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Sokolov AV, Schiöth HB. Decoding depression: a comprehensive multi-cohort exploration of blood DNA methylation using machine learning and deep learning approaches. Transl Psychiatry 2024; 14:287. [PMID: 39009577 PMCID: PMC11250806 DOI: 10.1038/s41398-024-02992-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
The causes of depression are complex, and the current diagnosis methods rely solely on psychiatric evaluations with no incorporation of laboratory biomarkers in clinical practices. We investigated the stability of blood DNA methylation depression signatures in six different populations using six public and two domestic cohorts (n = 1942) conducting mega-analysis and meta-analysis of the individual studies. We evaluated 12 machine learning and deep learning strategies for depression classification both in cross-validation (CV) and in hold-out tests using merged data from 8 separate batches, constructing models with both biased and unbiased feature selection. We found 1987 CpG sites related to depression in both mega- and meta-analysis at the nominal level, and the associated genes were nominally related to axon guidance and immune pathways based on enrichment analysis and eQTM data. Random forest classifiers achieved the highest performance (AUC 0.73 and 0.76) in CV and hold-out tests respectively on the batch-level processed data. In contrast, the methylation showed low predictive power (all AUCs < 0.57) for all classifiers in CV and no predictive power in hold-out tests when used with harmonized data. All models achieved significantly better performance (>14% gain in AUCs) with pre-selected features (selection bias), with some of the models (joint autoencoder-classifier) reaching AUCs of up to 0.91 in the final testing regardless of data preparation. Different algorithmic feature selection approaches may outperform limma, however, random forest models perform well regardless of the strategy. The results provide an overview over potential future biomarkers for depression and highlight many important methodological aspects for DNA methylation-based depression profiling including the use of machine learning strategies.
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Affiliation(s)
- Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden.
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2
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Singh MK, Gorelik AJ, Stave C, Gotlib IH. Genetics, epigenetics, and neurobiology of childhood-onset depression: an umbrella review. Mol Psychiatry 2024; 29:553-565. [PMID: 38102485 DOI: 10.1038/s41380-023-02347-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Depression is a serious and persistent psychiatric disorder that commonly first manifests during childhood. Depression that starts in childhood is increasing in frequency, likely due both to evolutionary trends and to increased recognition of the disorder. In this umbrella review, we systematically searched the extant literature for genetic, epigenetic, and neurobiological factors that contribute to a childhood onset of depression. We searched PubMed, EMBASE, OVID/PsychInfo, and Google Scholar with the following inclusion criteria: (1) systematic review or meta-analysis from a peer-reviewed journal; (2) inclusion of a measure assessing early age of onset of depression; and (3) assessment of neurobiological, genetic, environmental, and epigenetic predictors of early onset depression. Findings from 89 systematic reviews of moderate to high quality suggest that childhood-onset depressive disorders have neurobiological, genetic, environmental, and epigenetic roots consistent with a diathesis-stress theory of depression. This review identified key putative markers that may be targeted for personalized clinical decision-making and provide important insights concerning candidate mechanisms that might underpin the early onset of depression.
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Begni V, Marizzoni M, Creutzberg KC, Silipo DM, Papp M, Cattaneo A, Riva MA. Transcriptomic analyses of rats exposed to chronic mild stress: Modulation by chronic treatment with the antipsychotic drug lurasidone. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110885. [PMID: 37865392 DOI: 10.1016/j.pnpbp.2023.110885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Exposure to stressful experiences accounts for almost half of the risk for mental disorders. Hence, stress-induced alterations represent a key target for pharmacological interventions aimed at restoring brain function in affected individuals. We have previously demonstrated that lurasidone, a multi-receptor antipsychotic drug approved for the treatment of schizophrenia and bipolar depression, can normalize the functional and molecular impairments induced by stress exposure, representing a valuable tool for the treatment of stress-induced mental illnesses. However, the mechanisms that may contribute to the therapeutic effects of lurasidone are still poorly understood. Here, we performed a transcriptomic analysis on the prefrontal cortex (PFC) of adult male rats exposed to the chronic mild stress (CMS) paradigm and we investigated the impact of chronic lurasidone treatment on such changes. We found that CMS exposure leads to an anhedonic phenotype associated with a down-regulation of different pathways associated to neuronal guidance and synaptic plasticity within the PFC. Interestingly, a significant part of these alterations (around 25%) were counteracted by lurasidone treatment. In summary, we provided new insights on the transcriptional changes relevant for the therapeutic intervention with lurasidone, which may ultimately promote resilience.
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Affiliation(s)
- Veronica Begni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Moira Marizzoni
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy; Lab of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Kerstin Camile Creutzberg
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Diana Morena Silipo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
| | - Mariusz Papp
- Institute of Pharmacology and Polish Academy of Sciences, Smętna Street 12, Kraków 31-343, Poland
| | - Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy; Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Via Pilastroni 4, 25125 Brescia, Italy.
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4
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Colita D, Burdusel D, Glavan D, Hermann DM, Colită CI, Colita E, Udristoiu I, Popa-Wagner A. Molecular mechanisms underlying major depressive disorder and post-stroke affective disorders. J Affect Disord 2024; 344:149-158. [PMID: 37827260 DOI: 10.1016/j.jad.2023.10.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/24/2023] [Accepted: 10/08/2023] [Indexed: 10/14/2023]
Abstract
Two of the most common and incapacitating mental health disorders around the world are major depressive disorder (MDD) and post-stroke depression (PSD). MDD is thought to result from abnormal connectivity between the monoaminergic, glutamatergic, GABAergic, and/or cholinergic pathways. Additional factors include the roles of hormonal, immune, ageing, as well as the influence of cellular, molecular, and epigenetics in the development of mood disorders. This complexity of factors has been anticipated by the Swiss psychiatrists Paul Kielholz and Jules Angst who introduced a multimodal treatment of MDD. Depression is the predominant mood disorder, impacting around one-third of individuals who have experienced a stroke. MDD and PSD share common underlying biological mechanisms related to the disruption of monoaminergic pathways. The major contributor to PSD is the stroke lesion location, which can involve the disruption of the serotoninergic, dopaminergic, glutamatergic, GABAergic, or cholinergic pathways. Additionally, various other disorders such as mania, bipolar disorder, anxiety disorder, and apathy might occur post-stroke, although their prevalence is considerably lower. However, there are differences in the onset of MDD among mood disorders. Some mood disorders develop gradually and can persist for a lifetime, potentially culminating in suicide. In contrast, PSD has a rapid onset because of the severe disruption of neural pathways essential for mood behavior caused by the lesion. However, PSD might also spontaneously resolve several months after a stroke, though it is associated with higher mortality. This review also provides a brief overview of the treatments currently available in medical practice.
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Affiliation(s)
- Daniela Colita
- Doctoral School, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
| | - Daiana Burdusel
- Department of Psychiatry, University of Medicine and Pharmacy, 200349 Craiova, Romania; Chair of Vascular Neurology, Dementia and Ageing, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Daniela Glavan
- Department of Psychiatry, University of Medicine and Pharmacy, 200349 Craiova, Romania; Chair of Vascular Neurology, Dementia and Ageing, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Dirk M Hermann
- Chair of Vascular Neurology, Dementia and Ageing, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Cezar-Ivan Colită
- Doctoral School, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
| | - Eugen Colita
- Doctoral School, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
| | - Ion Udristoiu
- Department of Psychiatry, University of Medicine and Pharmacy, 200349 Craiova, Romania.
| | - Aurel Popa-Wagner
- Chair of Vascular Neurology, Dementia and Ageing, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
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Gonzales EL, Jeon SJ, Han KM, Yang SJ, Kim Y, Remonde CG, Ahn TJ, Ham BJ, Shin CY. Correlation between immune-related genes and depression-like features in an animal model and in humans. Brain Behav Immun 2023; 113:29-43. [PMID: 37379963 DOI: 10.1016/j.bbi.2023.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 06/01/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
A growing body of evidence suggests that immune-related genes play pivotal roles in the pathophysiology of depression. In the present study, we investigated a plausible connection between gene expression, DNA methylation, and brain structural changes in the pathophysiology of depression using a combined approach of murine and human studies. We ranked the immobility behaviors of 30 outbred Crl:CD1 (ICR) mice in the forced swim test (FST) and harvested their prefrontal cortices for RNA sequencing. Of the 24,532 analyzed genes, 141 showed significant correlations with FST immobility time, as determined through linear regression analysis with p ≤ 0.01. The identified genes were mostly involved in immune responses, especially interferon signaling pathways. Moreover, induction of virus-like neuroinflammation in the brains of two separate mouse cohorts (n = 30 each) using intracerebroventricular polyinosinic:polycytidylic acid injection resulted in increased immobility during FST and similar expression of top immobility-correlated genes. In human blood samples, candidate gene (top 5%) expression profiling using DNA methylation analysis found the interferon-related USP18 (cg25484698, p = 7.04 × 10-11, Δβ = 1.57 × 10-2; cg02518889, p = 2.92 × 10-3, Δβ = - 8.20 × 10-3) and IFI44 (cg07107453, p = 3.76 × 10-3, Δβ = - 4.94 × 10-3) genes to be differentially methylated between patients with major depressive disorder (n = 350) and healthy controls (n = 161). Furthermore, cortical thickness analyses using T1-weighted images revealed that the DNA methylation scores for USP18 were negatively correlated with the thicknesses of several cortical regions, including the prefrontal cortex. Our results reveal the important role of the interferon pathway in depression and suggest USP18 as a potential candidate target. The results of the correlation analysis between transcriptomic data and animal behavior carried out in this study provide insights that could enhance our understanding of depression in humans.
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Affiliation(s)
- Edson Luck Gonzales
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Republic of Korea
| | - Se Jin Jeon
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Republic of Korea; Department of Integrative Biotechnology, College of Science and Technology, Sahmyook University, Seoul 01795, Republic of Korea
| | - Kyu-Man Han
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Seung Jin Yang
- Department of Life Science, Handong Global University, Pohang 37554, Republic of Korea
| | - Yujeong Kim
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Republic of Korea
| | - Chilly Gay Remonde
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae Jin Ahn
- Department of Life Science, Handong Global University, Pohang 37554, Republic of Korea.
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Republic of Korea.
| | - Chan Young Shin
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Republic of Korea.
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Zhen Y, Pavez M, Li X. The role of Pcdh10 in neurological disease and cancer. J Cancer Res Clin Oncol 2023; 149:8153-8164. [PMID: 37058252 PMCID: PMC10374755 DOI: 10.1007/s00432-023-04743-w] [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: 03/06/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Protocadherin 10 (PCDH 10), a member of the superfamily of protocadherins, is a Ca2+-dependent homophilic cell-cell adhesion molecule expressed on the surface of cell membranes. Protocadherin 10 plays a critical role in the central nervous system including in cell adhesion, formation and maintenance of neural circuits and synapses, regulation of actin assembly, cognitive function and tumor suppression. Additionally, Pcdh10 can serve as a non-invasive diagnostic and prognostic indicator for various cancers. METHODS This paper collects and reviews relevant literature in Pubmed. CONCLUSION This review describes the latest research understanding the role of Pcdh10 in neurological disease and human cancer, highlighting the importance of scrutinizing its properties for the development of targeted therapies and identifying a need for further research to explore Pcdh10 functions in other pathways, cell types and human pathologies.
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Affiliation(s)
- Yilan Zhen
- Menzies Institute for Medical Research, University of Tasmania, Liverpool street, Hobart, 7000, Australia
| | - Macarena Pavez
- Department of Anatomy, University of Otago, Dunedin, Otago, New Zealand.
| | - Xinying Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China.
- School of Life Sciences, Anhui Medical University, Hefei, People's Republic of China.
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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Fries GR, Saldana VA, Finnstein J, Rein T. Molecular pathways of major depressive disorder converge on the synapse. Mol Psychiatry 2023; 28:284-297. [PMID: 36203007 PMCID: PMC9540059 DOI: 10.1038/s41380-022-01806-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023]
Abstract
Major depressive disorder (MDD) is a psychiatric disease of still poorly understood molecular etiology. Extensive studies at different molecular levels point to a high complexity of numerous interrelated pathways as the underpinnings of depression. Major systems under consideration include monoamines, stress, neurotrophins and neurogenesis, excitatory and inhibitory neurotransmission, mitochondrial dysfunction, (epi)genetics, inflammation, the opioid system, myelination, and the gut-brain axis, among others. This review aims at illustrating how these multiple signaling pathways and systems may interact to provide a more comprehensive view of MDD's neurobiology. In particular, considering the pattern of synaptic activity as the closest physical representation of mood, emotion, and conscience we can conceptualize, each pathway or molecular system will be scrutinized for links to synaptic neurotransmission. Models of the neurobiology of MDD will be discussed as well as future actions to improve the understanding of the disease and treatment options.
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Affiliation(s)
- Gabriel R. Fries
- grid.267308.80000 0000 9206 2401Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, Houston, TX 77054 USA ,grid.240145.60000 0001 2291 4776Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Ave, Houston, TX 77030 USA
| | - Valeria A. Saldana
- grid.262285.90000 0000 8800 2297Frank H. Netter MD School of Medicine at Quinnipiac University, 370 Bassett Road, North Haven, CT 06473 USA
| | - Johannes Finnstein
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Project Group Molecular Pathways of Depression, Max Planck Institute of Psychiatry, Kraepelinstr. 10, 80804 Munich, Germany
| | - Theo Rein
- Department of Translational Research in Psychiatry, Project Group Molecular Pathways of Depression, Max Planck Institute of Psychiatry, Kraepelinstr. 10, 80804, Munich, Germany.
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9
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Nijdam MJ, Vermetten E, McFarlane AC. Toward staging differentiation for posttraumatic stress disorder treatment. Acta Psychiatr Scand 2023; 147:65-80. [PMID: 36367112 PMCID: PMC10100486 DOI: 10.1111/acps.13520] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Several medical and psychiatric disorders have stage-based treatment decision-making methods. However, international treatment guidelines for posttraumatic stress disorder (PTSD) fail to give specific treatment recommendations based on chronicity or stage of the disorder. There is convincing evidence of a finite range of PTSD symptom trajectories, implying that different phenotypes of the disorder can be distinguished, which are highly relevant for a staging typology of PTSD. METHODS State-of-the-art review building on prior work on staging models in other disorders as a mapping tool to identify and synthesize toward PTSD. RESULTS We propose a four-stage model of PTSD ranging from stage 0: trauma-exposed asymptomatic but at risk to stage 4: severe unremitting illness of increasing chronicity. We favor a symptom description in various chronological characteristics based on neurobiological markers, information processing systems, stress reactivity, and consciousness dimensions. We also advocate for a separate phenomenology of treatment resistance since this can yield treatment recommendations. CONCLUSION A staging perspective in the field of PTSD is highly needed. This can facilitate the selection of interventions that are proportionate to patients' current needs and risk of illness progression and can also contribute to an efficient framework to organize biomarker data and guide service delivery. Therefore, we propose that a neurobiologically driven trajectory-based typology of PTSD can help deduct several treatment recommendations leading to a more personalized and refined grid to strategize, plan and evaluate treatment interventions.
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Affiliation(s)
- Mirjam J Nijdam
- Department of Psychiatry, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,ARQ National Psychotrauma Center, Diemen, The Netherlands
| | - Eric Vermetten
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander C McFarlane
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
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10
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Petrin AL, Zeng E, Thomas MA, Moretti-Ferreira D, Marazita ML, Xie XJ, Murray JC, Moreno-Uribe LM. DNA methylation differences in monozygotic twins with Van der Woude syndrome. FRONTIERS IN DENTAL MEDICINE 2023; 4:1120948. [PMID: 36936396 PMCID: PMC10019782 DOI: 10.3389/fdmed.2023.1120948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Introduction Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear. Methods We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A). Results and Discussion Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.
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Affiliation(s)
- A. L. Petrin
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
- CORRESPONDENCE A. L. Petrin
| | - E. Zeng
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - M. A. Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - D. Moretti-Ferreira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - M. L. Marazita
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - X. J. Xie
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
| | - J. C. Murray
- Carver College of Medicine, University of Iowa, Iowa, IA, United States
| | - L. M. Moreno-Uribe
- College of Dentistry and Dental Clinics, University of Iowa, Iowa, IA, United States
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Dissecting early life stress-induced adolescent depression through epigenomic approach. Mol Psychiatry 2023; 28:141-153. [PMID: 36517640 PMCID: PMC9812796 DOI: 10.1038/s41380-022-01907-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
Early life stress (ELS), such as abuse and neglect during childhood, can lead to psychiatric disorders in later life. Previous studies have suggested that ELS can cause profound changes in gene expression through epigenetic mechanisms, which can lead to psychiatric disorders in adulthood; however, studies on epigenetic modifications associated with ELS and psychiatric disorders in adolescents are limited. Moreover, how these epigenetic modifications can lead to psychiatric disorders in adolescents is not fully understood. Commonly, DNA methylation, histone modification, and the regulation of noncoding RNAs have been attributed to the reprogramming of epigenetic profiling associated with ELS. Although only a few studies have attempted to examine epigenetic modifications in adolescents with ELS, existing evidence suggests that there are commonalities and differences in epigenetic profiling between adolescents and adults. In addition, epigenetic modifications are sex-dependent and are influenced by the type of ELS. In this review, we have critically evaluated the current evidence on epigenetic modifications in adolescents with ELS, particularly DNA methylation and the expression of microRNAs in both preclinical models and humans. We have also clarified the impact of ELS on psychiatric disorders in adolescents to predict the development of neuropsychiatric disorders and to prevent and recover these disorders through personalized medicine.
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12
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Lee B, Shin E, Song I, Chang B. Depression in Adolescence and Brain-Derived Neurotrophic Factor. Front Mol Neurosci 2022; 15:947192. [PMID: 35875661 PMCID: PMC9302599 DOI: 10.3389/fnmol.2022.947192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/20/2022] [Indexed: 12/27/2022] Open
Abstract
The incidence of depression among adolescents has been rapidly increasing in recent years. Environmental and genetic factors have been identified as important risk factors for adolescent depression. However, the mechanisms underlying the development of adolescent depression that are triggered by these risk factors are not well understood. Clinical and preclinical studies have focused more on adult depression, and differences in depressive symptoms between adolescents and adults make it difficult to adequately diagnose and treat adolescent depression. Brain-derived neurotrophic factor (BDNF) is known to play a critical role in the pathophysiology of many psychiatric disorders, including depression. However, there are still few studies on adolescent depression. Therefore, in this review paper, the causes and treatment of adolescent depression and the function of BDNF are investigated.
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13
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Schiele MA, Lipovsek J, Schlosser P, Soutschek M, Schratt G, Zaudig M, Berberich G, Köttgen A, Domschke K. Epigenome-wide DNA methylation in obsessive-compulsive disorder. Transl Psychiatry 2022; 12:221. [PMID: 35650177 PMCID: PMC9160220 DOI: 10.1038/s41398-022-01996-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 01/02/2023] Open
Abstract
In adult patients with obsessive-compulsive disorder (OCD), altered DNA methylation has been discerned in several candidate genes, while DNA methylation on an epigenome-wide level has been investigated in only one Chinese study so far. Here, an epigenome-wide association study (EWAS) was performed in a sample of 76 OCD patients of European ancestry (37 women, age ± SD: 33.51 ± 10.92 years) and 76 sex- and age-matched healthy controls for the first time using the Illumina MethylationEPIC BeadChip. After quality control, nine epigenome-wide significant quantitative trait methylation sites (QTMs) and 21 suggestive hits were discerned in the final sample of 68 patients and 68 controls. The top hit (cg24159721) and four other significant QTMs (cg11894324, cg01070250, cg11330075, cg15174812) map to the region of the microRNA 12136 gene (MIR12136). Two additional significant CpG sites (cg05740793, cg20450977) are located in the flanking region of the MT-RNR2 (humanin) like 8 gene (MT-RNRL8), while two further QTMs (cg16267121, cg15890734) map to the regions of the MT-RNR2 (humanin) like 3 (MT-RNRL3) and MT-RNR2 (humanin) like 2 (MT-RNRL2) genes. Provided replication of the present findings in larger samples, the identified QTMs might provide more biological insight into the pathogenesis of OCD and thereby could in the future serve as peripheral epigenetic markers of OCD risk with the potential to inform targeted preventive and therapeutic efforts.
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Affiliation(s)
- Miriam A. Schiele
- grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104 Freiburg, Germany
| | - Jan Lipovsek
- grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104 Freiburg, Germany ,grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany
| | - Pascal Schlosser
- grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany ,grid.21107.350000 0001 2171 9311Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD USA
| | - Michael Soutschek
- grid.5801.c0000 0001 2156 2780ETH Zurich–D-HEST, Institute for Neuroscience, Systems Neuroscience, Building Y17 L48, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Gerhard Schratt
- grid.5801.c0000 0001 2156 2780ETH Zurich–D-HEST, Institute for Neuroscience, Systems Neuroscience, Building Y17 L48, Winterthurerstraße 190, 8057 Zurich, Switzerland
| | - Michael Zaudig
- Psychosomatic Hospital Windach, Schützenstraße 100, 86949 Windach, Germany
| | - Götz Berberich
- Psychosomatic Hospital Windach, Schützenstraße 100, 86949 Windach, Germany
| | - Anna Köttgen
- grid.7708.80000 0000 9428 7911Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center—University of Freiburg, Hugstetter Straße 49, 79106 Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstraße 5, 79104, Freiburg, Germany. .,Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.
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14
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Hoshina N, Johnson-Venkatesh EM, Rally VR, Sant J, Hoshina M, Seiglie MP, Umemori H. ASD/OCD-Linked Protocadherin-10 Regulates Synapse, But Not Axon, Development in the Amygdala and Contributes to Fear- and Anxiety-Related Behaviors. J Neurosci 2022; 42:4250-4266. [PMID: 35504727 PMCID: PMC9145243 DOI: 10.1523/jneurosci.1843-21.2022] [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: 09/11/2021] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
The Protocadherin-10 (PCDH10) gene is associated with autism spectrum disorder (ASD), obsessive-compulsive disorder (OCD), and major depression (MD). The PCDH10 protein is a homophilic cell adhesion molecule that belongs to the δ2-protocadherin family. PCDH10 is highly expressed in the developing brain, especially in the basolateral nucleus of the amygdala (BLA). However, the role of PCDH10 in vivo has been debatable: one paper reported that a Pcdh10 mutant mouse line showed changes in axonal projections; however, another Pcdh10 mutant mouse line was reported to have failed to detect axonal phenotypes. Therefore, the actual roles of PCDH10 in the brain remain to be elucidated. We established a new Pcdh10 KO mouse line using the CRISPR/Cas9 system, without inserting gene cassettes to avoid nonspecific effects, examined the roles of PCDH10 in the brain, and studied the behavioral consequences of Pcdh10 inactivation. Here, we show that Pcdh10 KO mice do not show defects in axonal development. Instead, we find that Pcdh10 KO mice exhibit impaired development of excitatory synapses in the dorsal BLA. We further demonstrate that male Pcdh10 KO mice exhibit reduced anxiety-related behaviors, impaired fear conditioning, decreased stress-coping responses, and mildly impaired social recognition and communication. These results indicate that PCDH10 plays a critical role in excitatory synapse development, but not axon development, in the dorsal BLA and that PCDH10 regulates anxiety-related, fear-related, and stress-related behaviors. Our results reveal the roles of PCDH10 in the brain and its relationship to relevant psychiatric disorders such as ASD, OCD, and MD.SIGNIFICANCE STATEMENTProtocadherin-10 (PCDH10) encodes a cell adhesion molecule and is implicated in autism spectrum disorder (ASD), obsessive-compulsive disorder (OCD), and major depression (MD). PCDH10 is highly expressed in the basolateral nucleus of the amygdala (BLA). However, the phenotypes of previously published Pcdh10 mutant mice are debatable, and some are possibly because of the nonspecific effects of the LacZ/Neo cassette inserted in the mice. We have generated a new Pcdh10 mutant mouse line without the LacZ/Neo cassette. Using our new mouse line, we reveal the roles of PCDH10 for excitatory synapse development in the BLA. The mutant mice exhibit anxiety-related, fear-related, and stress-related behaviors, which are relevant to ASD, OCD, and MD, suggesting a possible treatment strategy for such psychiatric disorders.
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Affiliation(s)
- Naosuke Hoshina
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Erin M Johnson-Venkatesh
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Veronica R Rally
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jaanvi Sant
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Miyuki Hoshina
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Mariel P Seiglie
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Hisashi Umemori
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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15
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Lancaster EE, Vladimirov VI, Riley BP, Landry JW, Roberson-Nay R, York TP. LARGE-SCALE INTEGRATION OF DNA METHYLATION AND GENE EXPRESSION ARRAY PLATFORMS IDENTIFIES BOTH cis AND trans RELATIONSHIPS. Epigenetics 2022; 17:1753-1773. [PMID: 35608069 PMCID: PMC9621057 DOI: 10.1080/15592294.2022.2079293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although epigenome-wide association studies (EWAS) have been successful in identifying DNA methylation (DNAm) patterns associated with disease states, any further characterization of etiologic mechanisms underlying disease remains elusive. This knowledge gap does not originate from a lack of DNAm–trait associations, but rather stems from study design issues that affect the interpretability of EWAS results. Despite known limitations in predicting the function of a particular CpG site, most EWAS maintain the broad assumption that altered DNAm results in a concomitant change of transcription at the most proximal gene. This study integrated DNAm and gene expression (GE) measurements in two cohorts, the Adolescent and Young Adult Twin Study (AYATS) and the Pregnancy, Race, Environment, Genes (PREG) study, to improve the understanding of epigenomic regulatory mechanisms. CpG sites associated with GE in cis were enriched in areas of transcription factor binding and areas of intermediate-to-low CpG density. CpG sites associated with trans GE were also enriched in areas of known regulatory significance, including enhancer regions. These results highlight issues with restricting DNAm-transcript annotations to small genomic intervals and question the validity of assuming a cis DNAm–GE pathway. Based on these findings, the interpretation of EWAS results is limited in studies without multi-omic support and further research should identify genomic regions in which GE-associated DNAm is overrepresented. An in-depth characterization of GE-associated CpG sites could improve predictions of the downstream functional impact of altered DNAm and inform best practices for interpreting DNAm–trait associations generated by EWAS.
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Affiliation(s)
- Eva E Lancaster
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220
| | | | - Brien P Riley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Psychology, Virginia Commonwealth University, Richmond, VA 23220
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23220
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16
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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:5856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene-environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
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Affiliation(s)
- Diana M. Manu
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, 751 24 Uppsala, Sweden; (J.M.); (H.B.S.)
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17
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England-Mason G, Merrill SM, Gladish N, Moore SR, Giesbrecht GF, Letourneau N, MacIsaac JL, MacDonald AM, Kinniburgh DW, Ponsonby AL, Saffery R, Martin JW, Kobor MS, Dewey D. Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 163:107183. [PMID: 35325772 DOI: 10.1016/j.envint.2022.107183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prenatal exposure to phthalates has been associated with adverse health and neurodevelopmental outcomes. DNA methylation (DNAm) alterations may be a mechanism underlying these effects, but prior investigations of prenatal exposure to phthalates and neonatal DNAm profiles are limited to placental tissue and umbilical cord blood. OBJECTIVE Conduct an epigenome-wide association study (EWAS) of the associations between prenatal exposure to phthalates and DNAm in two accessible infant tissues, venous buffy coat blood and buccal epithelial cells (BECs). METHODS Participants included 152 maternal-infant pairs from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Maternal second trimester urine samples were analyzed for nine phthalate metabolites. Blood (n = 74) or BECs (n = 78) were collected from 3-month-old infants and profiled for DNAm using the Infinium HumanMethylation450 (450K) BeadChip. Robust linear regressions were used to investigate the associations between high (HMWPs) and low molecular weight phthalates (LMWPs) and change in methylation levels at variable Cytosine-phosphate-Guanine (CpG) sites in infant tissues, as well as the sensitivity of associations to potential confounders. RESULTS One candidate CpG in gene RNF39 reported by a previous study examining prenatal exposure to phthalates and cord blood DNAm was replicated. The EWAS identified 12 high-confidence CpGs in blood and another 12 in BECs associated with HMWPs and/or LMWPs. Prenatal exposure to bisphenol A (BPA) associated with two of the CpGs associated with HMWPs in BECs. DISCUSSION Prenatal exposure to phthalates was associated with DNAm variation at CpGs annotated to genes associated with endocrine hormone activity (i.e., SLCO4A1, TPO), immune pathways and DNA damage (i.e., RASGEF1B, KAZN, HLA-A, MYO18A, DIP2C, C1or109), and neurodevelopment (i.e., AMPH, NOTCH3, DNAJC5). Future studies that characterize the stability of these associations in larger samples, multiple cohorts, across tissues, and investigate the potential associations between these biomarkers and relevant health and neurodevelopmental outcomes are needed.
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Affiliation(s)
- Gillian England-Mason
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah M Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, Faculty of Arts, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Södermanland, Sweden
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Deborah Dewey
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada.
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18
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Martins J, Czamara D, Sauer S, Rex-Haffner M, Dittrich K, Dörr P, de Punder K, Overfeld J, Knop A, Dammering F, Entringer S, Winter SM, Buss C, Heim C, Binder EB. Childhood adversity correlates with stable changes in DNA methylation trajectories in children and converges with epigenetic signatures of prenatal stress. Neurobiol Stress 2021; 15:100336. [PMID: 34095363 PMCID: PMC8163992 DOI: 10.1016/j.ynstr.2021.100336] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022] Open
Abstract
Childhood maltreatment (CM) is an established major risk factor for a number of negative health outcomes later in life. While epigenetic mechanisms, such as DNA methylation (DNAm), have been proposed as a means of embedding this environmental risk factor, little is known about its timing and trajectory, especially in very young children. It is also not clear whether additional environmental adversities, often experienced by these children, converge on similar DNAm changes. Here, we calculated a cumulative adversity score, which additionally to CM includes socioeconomic status (SES), other life events, parental psychopathology and epigenetic biomarkers of prenatal smoking and alcohol consumption. We investigated the effects of CM alone as well as the adversity score on longitudinal DNAm trajectories in the Berlin Longitudinal Child Study. This is a cohort of 173 children aged 3-5 years at baseline of whom 86 were exposed to CM. These children were followed-up for 2 years with extensive psychometric and biological assessments as well as saliva collection at 5 time points providing genome-wide DNAm levels. Overall, only a few DNAm patterns were stable over this timeframe, but less than 10 DNAm regions showed significant changes. At baseline, neither CM nor the adversity score associated with DNAm changes. However, in 6 differentially methylated regions (DMRs), CM and the adversity score significantly moderated DNAm trajectories over time. A number of these DMRs have previously been associated with adverse prenatal exposures. In our study, children exposed to CM also presented with epigenetic signatures indicative of increased prenatal exposure to tobacco and alcohol, as compared to non-CM exposed children. These epigenetic signatures of prenatal exposure strongly correlate with DNAm regions associated with CM and the adversity score. Finally, weighted correlation network analysis revealed a module of CpGs exclusively associated with CM. While our study identifies DNAm loci specifically associated with CM, especially within long non-coding RNAs, the majority of associations were found with the adversity score with convergent association with indicators of adverse prenatal exposures. This study highlights the importance of mapping not only of the epigenome but also the exposome and extending the observational timeframe to well before birth.
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Affiliation(s)
- Jade Martins
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Susann Sauer
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Katja Dittrich
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Peggy Dörr
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Karin de Punder
- Natura Foundation, Research and Development, Numansdrop, 3281, NC, Netherlands
| | - Judith Overfeld
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Andrea Knop
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Felix Dammering
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Sonja Entringer
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Sibylle M. Winter
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Claudia Buss
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Christine Heim
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- Dept. of Biobehavioral Health, College of Health & Human Development, The Pennsylvania State University, University Park, PA, USA
| | - Elisabeth B. Binder
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30329, USA
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19
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Howard DM, Pain O, Arathimos R, Barbu MC, Amador C, Walker RM, Jermy B, Adams MJ, Deary IJ, Porteous D, Campbell A, Sullivan PF, Evans KL, Arseneault L, Wray NR, Meaney M, McIntosh AM, Lewis CM. Methylome-wide association study of early life stressors and adult mental health. Hum Mol Genet 2021; 31:651-664. [PMID: 34523677 PMCID: PMC8863421 DOI: 10.1093/hmg/ddab274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/25/2022] Open
Abstract
The environment and events that we are exposed to in utero, during birth and in early childhood influence our future physical and mental health. The underlying mechanisms that lead to these outcomes are unclear, but long-term changes in epigenetic marks, such as DNA methylation, could act as a mediating factor or biomarker. DNA methylation data were assayed at 713 522 CpG sites from 9537 participants of the Generation Scotland: Scottish Family Health Study, a family-based cohort with extensive genetic, medical, family history and lifestyle information. Methylome-wide association studies of eight early life environment phenotypes and two adult mental health phenotypes (major depressive disorder and brief resilience scale) were conducted using DNA methylation data collected from adult whole blood samples. Two genes involved with different developmental pathways (PRICKLE2, Prickle Planar Cell Polarity Protein 2 and ABI1, Abl-Interactor-1) were annotated to CpG sites associated with preterm birth (P < 1.27 × 10−9). A further two genes important to the development of sensory pathways (SOBP, Sine Oculis Binding Protein Homolog and RPGRIP1, Retinitis Pigmentosa GTPase Regulator Interacting Protein) were annotated to sites associated with low birth weight (P < 4.35 × 10−8). The examination of methylation profile scores and genes and gene-sets annotated from associated CpGs sites found no evidence of overlap between the early life environment and mental health conditions. Birth date was associated with a significant difference in estimated lymphocyte and neutrophil counts. Previous studies have shown that early life environments influence the risk of developing mental health disorders later in life; however, this study found no evidence that this is mediated by stable changes to the methylome detectable in peripheral blood.
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Affiliation(s)
- David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Oliver Pain
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Ryan Arathimos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Chancellor's Building, 49 Little France Crescent, University of Edinburgh, Edinburgh, UK
| | - Bradley Jermy
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - David Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Michael Meaney
- Douglas Mental Health University Institute, McGill University, Montréal, QC, Canada.,Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, QC, Canada.,Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.,Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
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20
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Yamagishi S, Bando Y, Sato K. Involvement of Netrins and Their Receptors in Neuronal Migration in the Cerebral Cortex. Front Cell Dev Biol 2021; 8:590009. [PMID: 33520982 PMCID: PMC7843923 DOI: 10.3389/fcell.2020.590009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
In mammals, excitatory cortical neurons develop from the proliferative epithelium and progenitor cells in the ventricular zone and subventricular zone, and migrate radially to the cortical plate, whereas inhibitory GABAergic interneurons are born in the ganglionic eminence and migrate tangentially. The migration of newly born cortical neurons is tightly regulated by both extracellular and intracellular signaling to ensure proper positioning and projections. Non-cell-autonomous extracellular molecules, such as growth factors, axon guidance molecules, extracellular matrix, and other ligands, play a role in cortical migration, either by acting as attractants or repellents. In this article, we review the guidance molecules that act as cell-cell recognition molecules for the regulation of neuronal migration, with a focus on netrin family proteins, their receptors, and related molecules, including neogenin, repulsive guidance molecules (RGMs), Down syndrome cell adhesion molecule (DSCAM), fibronectin leucine-rich repeat transmembrane proteins (FLRTs), and draxin. Netrin proteins induce attractive and repulsive signals depending on their receptors. For example, binding of netrin-1 to deleted in colorectal cancer (DCC), possibly together with Unc5, repels migrating GABAergic neurons from the ventricular zone of the ganglionic eminence, whereas binding to α3β1 integrin promotes cortical interneuron migration. Human genetic disorders associated with these and related guidance molecules, such as congenital mirror movements, schizophrenia, and bipolar disorder, are also discussed.
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Affiliation(s)
- Satoru Yamagishi
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Bando
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohji Sato
- Department of Organ and Tissue Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
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21
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Vahid-Ansari F, Albert PR. Rewiring of the Serotonin System in Major Depression. Front Psychiatry 2021; 12:802581. [PMID: 34975594 PMCID: PMC8716791 DOI: 10.3389/fpsyt.2021.802581] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Serotonin is a key neurotransmitter that is implicated in a wide variety of behavioral and cognitive phenotypes. Originating in the raphe nuclei, 5-HT neurons project widely to innervate many brain regions implicated in the functions. During the development of the brain, as serotonin axons project and innervate brain regions, there is evidence that 5-HT plays key roles in wiring the developing brain, both by modulating 5-HT innervation and by influencing synaptic organization within corticolimbic structures. These actions are mediated by 14 different 5-HT receptors, with region- and cell-specific patterns of expression. More recently, the role of the 5-HT system in synaptic re-organization during adulthood has been suggested. The 5-HT neurons have the unusual capacity to regrow and reinnervate brain regions following insults such as brain injury, chronic stress, or altered development that result in disconnection of the 5-HT system and often cause depression, anxiety, and cognitive impairment. Chronic treatment with antidepressants that amplify 5-HT action, such as selective serotonin reuptake inhibitors (SSRIs), appears to accelerate the rewiring of the 5-HT system by mechanisms that may be critical to the behavioral and cognitive improvements induced in these models. In this review, we survey the possible 5-HT receptor mechanisms that could mediate 5-HT rewiring and assess the evidence that 5-HT-mediated brain rewiring is impacting recovery from mental illness. By amplifying 5-HT-induced rewiring processes using SSRIs and selective 5-HT agonists, more rapid and effective treatments for injury-induced mental illness or cognitive impairment may be achieved.
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Affiliation(s)
- Faranak Vahid-Ansari
- Ottawa Hospital Research Institute (Neuroscience), University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
| | - Paul R Albert
- Ottawa Hospital Research Institute (Neuroscience), University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
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22
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Okechukwu C. Deciphering and manipulating the epigenome for the treatment of Parkinson’s and Alzheimer’s disease. MGM JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/mgmj.mgmj_90_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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