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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: 0] [Impact Index Per Article: 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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2
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Kefayati F, Karimi Babaahmadi A, Mousavi T, Hodjat M, Abdollahi M. Epigenotoxicity: a danger to the future life. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:382-411. [PMID: 36942370 DOI: 10.1080/10934529.2023.2190713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Environmental toxicants can regulate gene expression in the absence of DNA mutations via epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs' (ncRNAs). Here, all three epigenetic modifications for seven important categories of diseases and the impact of eleven main environmental factors on epigenetic modifications were discussed. Epigenetic-related mechanisms are among the factors that could explain the root cause of a wide range of common diseases. Its overall impression on the development of diseases can help us diagnose and treat diseases, and besides, predict transgenerational and intergenerational effects. This comprehensive article attempted to address the relationship between environmental factors and epigenetic modifications that cause diseases in different categories. The studies main gap is that the precise role of environmentally-induced epigenetic alterations in the etiology of the disorders is unknown; thus, still more well-designed researches need to be accomplished to fill this gap. The present review aimed to first summarize the adverse effect of certain chemicals on the epigenome that may involve in the onset of particular disease based on in vitro and in vivo models. Subsequently, the possible adverse epigenetic changes that can lead to many human diseases were discussed.
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Affiliation(s)
- Farzaneh Kefayati
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Karimi Babaahmadi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Taraneh Mousavi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hodjat
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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3
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Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev 2021; 131:988-1004. [PMID: 34592258 DOI: 10.1016/j.neubiorev.2021.09.049] [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: 04/05/2021] [Revised: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/26/2022]
Abstract
The circadian rhythm of the human brain is attuned to sleep-wake cycles that entail global alterations in neuronal excitability. This periodicity involves a highly coordinated regulation of gene expression. A growing number of studies are documenting a fascinating connection between primate-specific retrotransposons (Alu elements) and key epigenetic regulatory processes in the primate brain. Collectively, these studies indicate that Alu elements embedded in the human neuronal genome mediate post-transcriptional processes that unite human-specific neuroepigenetic landscapes and circadian rhythm. Here, we review evidence linking Alu retrotransposon-mediated posttranscriptional pathways to circadian gene expression. We hypothesize that Alu retrotransposons participate in the organization of circadian brain function through multidimensional neuroepigenetic pathways. We anticipate that these pathways are closely tied to the evolution of human cognition and their perturbation contributes to the manifestation of human-specific neurological diseases. Finally, we address current challenges and accompanying opportunities in studying primate- and human-specific transposable elements.
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Affiliation(s)
- Manci Li
- University of Minnesota, St. Paul, MN, 55108, United States
| | - Peter A Larsen
- University of Minnesota, St. Paul, MN, 55108, United States.
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4
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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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5
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Chen Q, Li D, Jin W, Shi Y, Li Z, Ma P, Sun J, Chen S, Li P, Lin P. Research Progress on the Correlation Between Epigenetics and Schizophrenia. Front Neurosci 2021; 15:688727. [PMID: 34366776 PMCID: PMC8334178 DOI: 10.3389/fnins.2021.688727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose of the Review Nowadays, the incidence of schizophrenia is noticeably increased. If left undiagnosed and untreated, it will lead to impaired social functions, repeated hospital admissions, decline in quality of life and life expectancy. However, the diagnosis of schizophrenia is complicated and challenging. Both genetic and environmental factors are considered as important contributors to the development and progression of this disorder. The environmental factors have been linked to changes in gene expression through epigenetic modulations, which have raised more and more research interests in recent years. This review article is to summarize the current findings and understanding of epigenetic modulation associated with pathogenesis of schizophrenia, aiming to provide useful information for further research in developing biomarkers for schizophrenia. Recent Findings Three major types of epigenetic modulations have been described in this article. Firstly, both DNA hypermethylation and hypomethylated have been associated with schizophrenia via analyzing post-mortem brain tissues and peripheral blood of patients. Specific changes of non-coding RNAs, particularly microRNAs and long-chain non-coding RNAs, have been observed in central and peripheral samples of schizophrenia patients, indicating their significant diagnostic value for the disease, and may also potentially predict treatment response. The correlation between histone modification and schizophrenia, however, is largely unclear. Summary Epigenetic modulations, including DNA methylation, ncRNA transcriptional regulation and histone modification, play an important role in the pathogenesis of schizophrenia. Therefore, tests of these epigenetic alterations may be utilized to assist in the diagnosis and determination of strategies of individualized treatment in clinical practice.
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Affiliation(s)
- Qing Chen
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weifeng Jin
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Shi
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenhua Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peijun Ma
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaqi Sun
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuzi Chen
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Li
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Lin
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Pappalardo XG, Barra V. Losing DNA methylation at repetitive elements and breaking bad. Epigenetics Chromatin 2021; 14:25. [PMID: 34082816 PMCID: PMC8173753 DOI: 10.1186/s13072-021-00400-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome. Main body Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation. Conclusions Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125, Catania, Italy.,National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, 95125, Catania, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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Reszka E, Jabłońska E, Lesicka M, Wieczorek E, Kapelski P, Szczepankiewicz A, Pawlak J, Dmitrzak-Węglarz M. An altered global DNA methylation status in women with depression. J Psychiatr Res 2021; 137:283-289. [PMID: 33730603 DOI: 10.1016/j.jpsychires.2021.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/23/2022]
Abstract
Sparse studies have shown that specific biomarkers of a global DNA methylation status may be related to various mental diseases and states, including: bipolar disorder (BD), anxiety and major depression disorder (MDD). The objective of this study was to analyze potential variation of the above mentioned global methylation status in women with depression. 38 women with a current and clinically confirmed depressive episode suffering from BD type I, type II or MDD and 71 women from the general population and at similar age were recruited for the study. Alu and LINE-1 methylation was assayed with the quantitative methylation-specific PCR technique with TaqMan probes, while the 5-mC and 5-hmC level was determined using the ELISA-based method. Significantly higher levels of 5-mC, Alu and LINE-1 methylation were observed in the women with depression as compared to the controls; while the 5-hmC level revealed to be significantly lower. The BD type I patients presented the highest level of 5-mC of all the women with a depressive episode. 5-mC level in the patients was positively and significantly correlated with the severity of the symptoms of depression. Relationships between Alu or LINE-1 methylation and 5-mC level were statistically significant only in the case of the control women. Alu and LINE-1 methylation do not constitute suitable biomarkers of global DNA methylation in the investigated patients. These findings require confirmation in case-control and prospective epidemiological studies.
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Affiliation(s)
- Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Ewa Jabłońska
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Edyta Wieczorek
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Aleksandra Szczepankiewicz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
| | - Monika Dmitrzak-Węglarz
- Department of Psychiatric Genetics, Department of Psychiatry, University of Medical Sciences, Poznan, Poland
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8
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Legrand A, Iftimovici A, Khayachi A, Chaumette B. Epigenetics in bipolar disorder: a critical review of the literature. Psychiatr Genet 2021; 31:1-12. [PMID: 33290382 DOI: 10.1097/ypg.0000000000000267] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Bipolar disorder (BD) is a chronic, disabling disease characterised by alternate mood episodes, switching through depressive and manic/hypomanic phases. Mood stabilizers, in particular lithium salts, constitute the cornerstone of the treatment in the acute phase as well as for the prevention of recurrences. The pathophysiology of BD and the mechanisms of action of mood stabilizers remain largely unknown but several pieces of evidence point to gene x environment interactions. Epigenetics, defined as the regulation of gene expression without genetic changes, could be the molecular substrate of these interactions. In this literature review, we summarize the main epigenetic findings associated with BD and response to mood stabilizers. METHODS We searched PubMed, and Embase databases and classified the articles depending on the epigenetic mechanisms (DNA methylation, histone modifications and non-coding RNAs). RESULTS We present the different epigenetic modifications associated with BD or with mood-stabilizers. The major reported mechanisms were DNA methylation, histone methylation and acetylation, and non-coding RNAs. Overall, the assessments are poorly harmonized and the results are more limited than in other psychiatric disorders (e.g. schizophrenia). However, the nature of BD and its treatment offer excellent opportunities for epigenetic research: clear impact of environmental factors, clinical variation between manic or depressive episodes resulting in possible identification of state and traits biomarkers, documented impact of mood-stabilizers on the epigenome. CONCLUSION Epigenetic is a growing and promising field in BD that may shed light on its pathophysiology or be useful as biomarkers of response to mood-stabilizer.
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Affiliation(s)
- Adrien Legrand
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
| | - Anton Iftimovici
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
- Neurospin, CEA, Gif-sur-Yvette, France
| | - Anouar Khayachi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada
| | - Boris Chaumette
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France
- Department of Psychiatry, McGill University, Montreal, Canada
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9
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Abstract
Schizophrenia is a serious neuropsychiatric disorder with abnormal age-related neurodevelopmental (or neurodegenerative) trajectories. Although an accelerated aging hypothesis of schizophrenia has been proposed, the quantitative study of the disruption of the physiological trajectory caused by schizophrenia is inconclusive. In this study, we employed 3 "epigenetic clock" methods to quantify the epigenetic age of a large sample size of whole blood (1069 samples from patients with schizophrenia vs 1264 samples from unaffected controls) and brain tissues (500 samples from patients with schizophrenia vs 711 samples from unaffected controls). We observed significant positive correlations between epigenetic age and chronological age in both blood and brain tissues from unaffected controls and patients with schizophrenia, as estimated by 3 methods. Furthermore, we observed that epigenetic age acceleration was significantly delayed in schizophrenia from the whole blood samples (aged 20-90 years) and brain frontal cortex tissues (aged 20-39 years). Intriguingly, the genes regulated by the epigenetic clock also contained schizophrenia-associated genes, displaying differential expression and methylation in patients with schizophrenia and involving in the regulation of cell activation and development. These findings were further supported by the dysregulated leukocyte composition in patients with schizophrenia. Our study presents quantitative evidence for a neurodevelopmental model of schizophrenia from the perspective of a skewed "epigenetic clock." Moreover, landmark changes in an easily accessible biological sample, blood, reveal the value of these epigenetic clock genes as peripheral biomarkers for schizophrenia.
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Affiliation(s)
- Xiaohui Wu
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, and Guangdong Engineering and Technology Research Center for Genetic Testing, Southern Medical University, Guangzhou, Guangdong, China,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Junping; Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, and Guangdong Engineering and Technology Research Center for Genetic Testing, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, and Guangdong Engineering and Technology Research Center for Genetic Testing, Southern Medical University, Guangzhou, Guangdong, China,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, and Guangdong Engineering and Technology Research Center for Genetic Testing, Southern Medical University, Guangzhou, Guangdong, China,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China,To whom correspondence should be addressed; Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; tel: (8620)-62789519, fax: (8620)-62789519, e-mail:
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10
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Liu W, Li W, Cai X, Yang Z, Li H, Su X, Song M, Zhou DS, Li X, Zhang C, Shao M, Zhang L, Yang Y, Zhang Y, Zhao J, Chang H, Yao YG, Fang Y, Lv L, Li M, Xiao X. Identification of a functional human-unique 351-bp Alu insertion polymorphism associated with major depressive disorder in the 1p31.1 GWAS risk loci. Neuropsychopharmacology 2020; 45:1196-1206. [PMID: 32193514 PMCID: PMC7235090 DOI: 10.1038/s41386-020-0659-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/16/2020] [Accepted: 03/11/2020] [Indexed: 12/28/2022]
Abstract
Genome-wide association studies (GWAS) have reported substantial single-nucleotide polymorphisms (SNPs) associated with major depressive disorder (MDD), but the underlying functional variations in the GWAS risk loci are unclear. Here we show that the European MDD genome-wide risk-associated allele of rs12129573 at 1p31.1 is associated with MDD in Han Chinese, and this SNP is in strong linkage disequilibrium (LD) with a human-unique Alu insertion polymorphism (rs70959274) in the 5' flanking region of a long non-coding RNA (lncRNA) LINC01360 (Long Intergenic Non-Protein Coding RNA 1360), which is preferably expressed in human testis in the currently available expression datasets. The risk allele at rs12129573 is almost completely linked with the absence of this Alu insertion. The Alu insertion polymorphism (rs70959274) is significantly associated with a lower RNA level of LINC01360 and acts as a transcription silencer likely through modulating the methylation of its internal CpG sites. Luciferase assays confirm that the presence of Alu insertion at rs70959274 suppresses transcriptional activities in human cells, and deletion of the Alu insertion through CRISPR/Cas9-directed genome editing increases RNA expression of LINC01360. Deletion of the Alu insertion in human cells also leads to dysregulation of gene expression, biological processes and pathways relevant to MDD, such as the alterations of mRNA levels of DRD2 and FLOT1, transcription of genes involved in synaptic transmission, neurogenesis, learning or memory, and the PI3K-Akt signaling pathway. In summary, we identify a human-unique DNA repetitive polymorphism in robust LD with the MDD risk-associated SNP at the prominent 1p31.1 GWAS loci, and offer insights into the molecular basis of the illness.
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Affiliation(s)
- Weipeng Liu
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Wenqiang Li
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Xin Cai
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Zhihui Yang
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Huijuan Li
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Xi Su
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Meng Song
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Dong-Sheng Zhou
- 0000 0004 1782 599Xgrid.452715.0Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Xingxing Li
- 0000 0004 1782 599Xgrid.452715.0Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Chen Zhang
- 0000 0004 0368 8293grid.16821.3cShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minglong Shao
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Luwen Zhang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Yongfeng Yang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Yan Zhang
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Jingyuan Zhao
- 0000 0004 1808 322Xgrid.412990.7Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,0000 0004 1808 322Xgrid.412990.7Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Hong Chang
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yong-Gang Yao
- 0000000119573309grid.9227.eKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China ,0000000119573309grid.9227.eCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China ,0000000119573309grid.9227.eKIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yiru Fang
- 0000 0004 0368 8293grid.16821.3cShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China ,0000000119573309grid.9227.eCAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Province People's Hospital, Zhengzhou, Henan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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