suggest that whole-genome sequencing can identify novel, especially uncommon, variants associated with severe AUD phenotypes although the findings may be population specific.
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30
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Thaweethee-Sukjai B, Suttajit S, Thanoi S, Dalton CF, Reynolds GP, Nudmamud-Thanoi S. Parvalbumin Promoter Methylation Altered in Major Depressive Disorder. Int J Med Sci 2019; 16:1207-1214. [PMID: 31588185 PMCID: PMC6775273 DOI: 10.7150/ijms.36131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022] Open
Abstract
Aims: To determine the extent of DNA methylation of parvalbumin gene (PVALB) promoter in major depressive disorder (MDD) patients with and without suicide attempt in comparison with healthy controls. Methods: The extracted DNA from dried blood spots of MDD patients (n = 92) including non-suicidal MDD and suicidal-MDD subgroups (n = 45 and n = 47, respectively) and age-matched control subjects (n = 95) was used for DNA methylation analysis at four CpG sites in the promoter sequence of PVALB by pyrosequencing. Results: The PVALB methylation was significantly increased at CpG2 and decreased at CpG4 in the MDD group compared to the control group, while there was no difference between non-suicidal MDD and suicidal-MDD subgroups. A significant inverse correlation of severity of MDD was indicated only for CpG4. Conclusion: This study provides the first evidence of abnormalities of PVALB promoter methylation in MDD and its correlation with MDD severity indicating a role for epigenetics in this psychiatric disorder.
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Affiliation(s)
- Benjamard Thaweethee-Sukjai
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sirijit Suttajit
- Department of Psychiatry, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Samur Thanoi
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Caroline F Dalton
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Gavin P Reynolds
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.,Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Sutisa Nudmamud-Thanoi
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.,Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
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31
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Study Design and Rationale for the Mood and Methylation Study: A Platform for Multi-Omics Investigation of Depression in Twins. Twin Res Hum Genet 2018; 21:507-513. [DOI: 10.1017/thg.2018.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Major depression is a complex disorder with no single, direct causal mechanism. Morbidity has been linked to genetic processes, developmental history, and unique environmental exposures. Epigenetic mechanisms, especially DNA methylation, are also likely important factors in the pathogenesis of major depressive disorder (MDD). A community-based twin sample has many advantages for epigenetic studies, given the shared genetic and developmental histories of same-sex twin pairs. This article describes the rationale and study design for the Mood and Methylation Study in which 133 twin pairs (101 monozygotic and 32 dizygotic), both discordant and concordant for lifetime history of MDD, were evaluated on a large number of variables related to MDD. The twins also provided blood samples for an epigenome-wide association study of differentially methylated regions (DMR) relevant to MDD. Although MDD is typically considered a disorder of the central nervous system, it is unfeasible to obtain a large sample of brain tissues. However, epigenetic variation is not limited to the affected tissue but can also be detected in peripheral blood leukocytes. Thus, this study focused on monocytes for the major analyses. Additional plans for the study include gene expression analysis from the same set of twins using RNA-seq and validation of significant DMRs in postmortem brain tissues from a separate sample. Moreover, sufficient samples have been collected to perform future ‘multi-omic’ analyses, including metabolome, microbiome, and transcriptome. Our long-term goal is to understand how epigenomic and other ‘omic’ factors can be manipulated for diagnostic, preventive, and therapeutic purposes for MDD and its related conditions.
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32
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Epigenetic outlier profiles in depression: A genome-wide DNA methylation analysis of monozygotic twins. PLoS One 2018; 13:e0207754. [PMID: 30458022 PMCID: PMC6245788 DOI: 10.1371/journal.pone.0207754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 11/22/2022] Open
Abstract
Recent discoveries highlight the importance of stochastic epigenetic changes, as indexed by epigenetic outlier DNA methylation signatures, as a valuable tool to understand aberrant cell function and subsequent human pathology. There is evidence of such changes in different complex disorders as diverse as cancer, obesity and, to a lesser extent, depression. The current study was aimed at identifying outlying DNA methylation signatures of depressive psychopathology. Here, genome-wide DNA methylation levels were measured (by means of Illumina Infinium HumanMethylation450 Beadchip) in peripheral blood of thirty-four monozygotic twins informative for depressive psychopathology (lifetime DSM-IV diagnoses). This dataset was explored to identify outlying epigenetic signatures of depression, operationalized as extreme hyper- or hypo-methylation in affected co-twins from discordant pairs that is not observed across the rest of the study sample. After adjusting for blood cell count, there were thirteen CpG sites across which depressed co-twins from the discordant pairs exhibited outlying DNA methylation signatures. None of them exhibited a methylation outlier profile in the concordant and healthy pairs, and some of these loci spanned genes previously associated with neuropsychiatric phenotypes, such as GHSR and KCNQ1. This exploratory study provides preliminary proof-of-concept validation that epigenetic outlier profiles derived from genome-wide DNA methylation data may be related to depression risk.
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An epigenetic pathway approach to investigating associations between prenatal exposure to maternal mood disorder and newborn neurobehavior. Dev Psychopathol 2018; 30:881-890. [PMID: 30068429 DOI: 10.1017/s0954579418000688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Following recent advances in behavioral and psychiatric epigenetics, researchers are increasingly using epigenetic methods to study prenatal exposure to maternal mood disorder and its effects on fetal and newborn neurobehavior. Despite notable progress, various methodological limitations continue to obscure our understanding of the epigenetic mechanisms underpinning prenatal exposure to maternal mood disorder on newborn neurobehavioral development. Here we detail this problem, discussing limitations of the currently dominant analytical approaches (i.e., candidate epigenetic and epigenome-wide association studies), then present a solution that retains many benefits of existing methods while minimizing their shortcomings: epigenetic pathway analysis. We argue that the application of pathway-based epigenetic approaches that target DNA methylation at transcription factor binding sites could substantially deepen our mechanistic understanding of how prenatal exposures influence newborn neurobehavior.
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Fan SJ, Sun AB, Liu L. Epigenetic modulation during hippocampal development. Biomed Rep 2018; 9:463-473. [PMID: 30546873 DOI: 10.3892/br.2018.1160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/11/2018] [Indexed: 12/24/2022] Open
Abstract
The hippocampus is located in the limbic system and is vital in learning ability, memory formation and emotion regulation, and is associated with depression, epilepsy and mental retardation in an abnormal developmental situation. Several factors have been found to modulate the development of the hippocampus, and epigenetic modification have a crucial effect in this progress. The present review summarizes the epigenetic modifications, including DNA methylation, histone acetylation, and non-coding RNAs, regulating all stages of hippocampal development, focusing on the growth of Ammons horn and the dentate gyrus in humans and rodents. These modifications may significantly affect hippocampal development and health in addition to cognitive processes.
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Affiliation(s)
- Si-Jing Fan
- Department of Pharmacology, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - An-Bang Sun
- Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Department of Anatomy, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Lian Liu
- Department of Pharmacology, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China.,Laboratory of Neuronal and Brain Diseases Modulation, Yangtze University, Jingzhou, Hubei 434023, P.R. China
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Garg P, Joshi RS, Watson C, Sharp AJ. A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PLoS Genet 2018; 14:e1007707. [PMID: 30273333 PMCID: PMC6181428 DOI: 10.1371/journal.pgen.1007707] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 10/11/2018] [Accepted: 09/08/2018] [Indexed: 12/22/2022] Open
Abstract
While population studies have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We identified sites containing clusters of CpGs with high inter-individual epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3' UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 95 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 34 co-regulated VMRs comprising all four HOX gene clusters enriched for control of tissue growth; and in neurons a network of 18 VMRs enriched for roles in synaptic signaling. By culturing genetically-identical fibroblasts under varying environmental conditions, we experimentally demonstrated that some VMR networks are responsive to the environment, with methylation levels at these loci changing in a coordinated fashion in trans dependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10-80), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ricky S. Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Corey Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Ho KWD, Han S, Nielsen JV, Jancic D, Hing B, Fiedorowicz J, Weissman MM, Levinson DF, Potash JB. Genome-wide association study of seasonal affective disorder. Transl Psychiatry 2018; 8:190. [PMID: 30217971 PMCID: PMC6138666 DOI: 10.1038/s41398-018-0246-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/18/2018] [Accepted: 08/07/2018] [Indexed: 12/30/2022] Open
Abstract
Family and twin studies have shown a genetic component to seasonal affective disorder (SAD). A number of candidate gene studies have examined the role of variations within biologically relevant genes in SAD susceptibility, but few genome-wide association studies (GWAS) have been performed to date. The authors aimed to identify genetic risk variants for SAD through GWAS. The authors performed a GWAS for SAD in 1380 cases and 2937 controls of European-American (EA) origin, selected from samples for GWAS of major depressive disorder and of bipolar disorder. Further bioinformatic analyses were conducted to examine additional genomic and biological evidence associated with the top GWAS signals. No susceptibility loci for SAD were identified at a genome-wide significant level. The strongest association was at an intronic variant (rs139459337) within ZBTB20 (odds ratio (OR) = 1.63, p = 8.4 × 10-7), which encodes a transcriptional repressor that has roles in neurogenesis and in adult brain. Expression quantitative trait loci (eQTL) analysis showed that the risk allele "T" of rs139459337 is associated with reduced mRNA expression of ZBTB20 in human temporal cortex (p = 0.028). Zbtb20 is required for normal murine circadian rhythm and for entrainment to a shortened day. Of the 330 human orthologs of murine genes directly repressed by Zbtb20, there were 32 associated with SAD in our sample (at p < 0.05), representing a significant enrichment of ZBTB20 targets among our SAD genetic association signals (fold = 1.93, p = 0.001). ZBTB20 is a candidate susceptibility gene for SAD, based on a convergence of genetic, genomic, and biological evidence. Further studies are necessary to confirm its role in SAD.
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Affiliation(s)
- Kwo Wei David Ho
- Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Shizhong Han
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jakob V Nielsen
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
| | - Dubravka Jancic
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Benjamin Hing
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Jess Fiedorowicz
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Myrna M Weissman
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- The New York State Psychiatric Institute, New York, NY, USA
| | - Douglas F Levinson
- Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA, USA
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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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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Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder. Sci Rep 2018; 8:7620. [PMID: 29769613 PMCID: PMC5956073 DOI: 10.1038/s41598-018-26042-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/30/2018] [Indexed: 12/18/2022] Open
Abstract
As a childhood-onset psychiatric disorder, attention deficit hyperactivity disorder (ADHD) is complicated by phenotypic and genetic heterogeneity. Lifelong executive function deficits in ADHD are described in many literatures and have been proposed as endophenotypes of ADHD. However, its genetic basis is still elusive. In this study, we performed a genome-wide association study of executive function, rated with Behavioral Rating Inventory of Executive Function (BRIEF), in ADHD children. We identified one significant variant (rs852004, P = 2.51e-08) for the overall score of BRIEF. The association analyses for each component of executive function found this locus was more associated with inhibit and monitor components. Further principle component analysis and confirmatory factor analysis provided an ADHD-specific executive function pattern including inhibit and monitor factors. SNP rs852004 was mainly associated with the Behavioral Regulation factor. Meanwhile, we found the significant locus was associated with ADHD symptom. The Behavioral Regulation factor mediated its effect on ADHD symptom. Functional magnetic resonance imaging (fMRI) analyses further showed evidence that this variant affected the activity of inhibition control related brain regions. It provided new insights for the genetic basis of executive function in ADHD.
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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Roy B, Wang Q, Dwivedi Y. Long Noncoding RNA-Associated Transcriptomic Changes in Resiliency or Susceptibility to Depression and Response to Antidepressant Treatment. Int J Neuropsychopharmacol 2018; 21:461-472. [PMID: 29390069 PMCID: PMC5932471 DOI: 10.1093/ijnp/pyy010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Recent emergence of long noncoding RNAs in regulating gene expression and thereby modulating physiological functions in brain has manifested their possible role in psychiatric disorders. In this study, the roles of long noncoding RNAs in susceptibility and resiliency to develop stress-induced depression and their response to antidepressant treatment were examined. METHODS Microarray-based transcriptome-wide changes in long noncoding RNAs were determined in hippocampus of male Holtzman rats who showed susceptibility (learned helplessness) or resiliency (nonlearned helplessness) to develop depression. Changes in long noncoding RNA expression were also ascertained after subchronic administration of fluoxetine to learned helplessness rats. Bioinformatic and target prediction analyses (cis- and trans-acting) and qPCR-based assays were performed to decipher the functional role of altered long noncoding RNAs. RESULTS Group-wise comparison showed an overrepresented class of long noncoding RNAs that were uniquely associated with nonlearned helplessness or learned helplessness behavior. Chromosomal mapping within the 5-kbp flank region of the top 20 dysregulated long noncoding RNAs in the learned helplessness group showed several target genes that were regulated through cis- or trans-actions, including Zbtb20 and Zfp385b from zinc finger binding protein family. Genomic context of differentially expressed long noncoding RNAs showed an overall blunted response in the learned helplessness group regardless of the long noncoding RNA classes analyzed. Gene ontology exhibited the functional clustering for anatomical structure development, cellular architecture modulation, protein metabolism, and cellular communications. Fluoxetine treatment reversed learned helplessness-induced changes in many long noncoding RNAs and target genes. CONCLUSIONS The involvement of specific classes of long noncoding RNAs with distinctive roles in modulating target gene expression could confer the role of long noncoding RNAs in resiliency or susceptibility to develop depression with a reciprocal response to antidepressant treatment.
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Affiliation(s)
- Bhaskar Roy
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Qingzhong Wang
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama,Correspondence: Yogesh Dwivedi, PhD, Elesabeth Ridgely Shook Professor, Director of Translational Research, UAB Mood Disorder Program, Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, SC711 Sparks Center 1720 7th Avenue South, Birmingham, AL ()
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41
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Maulik U, Sen S, Mallik S, Bandyopadhyay S. Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus. BMC Genet 2018; 19:9. [PMID: 29357837 PMCID: PMC5776763 DOI: 10.1186/s12863-017-0574-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023] Open
Abstract
Background Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection. Results First of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis. Thereafter, we utilize weighted topological overlap matrix (TOM) measure and average linkage clustering consecutively on these genesets for intra- and inter-species study.We identify co-methylated and multi-stage co-methylated gene modules by using dynamic tree cut, for intra-and inter-species cases, respectively. Each module is represented by individual color in the dendrogram. Gene Ontology and KEGG pathway based analysis are then performed to identify biological functionalities of the identified modules. Finally, top ten regulator TFs and targeter miRNAs that are associated with the maximum number of gene modules, are determined for both intra-and inter-species analysis. Conclusions The novel TFs and miRNAs obtained from the analysis are: MYST3 and ZNF771 as TFs (for human intra-species analysis), BAZ2B, RCOR3 and ATF1 as TFs (for rhesus intra-species analysis), and mml-miR-768-3p and mml-miR-561 as miRs (for rhesus intra-species analysis); and MYST3 and ZNF771 as miRs(for inter-species study). Furthermore, the genes/TFs/miRNAs that are already found to be liable for several brain-related dreadful diseases as well as rare neglected diseases (e.g., wolf Hirschhorn syndrome, Joubarts Syndrome, Huntington’s disease, Simian Immunodeficiency Virus(SIV) mediated enchaphilits, Parkinsons Disease, Bipolar disorder and Schizophenia etc.) are mentioned. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0574-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India.
| | - Sagnik Sen
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
| | - Saurav Mallik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
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An epigenome-wide methylation study of healthy individuals with or without depressive symptoms. J Hum Genet 2018; 63:319-326. [PMID: 29305581 DOI: 10.1038/s10038-017-0382-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022]
Abstract
Major depressive disorder is a common psychiatric disorder that is thought to be triggered by both genetic and environmental factors. Depressive symptoms are an important public health problem and contribute to vulnerability to major depression. Although a substantial number of genetic and epigenetic studies have been performed to date, the detailed etiology of depression remains unclear and there are no validated biomarkers. DNA methylation is one of the major epigenetic modifications that play diverse roles in the etiology of complex diseases. In this study, we performed an epigenome-wide association study (EWAS) of DNA methylation on subjects with (N = 20) or without (N = 27) depressive symptoms in order to examine whether different levels of DNA methylation were associated with depressive tendencies. Employing methylation-array technology, a total of 363,887 methylation sites across the genomes were investigated and several candidate CpG sites associated with depressive symptoms were identified, especially annotated to genes linked to a G-protein coupled receptor protein signaling pathway. These data provide a strong impetus for validation studies using a larger cohort and support the possibility that G-protein coupled receptor protein signaling pathways are involved in the pathogenesis of depression.
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43
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Shadrina M, Bondarenko EA, Slominsky PA. Genetics Factors in Major Depression Disease. Front Psychiatry 2018; 9:334. [PMID: 30083112 PMCID: PMC6065213 DOI: 10.3389/fpsyt.2018.00334] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/02/2018] [Indexed: 12/22/2022] Open
Abstract
Depressive disorders (DDs) are one of the most widespread forms of psychiatric pathology. According to the World Health Organization, about 350 million people in the world are affected by this condition. Family and twin studies have demonstrated that the contribution of genetic factors to the risk of the onset of DDs is quite large. Various methodological approaches (analysis of candidate genes, genome-wide association analysis, genome-wide sequencing) have been used, and a large number of the associations between genes and different clinical DD variants and DD subphenotypes have been published. However, in most cases, these associations have not been confirmed in replication studies, and only a small number of genes have been proven to be associated with DD development risk. To ascertain the role of genetic factors in DD pathogenesis, further investigations of the relevant conditions are required. Special consideration should be given to the polygenic characteristics noted in whole-genome studies of the heritability of the disorder without a pronounced effect of the major gene. These observations accentuate the relevance of the analysis of gene-interaction roles in DD development and progression. It is important that association studies of the inherited variants of the genome should be supported by analysis of dynamic changes during DD progression. Epigenetic changes that cause modifications of a gene's functional state without changing its coding sequence are of primary interest. However, the opportunities for studying changes in the epigenome, transcriptome, and proteome during DD are limited by the nature of the disease and the need for brain tissue analysis, which is possible only postmortem. Therefore, any association studies between DD pathogenesis and epigenetic factors must be supplemented through the use of different animal models of depression. A threefold approach comprising the combination of gene association studies, assessment of the epigenetic state in DD patients, and analysis of different "omic" changes in animal depression models will make it possible to evaluate the contribution of genetic, epigenetic, and environmental factors to the development of different forms of depression and to help develop ways to decrease the risk of depression and improve the treatment of DD.
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Affiliation(s)
- Maria Shadrina
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena A Bondarenko
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Petr A Slominsky
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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44
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Chen X, Long F, Cai B, Chen X, Chen G. A novel relationship for schizophrenia, bipolar and major depressive disorder Part 3: Evidence from chromosome 3 high density association screen. J Comp Neurol 2017; 526:59-79. [PMID: 28856687 DOI: 10.1002/cne.24311] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 12/30/2022]
Abstract
Familial clustering of schizophrenia (SCZ), bipolar disorder (BPD), and major depressive disorder (MDD) was systematically reported (Aukes et al, Genet Med 2012, 14, 338-341) and convergent evidence from genetics, symptomatology, and psychopharmacology imply that there are intrinsic connections between these three major psychiatric disorders, for example, any two or even three of these disorders could co-exist in some families. A total of 60, 838 single-nucleotide polymorphisms (SNPs) on chromosome 3 were genotyped by Affymetrix Genome-Wide Human SNP array 6.0 on 119 SCZ, 253 BPD (type-I), 177 MDD patients and 1,000 controls. The population of Shandong province was formed in 14 century and believed that it belongs to homogenous population. Associated SNPs were systematically revealed and outstanding susceptibility genes (CADPS, GRM7,KALRN, LSAMP, NLGN1, PRICKLE2, ROBO2) were identified. Unexpectedly, flanking genes for the associated SNPs distinctive for BPD and/or MDD were replicated in an enlarged cohort of 986 SCZ patients. The evidence from this chromosome 3 analysis supports the notion that both of bipolar and MDD might be subtypes of schizophrenia rather than independent disease entity. Also, a similar finding was detected on chromosome 5, 6, 7, and 8 (Chen et al. Am J Transl Res 2017;9 (5):2473-2491; Curr Mol Med 2016;16(9):840-854; Behav Brain Res 2015;293:241-251; Mol Neurobiol 2016. doi: 10.1007/s12035-016-0102-1). Furthermore, PRICKLE2 play an important role in the pathogenesis of three major psychoses in this population.
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Affiliation(s)
- Xing Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Feng Long
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Bin Cai
- CapitalBio corporation, Beijing, People's Republic of China
| | - Xiaohong Chen
- CapitalBio corporation, Beijing, People's Republic of China
| | - Gang Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
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45
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Marcon F, Siniscalchi E, Andreoli C, Allione A, Fiorito G, Medda E, Guarrera S, Matullo G, Crebelli R. Telomerase activity, telomere length and hTERT DNA methylation in peripheral blood mononuclear cells from monozygotic twins with discordant smoking habits. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:551-559. [PMID: 28843010 DOI: 10.1002/em.22127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Increased telomerase expression has been implicated in the pathogenesis of lung cancer and, since the primary cause of lung cancer is smoking, an association between telomerase reactivation and tobacco smoke has been proposed. In this work an investigation has been performed to assess the relationship between tobacco smoke exposure and telomerase activity (TA) in peripheral blood mononuclear cells of healthy smokers. The methylation status of the catalytic subunit of telomerase hTERT was concurrently investigated to assess the possible association between epigenetic modifications of hTERT and TA. Besides, the association between smoke and telomere length (TL) has been evaluated. Healthy monozygotic twins with discordant smoking habits were selected as study population to minimize inter-individual differences because of demographic characteristics and genetic heterogeneity. Statistically significant higher values of TA and TL were observed in smokers compared to nonsmoker co-twins. The multivariate analysis of data showed, besides smoking habits (P = 0.02), an influence of gender (P = 0.006) and BMI (P = 0.001) on TA and a borderline effect of gender (P = 0.05) on TL. DNA methylation analysis, focused on 100 CpG sites mapping in hTERT, highlighted nine CpG sites differentially methylated in smokers. When co-twins were contrasted, selecting as variables the intra-twin difference in TA and hTERT DNA methylation, a statistically significant inverse correlation (P = 0.003) was observed between TA and DNA methylation at the cg05521538 site. In conclusion, these results indicate an association of tobacco smoke with TA and TL and suggest a possible association between smoke-induced epigenetic effects and TA in healthy smokers. Environ. Mol. Mutagen. 58:551-559, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Francesca Marcon
- Department of Environment and Primary Prevention, Surveillance and Health Promotion, Istituto Superiore di Sanità, V.le Regina Elena 299, Rome, 00161, Italy
| | - Ester Siniscalchi
- Department of Environment and Primary Prevention, Surveillance and Health Promotion, Istituto Superiore di Sanità, V.le Regina Elena 299, Rome, 00161, Italy
| | - Cristina Andreoli
- Department of Environment and Primary Prevention, Surveillance and Health Promotion, Istituto Superiore di Sanità, V.le Regina Elena 299, Rome, 00161, Italy
| | - Alessandra Allione
- Italian Institute for Genomic Medicine (IIGM, FKA HuGeF), Via Nizza 52, 10126 Torino and Dept. Medical Sciences, University of Turin, Via Santena 19, Turin, 10126, Italy
| | - Giovanni Fiorito
- Italian Institute for Genomic Medicine (IIGM, FKA HuGeF), Via Nizza 52, 10126 Torino and Dept. Medical Sciences, University of Turin, Via Santena 19, Turin, 10126, Italy
| | - Emanuela Medda
- National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità, V.le Regina Elena 299, Rome, 00161, Italy
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine (IIGM, FKA HuGeF), Via Nizza 52, 10126 Torino and Dept. Medical Sciences, University of Turin, Via Santena 19, Turin, 10126, Italy
| | - Giuseppe Matullo
- Italian Institute for Genomic Medicine (IIGM, FKA HuGeF), Via Nizza 52, 10126 Torino and Dept. Medical Sciences, University of Turin, Via Santena 19, Turin, 10126, Italy
| | - Riccardo Crebelli
- Department of Environment and Primary Prevention, Surveillance and Health Promotion, Istituto Superiore di Sanità, V.le Regina Elena 299, Rome, 00161, Italy
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Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C. Sci Rep 2017; 7:9709. [PMID: 28852164 PMCID: PMC5575306 DOI: 10.1038/s41598-017-10648-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/10/2017] [Indexed: 12/14/2022] Open
Abstract
DNA methylation changes play essential roles in regulating the activities of genes involved in immune responses. Understanding of variable DNA methylation linked to immune responses may contribute to identifying biologically promising epigenetic markers for pathogenesis of diseases. Here, we generated genome-wide DNA methylation and transcriptomic profiles of six pairs of polyinosinic-polycytidylic acid-treated pig peripheral blood mononuclear cell (PBMC) samples and corresponding controls using methylated DNA immunoprecipitation sequencing and RNA sequencing. Comparative methylome analyses identified 5,827 differentially methylated regions and 615 genes showing differential expression between the two groups. Integrative analyses revealed inverse associations between DNA methylation around transcriptional start site and gene expression levels. Furthermore, 70 differentially methylated and expressed genes were identified such as TNFRSF9, IDO1 and EBI3. Functional annotation revealed the enriched categories including positive regulation of immune system process and regulation of leukocyte activation. These findings demonstrated DNA methylation changes occurring in immune responses of PBMCs to poly I:C stimulation and a subset of genes potentially regulated by DNA methylation in the immune responses. The PBMC DNA methylome provides an epigenetic overview of this physiological system in response to viral infection, and we expect it to constitute a valuable resource for future epigenetic epidemiology studies in pigs.
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Epigenetic dysregulation of protocadherins in human disease. Semin Cell Dev Biol 2017; 69:172-182. [PMID: 28694114 DOI: 10.1016/j.semcdb.2017.07.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/12/2022]
Abstract
Protocadherins (Pcdhs) are a group of cell-cell adhesion molecules that are highly expressed in the nervous system and have a major function in dendrite development and neural circuit formation. However, the role protocadherins play in human health and disease remains unclear. Several recent studies have associated epigenetic dysregulation of protocadherins with possible implications for disease pathogenesis. In this review, we briefly recap the various epigenetic mechanisms regulating protocadherin genes, particularly the clustered Pcdhs. We further outline research describing altered epigenetic regulation of protocadherins in neurological and psychiatric disorders, as well as in cancer and during aging. We additionally present preliminary data on DNA methylation dynamics of clustered protocadherins during fetal brain development, as well as the epigenetic differences distinguishing adult neuronal and glial cells. A deeper understanding of the role of protocadherins in disease is crucial for designing novel diagnostic tools and therapies targeting brain disorders.
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48
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Kaut O, Sharma A, Schmitt I, Hurlemann R, Wüllner U. DNA methylation of DLG4 and GJA-1 of human hippocampus and prefrontal cortex in major depression is unchanged in comparison to healthy individuals. J Clin Neurosci 2017. [PMID: 28645745 DOI: 10.1016/j.jocn.2017.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Epigenetic alterations provide a potential mechanism to account for the numerous gene-environment interactions that have been reported in association with neuropsychiatric phenotypes. In context to major depression disorder (MDD), where postmortem and neuroimaging studies provide insights into dysfunctional brain regions, involvement of genetic heterogeneity also revealed the complexity of this disorder. Despite intensive research during the past several decades and information from genome wide studies, pathophysiology of depressive disorders remained elusive. To evaluate the impact of epigenetic pressure on this disease, we took advantage of DNA isolated from different sections of human brain (prefrontal cortex and hippocampus) from clinically well defined depressed patients and healthy individuals and performed pyrosequencing for DNA methylation analysis. Herein, we focused on two genes DLG4 (PSD-95) and GJA-1 (Connexin43) known to be associated with neuropsychiatric behavior. Comparing MDD with controls we found no differences of DNA methylation. Our results clearly demonstrate that DNA methylation levels on these particular genes are not associated with depression related phenotype.
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Affiliation(s)
- Oliver Kaut
- Department of Neurology, University Clinic Bonn, Bonn, Germany.
| | - Amit Sharma
- Department of Neurology, University Clinic Bonn, Bonn, Germany.
| | - Ina Schmitt
- Department of Neurology, University Clinic Bonn, Bonn, Germany.
| | - René Hurlemann
- Division of Medical Psychology, University of Bonn Medical Center, 53105 Bonn, Germany.
| | - Ullrich Wüllner
- Department of Neurology, University Clinic Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Oral & Dental Sciences, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK
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50
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An epigenome-wide DNA methylation study of PTSD and depression in World Trade Center responders. Transl Psychiatry 2017; 7:e1158. [PMID: 28654093 PMCID: PMC5537648 DOI: 10.1038/tp.2017.130] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 01/03/2023] Open
Abstract
Previous epigenome-wide association studies (EWAS) of posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) have been inconsistent. This may be due to small sample sizes, and measurement and tissue differences. The current two EWA analyses of 473 World Trade Center responders are the largest to date for both PTSD and MDD. These analyses investigated DNA methylation patterns and biological pathways influenced by differentially methylated genes associated with each disorder. Methylation was profiled on blood samples using Illumina 450 K Beadchip. Two EWA analyses compared current versus never PTSD, and current versus never MDD, adjusting for cell types and demographic confounders. Pathway and gene set enrichment analyses were performed to understand the complex biological systems of PTSD and MDD. No significant epigenome-wide associations were found for PTSD or MDD at an FDR P<0.05. The majority of genes with differential methylation at a suggestive threshold did not overlap between the two disorders. Pathways significant in PTSD included a regulator of synaptic plasticity, oxytocin signaling, cholinergic synapse and inflammatory disease pathways, while only phosphatidylinositol signaling and cell cycle pathways emerged in MDD. The failure of the current EWA analyses to detect significant epigenome-wide associations is in contrast with disparate findings from previous, smaller EWA and candidate gene studies of PTSD and MDD. Enriched gene sets involved in several biological pathways, including stress response, inflammation and physical health, were identified in PTSD, supporting the view that multiple genes play a role in this complex disorder.
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