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Nohesara S, Mostafavi Abdolmaleky H, Thiagalingam S. Substance-Induced Psychiatric Disorders, Epigenetic and Microbiome Alterations, and Potential for Therapeutic Interventions. Brain Sci 2024; 14:769. [PMID: 39199463 PMCID: PMC11352452 DOI: 10.3390/brainsci14080769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 09/01/2024] Open
Abstract
Substance use disorders (SUDs) are complex biopsychosocial diseases that cause neurocognitive deficits and neurological impairments by altering the gene expression in reward-related brain areas. Repeated drug use gives rise to alterations in DNA methylation, histone modifications, and the expression of microRNAs in several brain areas that may be associated with the development of psychotic symptoms. The first section of this review discusses how substance use contributes to the development of psychotic symptoms via epigenetic alterations. Then, we present more evidence about the link between SUDs and brain epigenetic alterations. The next section presents associations between paternal and maternal exposure to substances and epigenetic alterations in the brains of offspring and the role of maternal diet in preventing substance-induced neurological impairments. Then, we introduce potential therapeutic agents/approaches such as methyl-rich diets to modify epigenetic alterations for alleviating psychotic symptoms or depression in SUDs. Next, we discuss how substance use-gut microbiome interactions contribute to the development of neurological impairments through epigenetic alterations and how gut microbiome-derived metabolites may become new therapeutics for normalizing epigenetic aberrations. Finally, we address possible challenges and future perspectives for alleviating psychotic symptoms and depression in patients with SUDs by modulating diets, the epigenome, and gut microbiome.
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Affiliation(s)
- Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA;
- Mental Health Research Center, Psychosocial Health Research Institute, Department of Psychiatry, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA;
- Nutrition/Metabolism Laboratory, Department of Surgery, BIDMC, Harvard Medical School, Boston, MA 02215, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Pathology & Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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Mostafavi Abdolmaleky H, Alam R, Nohesara S, Deth RC, Zhou JR. iPSC-Derived Astrocytes and Neurons Replicate Brain Gene Expression, Epigenetic, Cell Morphology and Connectivity Alterations Found in Autism. Cells 2024; 13:1095. [PMID: 38994948 PMCID: PMC11240613 DOI: 10.3390/cells13131095] [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: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Excessive inflammatory reactions and oxidative stress are well-recognized molecular findings in autism and these processes can affect or be affected by the epigenetic landscape. Nonetheless, adequate therapeutics are unavailable, as patient-specific brain molecular markers for individualized therapies remain challenging. METHODS We used iPSC-derived neurons and astrocytes of patients with autism vs. controls (5/group) to examine whether they replicate the postmortem brain expression/epigenetic alterations of autism. Additionally, DNA methylation of 10 postmortem brain samples (5/group) was analyzed for genes affected in PSC-derived cells. RESULTS We found hyperexpression of TGFB1, TGFB2, IL6 and IFI16 and decreased expression of HAP1, SIRT1, NURR1, RELN, GPX1, EN2, SLC1A2 and SLC1A3 in the astrocytes of patients with autism, along with DNA hypomethylation of TGFB2, IL6, TNFA and EN2 gene promoters and a decrease in HAP1 promoter 5-hydroxymethylation in the astrocytes of patients with autism. In neurons, HAP1 and IL6 expression trended alike. While HAP1 promoter was hypermethylated in neurons, IFI16 and SLC1A3 promoters were hypomethylated and TGFB2 exhibited increased promoter 5-hydroxymethlation. We also found a reduction in neuronal arborization, spine size, growth rate, and migration, but increased astrocyte size and a reduced growth rate in autism. In postmortem brain samples, we found DNA hypomethylation of TGFB2 and IFI16 promoter regions, but DNA hypermethylation of HAP1 and SLC1A2 promoters in autism. CONCLUSION Autism-associated expression/epigenetic alterations in iPSC-derived cells replicated those reported in the literature, making them appropriate surrogates to study disease pathogenesis or patient-specific therapeutics.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Reza Alam
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Scuto M, Rampulla F, Reali GM, Spanò SM, Trovato Salinaro A, Calabrese V. Hormetic Nutrition and Redox Regulation in Gut-Brain Axis Disorders. Antioxidants (Basel) 2024; 13:484. [PMID: 38671931 PMCID: PMC11047582 DOI: 10.3390/antiox13040484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The antioxidant and anti-inflammatory effects of hormetic nutrition for enhancing stress resilience and overall human health have received much attention. Recently, the gut-brain axis has attracted prominent interest for preventing and therapeutically impacting neuropathologies and gastrointestinal diseases. Polyphenols and polyphenol-combined nanoparticles in synergy with probiotics have shown to improve gut bioavailability and blood-brain barrier (BBB) permeability, thus inhibiting the oxidative stress, metabolic dysfunction and inflammation linked to gut dysbiosis and ultimately the onset and progression of central nervous system (CNS) disorders. In accordance with hormesis, polyphenols display biphasic dose-response effects by activating at a low dose the Nrf2 pathway resulting in the upregulation of antioxidant vitagenes, as in the case of heme oxygenase-1 upregulated by hidrox® or curcumin and sirtuin-1 activated by resveratrol to inhibit reactive oxygen species (ROS) overproduction, microbiota dysfunction and neurotoxic damage. Importantly, modulation of the composition and function of the gut microbiota through polyphenols and/or probiotics enhances the abundance of beneficial bacteria and can prevent and treat Alzheimer's disease and other neurological disorders. Interestingly, dysregulation of the Nrf2 pathway in the gut and the brain can exacerbate selective susceptibility under neuroinflammatory conditions to CNS disorders due to the high vulnerability of vagal sensory neurons to oxidative stress. Herein, we aimed to discuss hormetic nutrients, including polyphenols and/or probiotics, targeting the Nrf2 pathway and vitagenes for the development of promising neuroprotective and therapeutic strategies to suppress oxidative stress, inflammation and microbiota deregulation, and consequently improve cognitive performance and brain health. In this review, we also explore interactions of the gut-brain axis based on sophisticated and cutting-edge technologies for novel anti-neuroinflammatory approaches and personalized nutritional therapies.
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Affiliation(s)
- Maria Scuto
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy; (F.R.); (G.M.R.); (S.M.S.); (V.C.)
| | | | | | | | - Angela Trovato Salinaro
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95124 Catania, Italy; (F.R.); (G.M.R.); (S.M.S.); (V.C.)
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Khoodoruth MAS, Chut-kai Khoodoruth WN, Al Alwani R. Exploring the epigenetic landscape: The role of 5-hydroxymethylcytosine in neurodevelopmental disorders. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e5. [PMID: 38699519 PMCID: PMC11062787 DOI: 10.1017/pcm.2024.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/18/2024] [Accepted: 03/16/2024] [Indexed: 05/05/2024]
Abstract
Recent advances in genetic and epigenetic research have underscored the significance of 5-hydroxymethylcytosine (5hmC) in neurodevelopmental disorders (NDDs), such as autism spectrum disorder (ASD) and intellectual disability (ID), revealing its potential as both a biomarker for early detection and a target for novel therapeutic strategies. This review article provides a comprehensive analysis of the role of 5hmC in NDDs by examining both animal models and human studies. By examining mouse models, studies have demonstrated that prenatal environmental challenges, such as maternal infection and food allergies, lead to significant epigenetic alterations in 5hmC levels, which were associated with NDDs in offspring, impacting social behavior, cognitive abilities and increasing ASD-like symptoms. In human studies, researchers have linked alterations in 5hmC levels NDDs through studies in individuals with ASD, fragile X syndrome, TET3 deficiency and ID, specifically identifying significant epigenetic modifications in genes such as GAD1, RELN, FMR1 and EN-2, suggesting that dysregulation of 5hmC played a critical role in the pathogenesis of these disorders and highlighted the potential for targeted therapeutic interventions. Moreover, we explore the implications of these findings for the development of epigenetic therapies aimed at modulating 5hmC levels. The review concludes with a discussion on future directions for research in this field, such as machine learning, emphasizing the need for further studies to elucidate the complex mechanisms underlying NDDs and to translate these findings into clinical practice. This paper not only advances our understanding of the epigenetic landscape of NDDs but also opens up new avenues for diagnosis and treatment, offering hope for individuals affected by these conditions.
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Affiliation(s)
- Mohamed Adil Shah Khoodoruth
- Department of Child and Adolescent Psychiatry, Hamad Medical Corporation, Doha, Qatar
- Division of Genomics and Precision Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Rafaa Al Alwani
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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Nohesara S, Abdolmaleky HM, Thiagalingam S. Epigenetic Aberrations in Major Psychiatric Diseases Related to Diet and Gut Microbiome Alterations. Genes (Basel) 2023; 14:1506. [PMID: 37510410 PMCID: PMC10379841 DOI: 10.3390/genes14071506] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Nutrition and metabolism modify epigenetic signatures like histone acetylation and DNA methylation. Histone acetylation and DNA methylation in the central nervous system (CNS) can be altered by bioactive nutrients and gut microbiome via the gut-brain axis, which in turn modulate neuronal activity and behavior. Notably, the gut microbiome, with more than 1000 bacterial species, collectively contains almost three million functional genes whose products interact with millions of human epigenetic marks and 30,000 genes in a dynamic manner. However, genetic makeup shapes gut microbiome composition, food/nutrient metabolism, and epigenetic landscape, as well. Here, we first discuss the effect of changes in the microbial structure and composition in shaping specific epigenetic alterations in the brain and their role in the onset and progression of major mental disorders. Afterward, potential interactions among maternal diet/environmental factors, nutrition, and gastrointestinal microbiome, and their roles in accelerating or delaying the onset of severe mental illnesses via epigenetic changes will be discussed. We also provide an overview of the association between the gut microbiome, oxidative stress, and inflammation through epigenetic mechanisms. Finally, we present some underlying mechanisms involved in mediating the influence of the gut microbiome and probiotics on mental health via epigenetic modifications.
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Affiliation(s)
- Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
| | - Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boson, MA 02215, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02218, USA; (S.N.); (S.T.)
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA 02218, USA
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Liu T, Du D, Zhao R, Xie Q, Dong Z. Gut microbes influence the development of central nervous system disorders through epigenetic inheritance. Microbiol Res 2023; 274:127440. [PMID: 37343494 DOI: 10.1016/j.micres.2023.127440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Central nervous system (CNS) disorders, such as depression, anxiety, and Alzheimer's disease (AD), affect quality of life of patients and pose significant economic and social burdens worldwide. Due to their obscure and complex pathogeneses, current therapies for these diseases have limited efficacy. Over the past decade, the gut microbiome has been shown to exhibit direct and indirect influences on the structure and function of the CNS, affecting multiple pathological pathways. In addition to the direct interactions between the gut microbiota and CNS, the gut microbiota and their metabolites can regulate epigenetic processes, including DNA methylation, histone modification, and regulation of non-coding RNAs. In this review, we discuss the tripartite relationship among gut microbiota, epigenetic inheritance, and CNS disorders. We suggest that gut microbes and their metabolites influence the pathogenesis of CNS disorders at the epigenetic level, which may inform the development of effective therapeutic strategies for CNS disorders.
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Affiliation(s)
- Tianyou Liu
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Dongru Du
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Rui Zhao
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Qinglian Xie
- Department of Outpatient, West China Hospital of Sichuan University, Chengdu 610041, PR China
| | - Zaiquan Dong
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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Vitetta L, Bambling M, Strodl E. Probiotics and Commensal Bacteria Metabolites Trigger Epigenetic Changes in the Gut and Influence Beneficial Mood Dispositions. Microorganisms 2023; 11:1334. [PMID: 37317308 DOI: 10.3390/microorganisms11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
The effect of the intestinal microbiome on the gut-brain axis has received considerable attention, strengthening the evidence that intestinal bacteria influence emotions and behavior. The colonic microbiome is important to health and the pattern of composition and concentration varies extensively in complexity from birth to adulthood. That is, host genetics and environmental factors are complicit in shaping the development of the intestinal microbiome to achieve immunological tolerance and metabolic homeostasis from birth. Given that the intestinal microbiome perseveres to maintain gut homeostasis throughout the life cycle, epigenetic actions may determine the effect on the gut-brain axis and the beneficial outcomes on mood. Probiotics are postulated to exhibit a range of positive health benefits including immunomodulating capabilities. Lactobacillus and Bifidobacterium are genera of bacteria found in the intestines and so far, the benefits afforded by ingesting bacteria such as these as probiotics to people with mood disorders have varied in efficacy. Most likely, the efficacy of probiotic bacteria at improving mood has a multifactorial dependency, relying namely on several factors that include the agents used, the dose, the pattern of dosing, the pharmacotherapy used, the characteristics of the host and the underlying luminal microbial environment (e.g., gut dysbiosis). Clarifying the pathways linking probiotics with improvements in mood may help identify the factors that efficacy is dependent upon. Adjunctive therapies with probiotics for mood disorders could, through DNA methylation molecular mechanisms, augment the intestinal microbial active cohort and endow its mammalian host with important and critical co-evolutionary redox signaling metabolic interactions, that are embedded in bacterial genomes, and that in turn can enhance beneficial mood dispositions.
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Affiliation(s)
- Luis Vitetta
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2005, Australia
| | - Matthew Bambling
- Faculty of Medicine and Health, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Esben Strodl
- Faculty of Health, Queensland University of Technology, Brisbane, QLD 4058, Australia
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Abdolmaleky HM, Martin M, Zhou JR, Thiagalingam S. Epigenetic Alterations of Brain Non-Neuronal Cells in Major Mental Diseases. Genes (Basel) 2023; 14:896. [PMID: 37107654 PMCID: PMC10137903 DOI: 10.3390/genes14040896] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The tissue-specific expression and epigenetic dysregulation of many genes in cells derived from the postmortem brains of patients have been reported to provide a fundamental biological framework for major mental diseases such as autism, schizophrenia, bipolar disorder, and major depression. However, until recently, the impact of non-neuronal brain cells, which arises due to cell-type-specific alterations, has not been adequately scrutinized; this is because of the absence of techniques that directly evaluate their functionality. With the emergence of single-cell technologies, such as RNA sequencing (RNA-seq) and other novel techniques, various studies have now started to uncover the cell-type-specific expression and DNA methylation regulation of many genes (e.g., TREM2, MECP2, SLC1A2, TGFB2, NTRK2, S100B, KCNJ10, and HMGB1, and several complement genes such as C1q, C3, C3R, and C4) in the non-neuronal brain cells involved in the pathogenesis of mental diseases. Additionally, several lines of experimental evidence indicate that inflammation and inflammation-induced oxidative stress, as well as many insidious/latent infectious elements including the gut microbiome, alter the expression status and the epigenetic landscapes of brain non-neuronal cells. Here, we present supporting evidence highlighting the importance of the contribution of the brain's non-neuronal cells (in particular, microglia and different types of astrocytes) in the pathogenesis of mental diseases. Furthermore, we also address the potential impacts of the gut microbiome in the dysfunction of enteric and brain glia, as well as astrocytes, which, in turn, may affect neuronal functions in mental disorders. Finally, we present evidence that supports that microbiota transplantations from the affected individuals or mice provoke the corresponding disease-like behavior in the recipient mice, while specific bacterial species may have beneficial effects.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marian Martin
- Department of Neurology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Jin-Rong Zhou
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Pathology & Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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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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Anne A, Saxena S, Mohan KN. Genome-wide methylation analysis of post-mortem cerebellum samples supports the role of peroxisomes in autism spectrum disorder. Epigenomics 2022; 14:1015-1027. [PMID: 36154275 DOI: 10.2217/epi-2022-0184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We tested the hypothesis that a subset of patients with autism spectrum disorder (ASD) contains candidate genes with high DNA methylation differences (effective values) that potentially affect one of the two alleles. Materials & methods: Genome-wide DNA methylation comparisons were made on cerebellum samples from 30 patients and 45 controls. Results: 12 genes with high effective values, including GSDMD, MMACHC, SLC6A5 and NKX6-2, implicated in ASD and other neuropsychiatric disorders were identified. Monoallelic promoter methylation and downregulation were observed for SERHL (serine hydrolase-like) and CAT (catalase) genes associated with peroxisome function. Conclusion: These data are consistent with the hypothesis implicating impaired peroxisome function/biogenesis for ASD. A similar approach holds promise for identifying rare epimutations in ASD and other complex disorders.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Sonal Saxena
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
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Saulnier K, Berner A, Liosi S, Earp B, Berrios C, Dyke SO, Dupras C, Joly Y. Studying Vulnerable Populations Through an Epigenetics Lens: Proceed with Caution. CANADIAN JOURNAL OF BIOETHICS 2022. [DOI: 10.7202/1087205ar] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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12
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Abdolmaleky HM, Zhou JR, Thiagalingam S. Cataloging recent advances in epigenetic alterations in major mental disorders and autism. Epigenomics 2021; 13:1231-1245. [PMID: 34318684 PMCID: PMC8738978 DOI: 10.2217/epi-2021-0074] [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: 02/24/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
During the last two decades, diverse epigenetic modifications including DNA methylation, histone modifications, RNA editing and miRNA dysregulation have been associated with psychiatric disorders. A few years ago, in a review we outlined the most common epigenetic alterations in major psychiatric disorders (e.g., aberrant DNA methylation of DTNBP1, HTR2A, RELN, MB-COMT and PPP3CC, and increased expression of miR-34a and miR-181b). Recent follow-up studies have uncovered other DNA methylation aberrations affecting several genes in mental disorders, in addition to dysregulation of many miRNAs. Here, we provide an update on new epigenetic findings and highlight potential origin of the diversity and inconsistencies, focusing on drug effects, tissue/cell specificity of epigenetic landscape and discuss shortcomings of the current diagnostic criteria in mental disorders.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Jin-Rong Zhou
- Department of Surgery, Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02215 MA, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, 02118 MA, USA
- Genetics & Genomics Graduate Program, Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, 02218 MA, USA
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Kichukova T, Petrov V, Popov N, Minchev D, Naimov S, Minkov I, Vachev T. Identification of serum microRNA signatures associated with autism spectrum disorder as promising candidate biomarkers. Heliyon 2021; 7:e07462. [PMID: 34286132 PMCID: PMC8278430 DOI: 10.1016/j.heliyon.2021.e07462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 06/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background MicroRNAs (miRNAs) are short non-coding RNA molecules with a well-recognized role in gene expression mostly at the post-transcriptional level. Recently, dysregulation of miRNAs and miRNA-mRNA interactions has been associated with CNS diseases, including numerous psychiatric disorders. Dynamic changes in the expression profiles of circulating miRNA are nowadays regarded as promising non-invasive biomarkers that may facilitate the accurate and timely diagnosis of complex conditions. Methods In this study, we investigated the gene expression patterns of four miRNAs, which were previously reported to be dysregulated in pooled serum samples taken from Autism Spectrum Disorder (ASD) patients and typically developing children. The performance of a diagnostic model for ASD based on these four miRNAs was assessed by a receiver operating characteristic (ROC) curve analysis, which evaluates the diagnostic accuracy of the investigated miRNA biomarkers for ASD. Finally, to examine the potential modulation of CNS-related biological pathways, we carried out target identification and pathway analyses of the selected miRNAs. Results Significant differential expression for all the four studied miRNAs: miR-500a-5p, miR-197-5p, miR-424-5p, and miR-664a-3p, was consistently measured in the samples from ASD patients. The ROC curve analysis demonstrated high sensitivity and specificity for miR-500a-5p, miR-197-5p, and miR-424-5p. With all miRNA expression data integrated into an additive ROC curve, the combination of miR-500a-5p and miR-197-5p provided the most powerful diagnostic model. On the other hand, the mRNA target mining showed that miR-424-5p and miR-500-5p regulate pools of target mRNA molecules which are enriched in a number of biological pathways associated with the development and differentiation of the nervous system. Conclusions The steady expression patterns of miR-500a-5p, miR-197-5p, miR-424-5p, and miR-664a-3p in ASD children suggest that these miRNAs can be considered good candidates for non-invasive molecular biomarkers in the study of ASD patients. The highest diagnostic potential is manifested by miR-500a-5p and miR-197-5p, whose combined ROC curve demonstrates very strong predictive accuracy.
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Affiliation(s)
- Tatyana Kichukova
- Department of Plant Physiology and Molecular Biology, "Paisii Hilendarski" University of Plovdiv, 24 Tzar Assen Street, Plovdiv, Bulgaria
| | - Veselin Petrov
- Department of Plant Physiology, Biochemistry and Genetics, Agricultural University of Plovdiv, Bulgaria
| | - Nikolay Popov
- Psychiatric Ward for Active Treatment of Men, State Psychiatry Hospital Pazardzhik, Pazardzhik, Bulgaria
| | - Danail Minchev
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, 15-A Vassil Aprilov Blvd., Plovdiv, Bulgaria.,Division of Molecular and Regenerative Medicine, Research Institute at Medical University of 12 Plovdiv, 15A Vasil Aprilov Blvd, Plovdiv, 4000, Bulgaria
| | - Samir Naimov
- Department of Plant Physiology and Molecular Biology, "Paisii Hilendarski" University of Plovdiv, 24 Tzar Assen Street, Plovdiv, Bulgaria
| | - Ivan Minkov
- Institute of Molecular Biology and Biotechnologies (IMBB), Plovdiv, Bulgaria
| | - Tihomir Vachev
- Department of Plant Physiology and Molecular Biology, "Paisii Hilendarski" University of Plovdiv, 24 Tzar Assen Street, Plovdiv, Bulgaria
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14
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Zhang YH, Li Z, Zeng T, Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One 2021; 16:e0250032. [PMID: 33886611 PMCID: PMC8062050 DOI: 10.1371/journal.pone.0250032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Pregnancy is a complicated and long procedure during one or more offspring development inside a woman. A short period of oxygen shortage after birth is quite normal for most babies and does not threaten their health. However, if babies have to suffer from a long period of oxygen shortage, then this condition is an indication of pathological fetal intolerance, which probably causes their death. The identification of the pathological fetal intolerance from the physical oxygen shortage is one of the important clinical problems in obstetrics for a long time. The clinical syndromes typically manifest five symptoms that indicate that the baby may suffer from fetal intolerance. At present, liquid biopsy combined with high-throughput sequencing or mass spectrum techniques provides a quick approach to detect real-time alteration in the peripheral blood at multiple levels with the rapid development of molecule sequencing technologies. Gene methylation is functionally correlated with gene expression; thus, the combination of gene methylation and expression information would help in screening out the key regulators for the pathogenesis of fetal intolerance. We combined gene methylation and expression features together and screened out the optimal features, including gene expression or methylation signatures, for fetal intolerance prediction for the first time. In addition, we applied various computational methods to construct a comprehensive computational pipeline to identify the potential biomarkers for fetal intolerance dependent on the liquid biopsy samples. We set up qualitative and quantitative computational models for the prediction for fetal intolerance during pregnancy. Moreover, we provided a new prospective for the detailed pathological mechanism of fetal intolerance. This work can provide a solid foundation for further experimental research and contribute to the application of liquid biopsy in antenatal care.
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Affiliation(s)
- Yu-Hang Zhang
- School of Life Sciences, Shanghai University, Shanghai, China
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Margarita Gamarra
- Department of Computational Science and Electronic, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Romany F. Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga, Egypt
| | - José Escorcia-Gutierrez
- Electronic and Telecommunicacions Program, Universidad Autónoma del Caribe, Barranquilla, Colombia
- * E-mail: (JEG); (TH); (YDC)
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- * E-mail: (JEG); (TH); (YDC)
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15
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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16
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Ragusa M, Santagati M, Mirabella F, Lauretta G, Cirnigliaro M, Brex D, Barbagallo C, Domini CN, Gulisano M, Barone R, Trovato L, Oliveri S, Mongelli G, Spitale A, Barbagallo D, Di Pietro C, Stefani S, Rizzo R, Purrello M. Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children. Int J Mol Sci 2020; 21:ijms21176203. [PMID: 32867322 PMCID: PMC7504581 DOI: 10.3390/ijms21176203] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/16/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Recent evidence has demonstrated that salivary molecules, as well as bacterial populations, can be perturbed by several pathological conditions, including neuro-psychiatric diseases. This relationship between brain functionality and saliva composition could be exploited to unveil new pathological mechanisms of elusive diseases, such as Autistic Spectrum Disorder (ASD). We performed a combined approach of miRNA expression profiling by NanoString technology, followed by validation experiments in qPCR, and 16S rRNA microbiome analysis on saliva from 53 ASD and 27 neurologically unaffected control (NUC) children. MiR-29a-3p and miR-141-3p were upregulated, while miR-16-5p, let-7b-5p, and miR-451a were downregulated in ASD compared to NUCs. Microbiome analysis on the same subjects revealed that Rothia, Filifactor, Actinobacillus, Weeksellaceae, Ralstonia, Pasteurellaceae, and Aggregatibacter increased their abundance in ASD patients, while Tannerella, Moryella and TM7-3 decreased. Variations of both miRNAs and microbes were statistically associated to different neuropsychological scores related to anomalies in social interaction and communication. Among miRNA/bacteria associations, the most relevant was the negative correlation between salivary miR-141-3p expression and Tannerella abundance. MiRNA and microbiome dysregulations found in the saliva of ASD children are potentially associated with cognitive impairments of the subjects. Furthermore, a potential cross-talking between circulating miRNAs and resident bacteria could occur in saliva of ASD.
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Affiliation(s)
- Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
- Oasi Research Institute—IRCCS, 94018 Troina, Italy
| | - Maria Santagati
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Federica Mirabella
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Giovanni Lauretta
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Matilde Cirnigliaro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Duilia Brex
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Carla Noemi Domini
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Mariangela Gulisano
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Rita Barone
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Laura Trovato
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Salvatore Oliveri
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Gino Mongelli
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
- Bio-nanotech Research and Innovation Tower (BRIT), University of Catania, 95123 Catania, Italy
| | - Ambra Spitale
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy; (M.S.); (L.T.); (S.O.); (G.M.); (A.S.); (S.S.)
| | - Renata Rizzo
- Department of Clinical and Experimental Medicine, Section of Child and Adolescent Psychiatry, University of Catania, 95123 Catania, Italy; (C.N.D.); (M.G.); (R.B.); (R.R.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, 95123 Catania, Italy; (M.R.); (F.M.); (G.L.); (M.C.); (D.B.); (C.B.); (D.B.); (C.D.P.)
- Correspondence:
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Hrovatin K, Kunej T, Dolžan V. Genetic variability of serotonin pathway associated with schizophrenia onset, progression, and treatment. Am J Med Genet B Neuropsychiatr Genet 2020; 183:113-127. [PMID: 31674148 DOI: 10.1002/ajmg.b.32766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 12/22/2022]
Abstract
Schizophrenia (SZ) onset and treatment outcome have important genetic components, however individual genes do not have strong effects on SZ phenotype. Therefore, it is important to use the pathway-based approach and study metabolic and signaling pathways, such as dopaminergic and serotonergic. Serotonin pathway has an important role in brain signaling, nevertheless, its role in SZ is not as thoroughly examined as that of dopamine pathway. In this study, we reviewed serotonin pathway genes and genetic variations associated with SZ, including variations at DNA, RNA, and epigenetic level. We obtained 30 serotonin pathway genes from Kyoto encyclopedia of genes and genomes and used these genes for the literature review. We extracted 20 protein coding serotonin pathway genes with genetic variations associated with SZ onset, development, and treatment from 31 research papers. Genes associated with SZ are present on all levels of serotonin pathway: serotonin synthesis, transport, receptor binding, intracellular signaling, and reuptake; however, regulatory genes are poorly researched. We summarized common challenges of genetic association studies and presented some solutions. The analysis of reported serotonin pathway-SZ associations revealed lack of information about certain serotonin pathway genes potentially associated with SZ. Furthermore, it is becoming clear that interactions among serotonin pathway genes and their regulators may bring further knowledge about their involvement in SZ.
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Affiliation(s)
- Karin Hrovatin
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Ljubljana, Slovenia
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Ljubljana, Slovenia
| | - Vita Dolžan
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, Pharmacogenetics Laboratory, Ljubljana, Slovenia
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18
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Zhang Y, Peng P, Ju Y, Li G, Calhoun VD, Wang YP. Canonical Correlation Analysis of Imaging Genetics Data Based on Statistical Independence and Structural Sparsity. IEEE J Biomed Health Inform 2020; 24:2621-2629. [PMID: 32071012 DOI: 10.1109/jbhi.2020.2972581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Current developments of neuroimaging and genetics promote an integrative and compressive study of schizophrenia. However, it is still difficult to explore how gene mutations are related to brain abnormalities due to the high dimension but low sample size of these data. Conventional approaches reduce the dimension of dataset separately and then calculate the correlation, but ignore the effects of the response variables and the structure of data. To improve the identification of risk genes and abnormal brain regions on schizophrenia, in this paper, we propose a novel method called Independence and Structural sparsity Canonical Correlation Analysis (ISCCA). ISCCA combines independent component analysis (ICA) and Canonical Correlation Analysis (CCA) to reduce the collinear effects, which also incorporate graph structure of the data into the model to improve the accuracy of feature selection. The results from simulation studies demonstrate its higher accuracy in discovering correlations compared with other competing methods. Moreover, applying ISCCA to a real imaging genetics dataset collected by Mind Clinical Imaging Consortium (MCIC), a set of distinct gene-ROI interactions are identified, which are verified to be both statistically and biologically significant.
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19
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Schiele MA, Gottschalk MG, Domschke K. The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention. Clin Psychol Rev 2020; 77:101830. [PMID: 32163803 DOI: 10.1016/j.cpr.2020.101830] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/11/2022]
Abstract
Mental disorders are highly complex and multifactorial in origin, comprising an elaborate interplay of genetic and environmental factors. Epigenetic mechanisms such as DNA modifications (e.g. CpG methylation), histone modifications (e.g. acetylation) and microRNAs function as a translator between genes and the environment. Indeed, environmental influences such as exposure to stress shape epigenetic patterns, and lifetime experiences continue to alter the function of the genome throughout the lifespan. Here, we summarize the recently burgeoning body of research regarding the involvement of aberrant epigenetic signatures in mediating an increased vulnerability to a wide range of mental disorders. We review the current knowledge of epigenetic changes to constitute useful markers predicting the clinical response to psychotherapeutic interventions, and of psychotherapy to alter - and potentially reverse - epigenetic risk patterns. Given first evidence pointing to a transgenerational transmission of epigenetic information, epigenetic alterations arising from successful psychotherapy might be transferred to future generations and thus contribute to the prevention of mental disorders. Findings are integrated into a multi-level framework highlighting challenges pertaining to the mechanisms of action and clinical implications of epigenetic research. Promising future directions regarding the prediction, prevention, and personalized treatment of mental disorders in line with a 'precision medicine' approach are discussed.
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Affiliation(s)
- Miriam A Schiele
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany
| | - Michael G Gottschalk
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany; Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Breisacher Straße 64, D-79106 Freiburg, Germany.
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20
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Thiagalingam S. Epigenetic memory in development and disease: Unraveling the mechanism. Biochim Biophys Acta Rev Cancer 2020; 1873:188349. [PMID: 31982403 DOI: 10.1016/j.bbcan.2020.188349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 01/14/2023]
Abstract
Epigenetic memory is an essential process of life that governs the inheritance of predestined functional characteristics of normal cells and the newly acquired properties of cells affected by cancer and other diseases from parental to progeny cells. Unraveling the molecular basis of epigenetic memory dictated by protein and RNA factors in conjunction with epigenetic marks that are erased and re-established during embryogenesis/development during the formation of somatic, stem and disease cells will have far reaching implications to our understanding of embryogenesis/development and various diseases including cancer. While there has been enormous progress made, there are still gaps in knowledge which includes, the identity of unique epigenetic memory factors (EMFs) and epigenome coding enzymes/co-factors/scaffolding proteins involved in the assembly of defined "epigenetic memorysomes" and the epigenome marks that constitute collections of gene specific epigenetic memories corresponding to specific cell types and physiological conditions. A better understanding of the molecular basis for epigenetic memory will play a central role in improving diagnostics and prognostics of disease states and aid the development of targeted therapeutics of complex diseases.
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Affiliation(s)
- Sam Thiagalingam
- Department of Medicine (Biomedical Genetics Section and Cancer Center), Department of Pathology & Laboratory Medicine, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America.
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21
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Zhang C, Rong H. Genetic Advance in Depressive Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1180:19-57. [PMID: 31784956 DOI: 10.1007/978-981-32-9271-0_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Major depressive disorder (MDD) and bipolar disorder (BPD) are both chronic, severe mood disorder with high misdiagnosis rate, leading to substantial health and economic burdens to patients around the world. There is a high misdiagnosis rate of bipolar depression (BD) just based on symptomology in depressed patients whose previous manic or mixed episodes have not been well recognized. Therefore, it is important for psychiatrists to identify these two major psychiatric disorders. Recently, with the accumulation of clinical sample sizes and the advances of methodology and technology, certain progress in the genetics of major depression and bipolar disorder has been made. This article reviews the candidate genes for MDD and BD, genetic variation loci, chromosome structural variation, new technologies, and new methods.
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Affiliation(s)
- Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Han Rong
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen, Guangdong, China
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22
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Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
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23
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Barros SP, Hefni E, Nepomuceno R, Offenbacher S, North K. Targeting epigenetic mechanisms in periodontal diseases. Periodontol 2000 2019; 78:174-184. [PMID: 30198133 DOI: 10.1111/prd.12231] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic factors are heritable genome modifications that potentially impact gene transcription, contributing to disease states. Epigenetic marks play an important role in chronic inflammatory conditions, as observed in periodontal diseases, by allowing microbial persistence or by permitting microbial insult to play a role in the so-called 'hit-and-run' infectious mechanism, leading to lasting pathogen interference with the host genome. Epigenetics also affects the health sciences by providing a dynamic mechanistic framework to explain the way in which environmental and behavioral factors interact with the genome to alter disease risk. In this article we review current knowledge of epigenome regulation in light of the multifactorial nature of periodontal diseases. We discuss epigenetic tagging in identified genes, and consider the potential implications of epigenetic changes on host-microbiome dynamics in chronic inflammatory states and in response to environmental stressors. The most recent advances in genomic technologies have placed us in a position to analyze interaction effects (eg, between periodontal disease and type 2 diabetes mellitus), which can be investigated through epigenome-wide association analysis. Finally, because of the individualized traits of epigenetic biomarkers, pharmacoepigenomic perspectives are also considered as potentially novel therapeutic approaches for improving periodontal disease status.
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Affiliation(s)
- Silvana P Barros
- Department of Periodontology, University of North Carolina, Chapel Hil, NC, USA
| | - Eman Hefni
- Department of Periodontology, School of Dentistry, Umm Al Qura University, Makkah, Saudi Arabia
| | - Rafael Nepomuceno
- Department of Periodontology, University of North Carolina, Chapel Hil, NC, USA
| | - Steven Offenbacher
- Department of Periodontology, University of North Carolina, Chapel Hil, NC, USA
| | - Kari North
- Department of Epidemiology and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
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24
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Abdolmaleky HM, Gower AC, Wong CK, Cox JW, Zhang X, Thiagalingam A, Shafa R, Sivaraman V, Zhou JR, Thiagalingam S. Aberrant transcriptomes and DNA methylomes define pathways that drive pathogenesis and loss of brain laterality/asymmetry in schizophrenia and bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2019; 180:138-149. [PMID: 30468562 PMCID: PMC6386618 DOI: 10.1002/ajmg.b.32691] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/23/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022]
Abstract
Although the loss of brain laterality is one of the most consistent modalities in schizophrenia (SCZ) and bipolar disorder (BD), its molecular basis remains elusive. Our limited previous studies indicated that epigenetic modifications are key to the asymmetric transcriptomes of brain hemispheres. We used whole-genome expression microarrays to profile postmortem brain samples from subjects with SCZ, psychotic BD [BD[+]] or non-psychotic BD [BD(-)], or matched controls (10/group) and performed whole-genome DNA methylation (DNAM) profiling of the same samples (3-4/group) to identify pathways associated with SCZ or BD[+] and genes/sites susceptible to epigenetic regulation. qRT-PCR and quantitative DNAM analysis were employed to validate findings in larger sample sets (35/group). Gene Set Enrichment Analysis (GSEA) demonstrated that BMP signaling and astrocyte and cerebral cortex development are significantly (FDR q < 0.25) coordinately upregulated in both SCZ and BD[+], and glutamate signaling and TGFβ signaling are significantly coordinately upregulated in SCZ. GSEA also indicated that collagens are downregulated in right versus left brain of controls, but not in SCZ or BD[+] patients. Ingenuity Pathway Analysis predicted that TGFB2 is an upstream regulator of these genes (p = .0012). While lateralized expression of TGFB2 in controls (p = .017) is associated with a corresponding change in DNAM (p ≤ .023), lateralized expression and DNAM of TGFB2 are absent in SCZ or BD. Loss of brain laterality in SCZ and BD corresponds to aberrant epigenetic regulation of TGFB2 and changes in TGFβ signaling, indicating potential avenues for disease prevention/treatment.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA,Nutrition/Metabolism Laboratory, BIDMC, Harvard Medical School, Boston, MA,Corresponding Authors: Hamid Mostafavi Abdolmaleky () and Sam Thiagalingam ()
| | - Adam Chapin Gower
- Clinical and Translational Science Institute, Boston University School of Medicine, Boston, MA
| | - Chen Khuan Wong
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA,Genetics & Genomics Graduate Program, Boston University School of Medicine, Boston, MA
| | - Jiayi Wu Cox
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA,Bioinformatics Graduate Program, Boston University, Boston, MA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA
| | - Arunthathi Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA
| | | | - Vadivelu Sivaraman
- Critical Care Medicine, Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, MD
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, BIDMC, Harvard Medical School, Boston, MA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA,Genetics & Genomics Graduate Program, Boston University School of Medicine, Boston, MA,Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA,Corresponding Authors: Hamid Mostafavi Abdolmaleky () and Sam Thiagalingam ()
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25
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Abstract
Tourette syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females. Previous family and twin studies have shown that the majority of cases of TS are inherited. TS was previously thought to have an autosomal dominant pattern of inheritance. However, several decades of research have shown that this is unlikely the case. Instead, TS most likely results from a variety of genetic and environmental factors, not changes in a single gene. In the past decade, there has been a rapid development of innovative genetic technologies and methodologies, as well as significant progress in genetic studies of psychiatric disorders. In this review, we will briefly summarize previous genetic epidemiological studies of TS and related disorders. We will also review previous genetic studies based on genome-wide linkage analyses and candidate gene association studies to comment on problems of previous methodological and strategic issues. Our main purpose for this review will be to summarize the new genetic discoveries of TS based on novel genetic methods and strategies, such as genome-wide association studies (GWASs), whole exome sequencing (WES), and whole genome sequencing (WGS). We will also compare the new genetic discoveries of TS with other major psychiatric disorders in order to understand the current status of TS genetics and its relationship with other psychiatric disorders.
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26
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Ziegler C, Schiele MA, Domschke K. Patho- und Therapieepigenetik psychischer Erkrankungen. DER NERVENARZT 2018; 89:1303-1314. [DOI: 10.1007/s00115-018-0625-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
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28
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Gillet V, Hunting DJ, Takser L. Turing Revisited: Decoding the microRNA Messages in Brain Extracellular Vesicles for Early Detection of Neurodevelopmental Disorders. Curr Environ Health Rep 2018; 3:188-201. [PMID: 27301443 DOI: 10.1007/s40572-016-0093-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The prevention of neurodevelopmental disorders (NDD) of prenatal origin suffers from the lack of objective tools for early detection of susceptible individuals and the long time lag, usually in years, between the neurotoxic exposure and the diagnosis of mental dysfunction. Human data on the effects of alcohol, lead, and mercury and experimental data from animals on developmental neurotoxins and their long-term behavioral effects have achieved a critical mass, leading to the concept of the Developmental Origin of Health and Disease (DOHaD). However, there is currently no way to evaluate the degree of brain damage early after birth. We propose that extracellular vesicles (EVs) and particularly exosomes, released by brain cells into the fetal blood, may offer us a non-invasive means of assessing brain damage by neurotoxins. We are inspired by the strategy applied by Alan Turing (a cryptanalyst working for the British government), who created a first computer to decrypt German intelligence communications during World War II. Given the growing evidence that microRNAs (miRNAs), which are among the molecules carried by EVs, are involved in cell-cell communication, we propose that decrypting messages from EVs can allow us to detect damage thus offering an opportunity to cure, reverse, or prevent the development of NDD. This review summarizes recent findings on miRNAs associated with selected environmental toxicants known to be involved in the pathophysiology of NDD.
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Affiliation(s)
- Virginie Gillet
- Département Pédiatrie, Faculté de Médecine et Sciences de la Santé de l'Université de Sherbrooke, 3001, 12ème avenue Nord, Sherbrooke, Québec, Canada, J1H 5N4
| | - Darel John Hunting
- Département Radiobiologie, Faculté de Médecine et Sciences de la Santé de l'Université de Sherbrooke, 3001, 12ème avenue Nord, Sherbrooke, Québec, Canada, J1H 5N4
| | - Larissa Takser
- Département Pédiatrie, Faculté de Médecine et Sciences de la Santé de l'Université de Sherbrooke, 3001, 12ème avenue Nord, Sherbrooke, Québec, Canada, J1H 5N4.
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29
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Kernaleguen M, Daviaud C, Shen Y, Bonnet E, Renault V, Deleuze JF, Mauger F, Tost J. Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution. Methods Mol Biol 2018. [PMID: 29524144 DOI: 10.1007/978-1-4939-7774-1_18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here we provide two detailed protocols based on commercial kits for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. If only DNA methylation is of interest, sequencing libraries can be constructed from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For samples with significant levels of hydroxymethylation such as stem cells or brain tissue, we describe the protocol of oxidative bisulfite sequencing (OxBs-seq), which in its current version uses a post-bisulfite adaptor tagging (PBAT) approach. Two methylomes need to be generated: a classic methylome following bisulfite conversion and analyzing both methylated and hydroxymethylated cytosines and a methylome analyzing only methylated cytosines, respectively. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocols have been successfully applied to different human samples and yield robust and reproducible results.
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Affiliation(s)
- Magali Kernaleguen
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Yimin Shen
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Eric Bonnet
- Laboratory for Bio-analysis, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France.,Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, Paris, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Evry, France.
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30
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Daviaud C, Renault V, Mauger F, Deleuze JF, Tost J. Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol. Methods Mol Biol 2018; 1708:83-104. [PMID: 29224140 DOI: 10.1007/978-1-4939-7481-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. The converted library is then amplified with an optimal number of PCR cycles to ensure high sequence diversity and low duplicate rates. Spike-in of unmethylated DNA allows for the precise estimation of bisulfite conversion rates. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human samples as well as DNA extracted from plant tissues and yields robust and reproducible results.
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Affiliation(s)
- Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Victor Renault
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, Paris, 75010, France
| | - Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
- Laboratory for Bioinformatics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, Paris, 75010, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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31
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Schmitz J, Metz GA, Güntürkün O, Ocklenburg S. Beyond the genome—Towards an epigenetic understanding of handedness ontogenesis. Prog Neurobiol 2017; 159:69-89. [DOI: 10.1016/j.pneurobio.2017.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/18/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022]
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32
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Systematic Review of Epigenetic Effects of Pharmacological Agents for Bipolar Disorders. Brain Sci 2017; 7:brainsci7110154. [PMID: 29156546 PMCID: PMC5704161 DOI: 10.3390/brainsci7110154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023] Open
Abstract
Epigenetic effects of medications are an evolving field of medicine, and can change the landscape of drug development. The aim of this paper is to systematically review the literature of the relationship between common medications used for treatment of bipolar disorders and epigenetic modifications. MedLine/PubMed searches were performed based on pre-specified inclusion criteria from inception to November 2017. Six animal and human studies met the inclusion criteria. These studies examined the epigenetic changes in the main classes of medications that are used in bipolar disorders, namely mood stabilizers and antipsychotics. Although these initial studies have small to moderate sample size, they generally suggest an evolving and accumulating evidence of epigenetic changes that are associated with several of the medications that are used in bipolar I and II disorders. In this manuscript, we describe the specific epigenetic changes that are associated with the medications studied. Of the studies reviewed, five of the six studies revealed epigenetic changes associated with the use of mood stabilizers or antipsychotic medications. This review contributes to future research directions. Further understanding of the complexities of the epigenome and the untangling of the effects and contributions of disease states versus medications is crucial for the future of drug design and the development of new therapeutics. Epigenetic therapeutics hold great promise for complex disease treatment and personalized interventions, including psychiatric diseases.
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33
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Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Arking DE, Ladd-Acosta C, Fallin MD. Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. Nat Commun 2017; 8:1011. [PMID: 29066808 PMCID: PMC5654961 DOI: 10.1038/s41467-017-00868-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/28/2017] [Indexed: 01/07/2023] Open
Abstract
Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; P < 0.001) and peripheral blood meQTLs (OR = 1.58; P < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly. “There have been a number of recent epigenetic studies on autism spectrum disorder. Here, the authors integrate genetic and epigenetic data from cord and peripheral blood and also from brain tissues to show the potential of blood-based epigenetic data to provide insights into psychiatric disorders.”
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Affiliation(s)
- Shan V Andrews
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Shannon E Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Brooke Sheppard
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis, 4610 X St, Sacramento, CA, 95817, USA.,MIND Institute, University of California Davis, 2825 50th St, Sacramento, CA, 95817, USA
| | - Craig J Newschaffer
- AJ Drexel Autism Institute, Drexel University, 3020 Market St #560, Philadelphia, PA, 19104, USA.,Department of Epidemiology and Biostatistics, Drexel University Dornsife School of Public Health, 3125 Market St, Philadelphia, PA, 19104, USA
| | - Andrew P Feinberg
- Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Dan E Arking
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe St, Baltimore, MD, 21205, USA. .,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA.
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA. .,Center for Epigenetics, Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA.
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34
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Qi Y, Zheng Y, Li Z, Xiong L. Progress in Genetic Studies of Tourette's Syndrome. Brain Sci 2017; 7:E134. [PMID: 29053637 PMCID: PMC5664061 DOI: 10.3390/brainsci7100134] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/23/2022] Open
Abstract
Tourette's Syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females. Previous family and twin studies have shown that the majority of cases of TS are inherited. TS was previously thought to have an autosomal dominant pattern of inheritance. However, several decades of research have shown that this is unlikely the case. Instead TS most likely results from a variety of genetic and environmental factors, not changes in a single gene. In the past decade, there has been a rapid development of innovative genetic technologies and methodologies, as well as significant progresses in genetic studies of psychiatric disorders. In this review, we will briefly summarize previous genetic epidemiological studies of TS and related disorders. We will also review previous genetic studies based on genome-wide linkage analyses and candidate gene association studies to comment on problems of previous methodological and strategic issues. Our main purpose for this review will be to summarize the new genetic discoveries of TS based on novel genetic methods and strategies, such as genome-wide association studies (GWASs), whole exome sequencing (WES) and whole genome sequencing (WGS). We will also compare the new genetic discoveries of TS with other major psychiatric disorders in order to understand the current status of TS genetics and its relationship with other psychiatric disorders.
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Affiliation(s)
- Yanjie Qi
- Laboratoire de Neurogénétique, Centre de Recherche, Institut Universitaire en Santé Mentale de Montréal, Montreal, QC H1N 3V2, Canada.
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
| | - Yi Zheng
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
- Center of Schizophrenia, Beijing Institute for Brain Disorders, Beijing 100088, China.
| | - Zhanjiang Li
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China.
- Center of Schizophrenia, Beijing Institute for Brain Disorders, Beijing 100088, China.
| | - Lan Xiong
- Laboratoire de Neurogénétique, Centre de Recherche, Institut Universitaire en Santé Mentale de Montréal, Montreal, QC H1N 3V2, Canada.
- Département de Psychiatrie, Faculté de Médecine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada.
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35
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Alam R, Abdolmaleky HM, Zhou JR. Microbiome, inflammation, epigenetic alterations, and mental diseases. Am J Med Genet B Neuropsychiatr Genet 2017; 174:651-660. [PMID: 28691768 PMCID: PMC9586840 DOI: 10.1002/ajmg.b.32567] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022]
Abstract
Major mental diseases such as autism, bipolar disorder, schizophrenia, and major depressive disorder are debilitating illnesses with complex etiologies. Recent findings show that the onset and development of these illnesses cannot be well described by the one-gene; one-disease approach. Instead, their clinical presentation is thought to result from the regulative interplay of a large number of genes. Even though the involvement of many genes are likely, up regulating and activation or down regulation and silencing of these genes by the environmental factors play a crucial role in contributing to their pathogenesis. Much of this interplay may be moderated by epigenetic changes. Similar to genetic mutations, epigenetic modifications such as DNA methylation, histone modifications, and RNA interference can influence gene expression and therefore may cause behavioral and neuronal changes observed in mental disorders. Environmental factors such as diet, gut microbiota, and infections have significant role in these epigenetic modifications. Studies show that bioactive nutrients and gut microbiota can alter either DNA methylation and histone signatures through a variety of mechanisms. Indeed, microbes within the human gut may play a significant role in the regulation of various elements of "gut-brain axis," via their influence on inflammatory cytokines and production of antimicrobial peptides that affect the epigenome through their involvement in generating short chain fatty acids, vitamin synthesis, and nutrient absorption. In addition, they may participate in-gut production of many common neurotransmitters. In this review we will consider the potential interactions of diet, gastrointestinal microbiome, inflammation, and epigenetic alterations in psychiatric disorders.
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Affiliation(s)
- Reza Alam
- Nutrition/Metabolism Laboratory; Beth Israel Deaconess Medical Center; Harvard Medical School; Boston Massachusetts
| | - Hamid M. Abdolmaleky
- Nutrition/Metabolism Laboratory; Beth Israel Deaconess Medical Center; Harvard Medical School; Boston Massachusetts
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory; Beth Israel Deaconess Medical Center; Harvard Medical School; Boston Massachusetts
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36
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Gomes KMS, Costa IC, Santos JFD, Dourado PMM, Forni MF, Ferreira JCB. Induced pluripotent stem cells reprogramming: Epigenetics and applications in the regenerative medicine. Rev Assoc Med Bras (1992) 2017; 63:180-189. [PMID: 28355380 DOI: 10.1590/1806-9282.63.02.180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 05/30/2016] [Indexed: 12/20/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are somatic cells reprogrammed into an embryonic-like pluripotent state by the expression of specific transcription factors. iPSC technology is expected to revolutionize regenerative medicine in the near future. Despite the fact that these cells have the capacity to self-renew, they present low efficiency of reprogramming. Recent studies have demonstrated that the previous somatic epigenetic signature is a limiting factor in iPSC performance. Indeed, the process of effective reprogramming involves a complete remodeling of the existing somatic epigenetic memory, followed by the establishment of a "new epigenetic signature" that complies with the new type of cell to be differentiated. Therefore, further investigations of epigenetic modifications associated with iPSC reprogramming are required in an attempt to improve their self-renew capacity and potency, as well as their application in regenerative medicine, with a new strategy to reduce the damage in degenerative diseases. Our review aimed to summarize the most recent findings on epigenetics and iPSC, focusing on DNA methylation, histone modifications and microRNAs, highlighting their potential in translating cell therapy into clinics.
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Affiliation(s)
- Kátia Maria Sampaio Gomes
- Department of Anatomy, Institute of Biomedical Sciences III, Universidade de São Paulo (ICB III/USP), São Paulo, SP, Brazil
| | - Ismael Cabral Costa
- Department of Anatomy, Institute of Biomedical Sciences III, Universidade de São Paulo (ICB III/USP), São Paulo, SP, Brazil
| | | | | | | | - Julio Cesar Batista Ferreira
- Department of Anatomy, Institute of Biomedical Sciences III, Universidade de São Paulo (ICB III/USP), São Paulo, SP, Brazil
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Cirnigliaro M, Barbagallo C, Gulisano M, Domini CN, Barone R, Barbagallo D, Ragusa M, Di Pietro C, Rizzo R, Purrello M. Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:250. [PMID: 28848387 PMCID: PMC5554380 DOI: 10.3389/fnmol.2017.00250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Given its prevalence and social impact, Autism Spectrum Disorder (ASD) is drawing much interest. Molecular basis of ASD is heterogeneous and only partially known. Many factors, including disorders comorbid with ASD, like TS (Tourette Syndrome), complicate ASD behavior-based diagnosis and make it vulnerable to bias. To further investigate ASD etiology and to identify potential biomarkers to support its precise diagnosis, we used TaqMan Low Density Array technology to profile serum miRNAs from ASD, TS, and TS+ASD patients, and unaffected controls (NCs). Through validation assays in 30 ASD, 24 TS, and 25 TS+ASD patients and 25 NCs, we demonstrated that miR-140-3p is upregulated in ASD vs.: NC, TS, and TS+ASD (Tukey's test, p-values = 0.03, = 0.01, < 0.0001, respectively). ΔCt values for miR-140-3p and YGTSS (Yale Global Tic Severity Scale) scores are positively correlated (Spearman r = 0.33; Benjamini-Hochberg p = 0.008) and show a linear relationship (p = 0.002). Network functional analysis showed that nodes controlled by miR-140-3p, especially CD38 and NRIP1 which are its validated targets, are involved in processes convergingly dysregulated in ASD, such as synaptic plasticity, immune response, and chromatin binding. Biomarker analysis proved that serum miR-140-3p can discriminate among: (1) ASD and NC (Area under the ROC curve, AUC: 0.70; sensitivity: 63.33%; specificity: 68%); (2) ASD and TS (AUC: 0.72; sensitivity: 66.66%; specificity: 70.83%); (3) ASD and TS+ASD (AUC: 0.78; sensitivity: 73.33%; specificity: 76%). Characterization of miR-140-3p network would contribute to further clarify ASD etiology. Serum miR-140-3p could represent a potential non-invasive biomarker for ASD, easy to test through liquid biopsy.
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Affiliation(s)
- Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Mariangela Gulisano
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Carla N Domini
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Rita Barone
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy.,Associazione Oasi Maria SS. Onlus (IRCCS), Institute for Research on Mental Retardation and Brain AgingTroina, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
| | - Renata Rizzo
- Section of Child and Adolescent Psychiatry, Department of Clinical and Experimental Medicine, University of CataniaCatania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of CataniaCatania, Italy
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Hamza M, Halayem S, Mrad R, Bourgou S, Charfi F, Belhadj A. Implication de l’épigénétique dans les troubles du spectre autistique : revue de la littérature. Encephale 2017; 43:374-381. [DOI: 10.1016/j.encep.2016.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 01/24/2023]
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Differences in 5-HT2A and mGlu2 Receptor Expression Levels and Repressive Epigenetic Modifications at the 5-HT2A Promoter Region in the Roman Low- (RLA-I) and High- (RHA-I) Avoidance Rat Strains. Mol Neurobiol 2017; 55:1998-2012. [PMID: 28265857 DOI: 10.1007/s12035-017-0457-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 01/12/2023]
Abstract
The serotonin 2A (5-HT2A) and metabotropic glutamate 2 (mGlu2) receptors regulate each other and are associated with schizophrenia. The Roman high- (RHA-I) and the Roman low- (RLA-I) avoidance rat strains present well-differentiated behavioral profiles, with the RHA-I strain emerging as a putative genetic rat model of schizophrenia-related features. The RHA-I strain shows increased 5-HT2A and decreased mGlu2 receptor binding levels in prefrontal cortex (PFC). Here, we looked for differences in gene expression and transcriptional regulation of these receptors. The striatum (STR) was included in the analysis. 5-HT2A, 5-HT1A, and mGlu2 mRNA and [3H]ketanserin binding levels were measured in brain homogenates. As expected, 5-HT2A binding was significantly increased in PFC in the RHA-I rats, while no difference in binding was observed in STR. Surprisingly, 5-HT2A gene expression was unchanged in PFC but significantly decreased in STR. mGlu2 receptor gene expression was significantly decreased in both PFC and STR. No differences were observed for the 5-HT1A receptor. Chromatin immunoprecipitation assay revealed increased trimethylation of histone 3 at lysine 27 (H3K27me3) at the promoter region of the HTR2A gene in the STR. We further looked at the Akt/GSK3 signaling pathway, a downstream point of convergence of the serotonin and glutamate system, and found increased phosphorylation levels of GSK3β at tyrosine 216 and increased β-catenin levels in the PFC of the RHA-I rats. These results reveal region-specific regulation of the 5-HT2A receptor in the RHA-I rats probably due to absence of mGlu2 receptor that may result in differential regulation of downstream pathways.
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Ueda J, Murata Y, Bundo M, Oh-Nishi A, Kassai H, Ikegame T, Zhao Z, Jinde S, Aiba A, Suhara T, Kasai K, Kato T, Iwamoto K. Use of human methylation arrays for epigenome research in the common marmoset (Callithrix jacchus). Neurosci Res 2017; 120:60-65. [PMID: 28215819 DOI: 10.1016/j.neures.2017.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/20/2017] [Accepted: 02/14/2017] [Indexed: 01/16/2023]
Abstract
We examined the usefulness of commercially available DNA methylation arrays designed for the human genome (Illumina HumanMethylation450 and MethylationEPIC) for high-throughput epigenome analysis of the common marmoset, a nonhuman primate suitable for research on neuropsychiatric disorders. From among the probes on the methylation arrays, we selected those available for the common marmoset. DNA methylation data were obtained from genomic DNA extracted from the frontal cortex and blood samples of adult common marmosets as well as the frontal cortex of neonatal marmosets. About 10% of the probes on the arrays were estimated to be useful for DNA methylation assay in the common marmoset. Strong correlations existed between human and marmoset DNA methylation data. Illumina methylation arrays are useful for epigenome research using the common marmoset.
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Affiliation(s)
- Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako City, Saitama, 351-0198, Japan
| | - Yui Murata
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan; Department of Molecular Brain Science, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto City, Kumamoto, 860-8556, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto City, Kumamoto, 860-8556, Japan
| | - Arata Oh-Nishi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Sciences and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba, 263-8555, Japan
| | - Hidetoshi Kassai
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Zhilei Zhao
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Seiichiro Jinde
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tetsuya Suhara
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institute for Quantum and Radiological Sciences and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba, 263-8555, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako City, Saitama, 351-0198, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto City, Kumamoto, 860-8556, Japan.
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Abstract
BACKGROUND Epigenetics refers to the study of heritable changes in gene expression not involving changes in DNA sequence and is presently an active area of research in biology and medicine. There is increasing evidence that epigenetics is involved in the pathogenesis of psychiatric disorders. AIMS AND METHODS Several studies conducted to date have suggested that psychosocial factors act by modifying epigenetic mechanisms of gene expression in the brain in the pathogenesis of psychiatric disorders. Such studies have been conducted both on brain tissues and also using peripheral tissues as substitutes for brain tissues. This article reviews such studies. RESULTS AND CONCLUSION Epigenetic mechanisms of gene expression in the brain appear to link one individual with another in the context of social psychiatry. Epigenetics appears to be of major importance to the field of social psychiatry.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College Vellore, Vellore, India
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Nassan M, Li Q, Croarkin PE, Chen W, Colby CL, Veldic M, McElroy SL, Jenkins GD, Ryu E, Cunningham JM, Leboyer M, Frye MA, Biernacka JM. A genome wide association study suggests the association of muskelin with early onset bipolar disorder: Implications for a GABAergic epileptogenic neurogenesis model. J Affect Disord 2017; 208:120-129. [PMID: 27769005 DOI: 10.1016/j.jad.2016.09.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/22/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Although multiple genes have been implicated in bipolar disorder (BD), they explain only a small proportion of its heritability. Identifying additional BD risk variants may be impaired by phenotypic heterogeneity, which is usually not taken into account in genome-wide association studies (GWAS). BD with early age at onset is a more homogeneous familial form of the disorder associated with greater symptom severity. METHODS We conducted a GWAS of early-onset BD (onset of mania/hypomania ≤19 years old) in a discovery sample of 419 cases and 1034 controls and a replication sample of 181 cases and 777 controls. These two samples were meta-analyzed, followed by replication of one signal in a third independent sample of 141 cases and 746 controls. RESULTS No single nucleotide polymorphism (SNP) associations were genome-wide significant in the discovery sample. Of the top 15 SNPs in the discovery analysis, rs114034759 in the muskelin (MKLN1) gene was nominally significant in the replication analysis, and was among the top associations in the meta-analysis (p=2.63E-06, OR=1.9). In the third sample, this SNP was again associated with early-onset BD (p=0.036, OR=1.6). Gene expression analysis showed that the rs114034759 risk allele is associated with decreased hippocampal MKLN1 expression. LIMITATIONS The sample sizes of the early-onset BD subgroups were relatively small. CONCLUSIONS Our results suggest MKLN1 is associated with early-onset BD. MKLN1 regulates cellular trafficking of GABA-A receptors, which is involved in synaptic transmission and plasticity, and is implicated in the mechanism of action of a group of antiepileptic mood stabilizers. These results therefore indicate that GABAergic neurotransmission may be implicated in early-onset BD. We propose that an increase in GABA-A receptors in the hippocampus in BD patients due to lower MKLN1 expression might increase the excitability during the GABA-excited early phase of young neurons, leading to an increased risk of developing a manic/hypomanic episode. Further studies are needed to test this model.
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Affiliation(s)
- Malik Nassan
- Department of Psychiatry & Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States.
| | - Qingqin Li
- Janssen Research & Development, LLC, Titusville, NJ, United States
| | - Paul E Croarkin
- Department of Psychiatry & Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Wenan Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Colin L Colby
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Marin Veldic
- Department of Psychiatry & Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Susan L McElroy
- Lindner Center of HOPE, Mason, OH and Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, United States
| | - Gregory D Jenkins
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Julie M Cunningham
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Marion Leboyer
- Université Paris-Est Créteil Val de Marne, Créteil, France
| | - Mark A Frye
- Department of Psychiatry & Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States
| | - Joanna M Biernacka
- Department of Psychiatry & Psychology, Mayo Clinic Depression Center, Mayo Clinic, Rochester, MN, United States; Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States.
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Abu-Akel A, Clark J, Perry A, Wood SJ, Forty L, Craddock N, Jones I, Gordon-Smith K, Jones L. Autistic and schizotypal traits and global functioning in bipolar I disorder. J Affect Disord 2017; 207:268-275. [PMID: 27736738 DOI: 10.1016/j.jad.2016.09.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 08/17/2016] [Accepted: 09/05/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To determine the expression of autistic and positive schizotypal traits in a large sample of adults with bipolar I disorder (BD I), and the effect of co-occurring autistic and positive schizotypal traits on global functioning in BD I. METHOD Autistic and positive schizotypal traits were self-assessed in 797 individuals with BD-I recruited by the Bipolar Disorder Research Network. Differences in global functioning (rated using the Global Assessment Scale) during lifetime worst depressive and manic episodes (GASD and GASM respectively) were calculated in groups with high/low autistic and positive schizotypal traits. Regression analyses assessed the interactive effect of autistic and positive schizotypal traits on global functioning. RESULTS 47.2% (CI=43.7-50.7%) showed clinically significant levels of autistic traits, and 23.22% (95% CI=20.29-26.14) showed clinically significant levels of positive schizotypal traits. In the worst episode of mania, the high autistic, high positive schizotypal group had better global functioning compared to the other groups. Individual differences analyses showed that high levels of both traits were associated with better global functioning in both mood states. LIMITATIONS Autistic and schizotypal traits were assessed using self-rated questionnaires. CONCLUSIONS Expression of autistic and schizotypal traits in adults with BD I is prevalent, and may be important to predict illness aetiology, prognosis, and diagnostic practices in this population. Future work should focus on replicating these findings in independent samples, and on the biological and/or psychosocial mechanisms underlying better global functioning in those who have high levels of both autistic and positive schizotypal traits.
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Affiliation(s)
- Ahmad Abu-Akel
- School of Psychology, University of Birmingham, Birmingham, United Kingdom
| | - Jennifer Clark
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Amy Perry
- Department of Psychological Medicine, University of Worcester, Worcester, United Kingdom
| | - Stephen J Wood
- School of Psychology, University of Birmingham, Birmingham, United Kingdom; Melbourne Neuropsychiatry Centre, University of Melbourne and Melbourne Health, Melbourne, Victoria, Australia
| | - Liz Forty
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Nick Craddock
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Ian Jones
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Katherine Gordon-Smith
- Department of Psychological Medicine, University of Worcester, Worcester, United Kingdom
| | - Lisa Jones
- Department of Psychological Medicine, University of Worcester, Worcester, United Kingdom.
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Nohesara S, Ghadirivasfi M, Barati M, Ghasemzadeh MR, Narimani S, Mousavi-Behbahani Z, Joghataei M, Soleimani M, Taban M, Mehrabi S, Thiagalingam S, Abdolmaleky HM. Methamphetamine-induced psychosis is associated with DNA hypomethylation and increased expression of AKT1 and key dopaminergic genes. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1180-1189. [PMID: 27753212 PMCID: PMC7115129 DOI: 10.1002/ajmg.b.32506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Abstract
Methamphetamine, one of the most frequently used illicit drugs worldwide, can induce psychosis in a large fraction of abusers and it is becoming a major problem for the health care institutions. There is some evidence that genetic and epigenetic factors may play roles in methamphetamine psychosis. In this study, we examined methamphetamine-induced epigenetic and expression changes of several key genes involved in psychosis. RNA and DNA extracted from the saliva samples of patients with methamphetamine dependency with and without psychosis as well as control subjects (each group 25) were analyzed for expression and promoter DNA methylation status of DRD1, DRD2, DRD3, DRD4, MB-COMT, GAD1, and AKT1 using qRT-PCR and q-MSP, respectively. We found statistically significant DNA hypomethylation of the promoter regions of DRD3 (P = 0.032), DRD4 (P = 0.05), MB-COMT (P = 0.009), and AKT1 (P = 0.0008) associated with increased expression of the corresponding genes in patients with methamphetamine psychosis (P = 0.022, P = 0.034, P = 0.035, P = 0.038, respectively), and to a lesser degree in some of the candidate genes in non-psychotic patients versus the control subjects. In general, methamphetamine dependency is associated with reduced DNA methylation and corresponding increase in expression of several key genes involved in the pathogenesis of psychotic disorders. While these epigenetic changes can be useful diagnostic biomarkers for psychosis in methamphetamine abusers, it is also consistent with the use of methyl rich diet for prevention or suppression of psychosis in these patients. However, this needs to be confirmed in future studies. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shabnam Nohesara
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ghadirivasfi
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmood Barati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Ghasemzadeh
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Narimani
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Mousavi-Behbahani
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadtaghi Joghataei
- Faculty of Medicine, Department of Anatomy and Neuroscience, Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mansoureh Soleimani
- Faculty of Medicine, Department of Anatomy and Neuroscience, Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mozhgan Taban
- Mental Health Research Center and Department of Psychiatry, Iran University of Medical Sciences, Tehran, Iran
| | - Soraya Mehrabi
- Department of Neuroscience, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts,Correspondence to: Sam Thiagalingam and Hamid Mostafavi Abdolmaleky, Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118., (S.T.); (H.M.A.)
| | - Hamid Mostafavi Abdolmaleky
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts,Correspondence to: Sam Thiagalingam and Hamid Mostafavi Abdolmaleky, Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118., (S.T.); (H.M.A.)
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Dissecting bipolar disorder complexity through epigenomic approach. Mol Psychiatry 2016; 21:1490-1498. [PMID: 27480490 PMCID: PMC5071130 DOI: 10.1038/mp.2016.123] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 01/16/2023]
Abstract
In recent years, numerous studies of gene regulation mechanisms have emerged in neuroscience. Epigenetic modifications, described as heritable but reversible changes, include DNA methylation, DNA hydroxymethylation, histone modifications and noncoding RNAs. The pathogenesis of psychiatric disorders, such as bipolar disorder, may be ascribed to a complex gene-environment interaction (G × E) model, linking the genome, environmental factors and epigenetic marks. Both the high complexity and the high heritability of bipolar disorder make it a compelling candidate for neurobiological analyses beyond DNA sequencing. Questions that are being raised in this review are the precise phenotype of the disorder in question, and also the trait versus state debate and how these concepts are being implemented in a variety of study designs.
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Cureau N, AlJahdali N, Vo N, Carbonero F. Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives. Epigenomics 2016; 8:1259-73. [DOI: 10.2217/epi-2016-0057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human microbiota and epigenetic processes have both been shown to play a crucial role in health and disease. However, there is extremely scarce information on epigenetic modulation of microbiota members except for a few pathogens. Mainly DNA adenine methylation has been described extensively in modulating the virulence of pathogenic bacteria in particular. It would thus appear likely that such mechanisms are widespread for most bacterial members of the microbiota. This review will present briefly the current knowledge on epigenetic processes in bacteria, give examples of known methylation processes in microbial members of the human microbiota and summarize the knowledge on regulation of host epigenetic processes by the human microbiota.
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Affiliation(s)
- Natacha Cureau
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nesreen AlJahdali
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nguyen Vo
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
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Dobrowolski SF, Lyons-Weiler J, Spridik K, Vockley J, Skvorak K, Biery A. DNA methylation in the pathophysiology of hyperphenylalaninemia in the PAH(enu2) mouse model of phenylketonuria. Mol Genet Metab 2016; 119:1-7. [PMID: 26822703 PMCID: PMC8958364 DOI: 10.1016/j.ymgme.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/31/2015] [Accepted: 01/01/2016] [Indexed: 12/25/2022]
Abstract
Phenylalanine hydroxylase deficient phenylketonuria (PKU) is the paradigm for a treatable inborn error of metabolism where maintaining plasma phenylalanine (Phe) in the therapeutic range relates to improved clinical outcomes. While Phe is the presumed intoxicating analyte causal in neurologic damage, the mechanism(s) of Phe toxicity has remained elusive. Altered DNA methylation is a recognized response associated with exposure to numerous small molecule toxic agents. Paralleling this effect, we hypothesized that chronic Phe over-exposure in the brain would lead to aberrant DNA methylation with secondary influence upon gene regulation that would ultimately contribute to PKU neuropathology. The PAH(enu2) mouse models human PKU with intrinsic hyperphenylalaninemia, abnormal response to Phe challenge, and neurologic deficit. To examine this hypothesis, we assessed DNA methylation patterns in brain tissues using methylated DNA immunoprecipitation and paired end sequencing in adult PAH(enu2) animals maintained under either continuous dietary Phe restriction or chronic hyperphenylalaninemia. Heterozygous PAH(enu2/WT) litter mates served as controls for normal Phe exposure. Extensive repatterning of DNA methylation was observed in brain tissue of hyperphenylalaninemic animals while Phe restricted animals displayed an attenuated pattern of aberrant DNA methylation. Affected gene coding regions displayed aberrant hypermethylation and hypomethylation. Gene body methylation of noncoding RNA genes was observed and among these microRNA genes were prominent. Of particular note, observed only in hyperphenylalaninemic animals, was hypomethylation of miRNA genes within the imprinted Dlk1-Dio3 locus on chromosome 12. Aberrant methylation of microRNA genes influenced their expression which has secondary effects upon the expression of targeted protein coding genes. Differential hypermethylation of gene promoters was exclusive to hyperphenylalaninemic PAH(enu2) animals. Genes with synaptic involvement were targets of promoter hypermethylation that resulted in down-regulation of their expression. Gene dysregulation secondary to abnormal DNA methylation may be contributing to PKU neuropathology. These results suggest drugs that prevent or correct aberrant DNA methylation may offer a novel therapeutic option to management of neurological symptoms in PKU patients.
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Affiliation(s)
- S F Dobrowolski
- Department of Pathology, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States.
| | - J Lyons-Weiler
- Genomics and Proteomics Core Laboratories, University of Pittsburgh, 3343 Forbes Avenue, Pittsburgh, PA 15260, United States
| | - K Spridik
- Department of Pathology, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - J Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - K Skvorak
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - A Biery
- Department of Pathology, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
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Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". Curr Behav Neurosci Rep 2016; 3:264-274. [PMID: 28093577 DOI: 10.1007/s40473-016-0083-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Evidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages. RECENT FINDINGS Brain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important. SUMMARY Epigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Alycia Halladay
- Autism Science Foundation, New York City, New York, USA; Department of Pharmacology and Toxicology, Rutgers University, New Brunswick, New Jersey, USA
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK; Institute for Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Luoni A, Riva MA. MicroRNAs and psychiatric disorders: From aetiology to treatment. Pharmacol Ther 2016; 167:13-27. [PMID: 27452338 DOI: 10.1016/j.pharmthera.2016.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023]
Abstract
The emergence of psychiatric disorders relies on the interaction between genetic vulnerability and environmental adversities. Several studies have demonstrated a crucial role for epigenetics (e.g. DNA methylation, post-translational histone modifications and microRNA-mediated post-transcriptional regulation) in the translation of environmental cues into adult behavioural outcome, which can prove to be harmful thus increasing the risk to develop psychopathology. Within this frame, non-coding RNAs, especially microRNAs, came to light as pivotal regulators of many biological processes occurring in the Central Nervous System, both during the neuronal development as well as in the regulation of adult function, including learning, memory and neuronal plasticity. On these basis, in recent years it has been hypothesised a central role for microRNA modulation and expression regulation in many brain disorders, including neurodegenerative disorders and mental illnesses. Indeed, the aim of the present review is to present the most recent state of the art regarding microRNA involvement in psychiatric disorders. We will first describe the mechanisms that regulate microRNA biogenesis and we will report evidences of microRNA dysregulation in peripheral body fluids, in postmortem brain tissues from patients suffering from psychopathology as well as in animal models. Last, we will discuss the potential to consider microRNAs as putative target for pharmacological intervention, using common psychotropic drugs or more specific tools, with the aim to normalize functions that are disrupted in different psychiatric conditions.
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Affiliation(s)
- Alessia Luoni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy
| | - Marco Andrea Riva
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milan, Italy.
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Alternatively Spliced Methionine Synthase in SH-SY5Y Neuroblastoma Cells: Cobalamin and GSH Dependence and Inhibitory Effects of Neurotoxic Metals and Thimerosal. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:6143753. [PMID: 26989453 PMCID: PMC4775819 DOI: 10.1155/2016/6143753] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/28/2015] [Accepted: 01/10/2016] [Indexed: 12/05/2022]
Abstract
The folate and cobalamin (Cbl-) dependent enzyme methionine synthase (MS) is highly sensitive to oxidation and its activity affects all methylation reactions. Recent studies have revealed alternative splicing of MS mRNA in human brain and patient-derived fibroblasts. Here we show that MS mRNA in SH-SY5Y human neuroblastoma cells is alternatively spliced, resulting in three primary protein species, thus providing a useful model to examine cofactor dependence of these variant enzymes. MS activity was dependent upon methylcobalamin (MeCbl) or the combination of hydroxocobalamin (OHCbl) and S-adenosylmethionine (SAM). OHCbl-based activity was eliminated by depletion of the antioxidant glutathione (GSH) but could be rescued by provision of either glutathionylcobalamin (GSCbl) or MeCbl. Pretreatment of cells with lead, arsenic, aluminum, mercury, or the ethylmercury-containing preservative thimerosal lowered GSH levels and inhibited MS activity in association with decreased uptake of cysteine, which is rate-limiting for GSH synthesis. Thimerosal treatment decreased cellular levels of GSCbl and MeCbl. These findings indicate that the alternatively spliced form of MS expressed in SH-SY5Y human neuronal cells is sensitive to inhibition by thimerosal and neurotoxic metals, and lower GSH levels contribute to their inhibitory action.
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