1
|
Yuan M, Yang B, Rothschild G, Mann JJ, Sanford LD, Tang X, Huang C, Wang C, Zhang W. Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential. Signal Transduct Target Ther 2023; 8:309. [PMID: 37644009 PMCID: PMC10465587 DOI: 10.1038/s41392-023-01519-z] [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: 11/17/2022] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 08/31/2023] Open
Abstract
Major depressive disorder (MDD) is a chronic, generally episodic and debilitating disease that affects an estimated 300 million people worldwide, but its pathogenesis is poorly understood. The heritability estimate of MDD is 30-40%, suggesting that genetics alone do not account for most of the risk of major depression. Another factor known to associate with MDD involves environmental stressors such as childhood adversity and recent life stress. Recent studies have emerged to show that the biological impact of environmental factors in MDD and other stress-related disorders is mediated by a variety of epigenetic modifications. These epigenetic modification alterations contribute to abnormal neuroendocrine responses, neuroplasticity impairment, neurotransmission and neuroglia dysfunction, which are involved in the pathophysiology of MDD. Furthermore, epigenetic marks have been associated with the diagnosis and treatment of MDD. The evaluation of epigenetic modifications holds promise for further understanding of the heterogeneous etiology and complex phenotypes of MDD, and may identify new therapeutic targets. Here, we review preclinical and clinical epigenetic findings, including DNA methylation, histone modification, noncoding RNA, RNA modification, and chromatin remodeling factor in MDD. In addition, we elaborate on the contribution of these epigenetic mechanisms to the pathological trait variability in depression and discuss how such mechanisms can be exploited for therapeutic purposes.
Collapse
Affiliation(s)
- Minlan Yuan
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Biao Yang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY, 10032, USA
- Department of Radiology, Columbia University, New York, NY, 10032, USA
| | - Larry D Sanford
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Xiangdong Tang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Canhua Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuang Wang
- Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Wei Zhang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Medical Big Data Center, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
2
|
Cao R, Takechi M, Wang X, Furutera T, Nojiri T, Koyabu D, Li J. Temporal and regulatory dynamics of the inner ear transcriptome during development in mice. Sci Rep 2022; 12:21196. [PMID: 36476755 PMCID: PMC9729293 DOI: 10.1038/s41598-022-25808-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
The inner ear controls hearing and balance, while the temporal molecular signatures and transcriptional regulatory dynamics underlying its development are still unclear. In this study, we investigated time-series transcriptome in the mouse inner ear from embryonic day 11.5 (E11.5) to postnatal day 7 (P7) using bulk RNA-Seq. A total of 10,822 differentially expressed genes were identified between pairwise stages. We identified nine significant temporal expression profiles using time-series expression analysis. The constantly down-regulated profiles throughout the development are related to DNA activity and neurosensory development, while the constantly upregulated profiles are related to collagen and extracellular matrix. Further co-expression network analysis revealed that several hub genes, such as Pnoc, Cd9, and Krt27, are related to the neurosensory development, cell adhesion, and keratinization. We uncovered three important transcription regulatory paths during mice inner ear development. Transcription factors related to Hippo/TGFβ signaling induced decreased expressions of genes related to the neurosensory and inner ear development, while a series of INF genes activated the expressions of genes in immunoregulation. In addition to deepening our understanding of the temporal and regulatory mechanisms of inner ear development, our transcriptomic data could fuel future multi-species comparative studies and elucidate the evolutionary trajectory of auditory development.
Collapse
Affiliation(s)
- Rui Cao
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Masaki Takechi
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
- Department of Molecular Craniofacial Embryology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Xiuwan Wang
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Toshiko Furutera
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Taro Nojiri
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Daisuke Koyabu
- Department of Molecular Craniofacial Embryology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba-shi, Ibaraki, 305-8550, Japan.
| | - Jun Li
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen, China.
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.
- School of Data Science, City University of Hong Kong, Kowloon, Hong Kong, China.
| |
Collapse
|
3
|
Xu P, Tao Y, Zhang H, Jin M, Xu H, Zou S, Deng F, Huang L, Zhang H, Wang X, Tang X, Dong Z, Wang Y, Yin L, Sun X. RPS6KA5 methylation predict response to 6-week treatment for adolescent MDD patients. BMC Psychiatry 2022; 22:561. [PMID: 35986314 PMCID: PMC9392312 DOI: 10.1186/s12888-022-04196-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/06/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE We aimed to investigate the effect of differentially methylated genes and chronic childhood stress on the development of depressive symptoms in Chinese adolescents, as well as to test whether methylation at baseline can be used as a predictor of remission at follow-up after six weeks of treatment. METHODS After recruiting 87 MDD patients and 53 healthy controls, we compared demographic and baseline clinical characteristics. The Childhood Chronic Stress Questionnaire was used to assess stress caused by early-life events. MDD patients underwent six weeks of treatment, and response to treatment was assessed using the Beck Depression Inventory-II. In addition, four MDD patients and five controls were randomly chosen for genome-wide methylation analysis. RESULTS The gene RPS6KA5 showed significant methylation differences between the two groups. Severity of chronic childhood stress was significantly associated with increased risk of depression in adolescents, but not with treatment response. Baseline RPS6KA5 methylation can predict remission after six weeks of treatment. We did not observe any interaction between RPS6KA5 methylation and chronic childhood stress. CONCLUSIONS Our results suggest that RPS6KA5 methylation can be used as a predictor of response to treatment in adolescent MDD patients. Here we offer new evidence for the role of epigenetics in early response to treatment of depression. TRIAL REGISTRATION ChiCTR, ChiCTR2000033402, 31/05/2020, http://www.chictr.org.cn/index.aspx.
Collapse
Affiliation(s)
- Peiwei Xu
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Yuanmei Tao
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Hang Zhang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Meijiang Jin
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Hanmei Xu
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Shoukang Zou
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Fang Deng
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Lijuan Huang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Hong Zhang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Xiaolan Wang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Xiaowei Tang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Zaiquan Dong
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Yanping Wang
- grid.412901.f0000 0004 1770 1022Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041 Sichuan China
| | - Li Yin
- Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041, Sichuan, China. .,Frontier Science Center for Disease-Related Molecular Networks, Chengdu, 610041, Sichuan, China. .,Sichuan Clinical Medical Research Center for Mental Disorders, Chengdu, 610041, Sichuan, China.
| | - Xueli Sun
- Department of Psychiatry, West China Hospital of Sichuan University, No. 28 Dianxin South Street, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
4
|
Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:ijms23105856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene–environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
Collapse
|
5
|
Early life and adult stress promote sex dependent changes in hypothalamic miRNAs and environmental enrichment prevents stress-induced miRNA and gene expression changes in rats. BMC Genomics 2021; 22:701. [PMID: 34583641 PMCID: PMC8480023 DOI: 10.1186/s12864-021-08003-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The hypothalamus plays a key role in the stress response. While early life stress (ELS) increases susceptibility to psychiatric disorders including major depressive disorder (MDD), acute stress during adulthood can also precipitate MDD after ELS. AIM Here, we tested the expression of miRNAs following ELS and susceptibility to depression-like behavior and whether sex or acute stress exacerbates this response. We also tested whether environmental enrichment (Enr) promotes early life and adult behavioral stress resilience and its effect on hypothalamic miRNA and gene expression. Following rat maternal separation (MS) as an ELS model, Enr from weaning through adulthood, and restraint (RS) as acute adult stress, we tested both animal behavior and miRNA expression in the hypothalamus. Target genes and their enrichment and ontology were analyzed using bioinformatic tools. Target gene expression changes were tested using qPCR, and miRNA promoter methylation was studied using methylated-DNA immunoprecipitation qPCR. RESULTS MS, Enr, RS, and sex altered hypothalamic miRNAs, including several previously reported in MS literature: miRs-29, - 124, - 132, - 144, - 504. Sex had a significant effect on the greatest number of miRNAs. Also, Enr reversed downregulation of miR-29b-1-5p and -301b-3p in MS. qPCR showed that MAPK6 and MMP19, targets of miR-301b-3p, were upregulated in MS and reversed by Enr. Additionally, miR-219a was hypermethylated in MS coinciding with decreased miR-219a expression. CONCLUSIONS This study found that sex plays a critical role in the hypothalamic miRNA response to both ELS and acute stress, with males expressing greater changes following postnatal stress. Moreover, enrichment significantly altered behavior as well as hypothalamic miRNA expression and their gene targets. Because of its role as the initiator of the autonomic stress response and connection to hedonic and motivational behavior, the hypothalamic miRNA landscape may significantly alter both the short and long-term behavioral response to stress.
Collapse
|
6
|
Emerging role of microRNAs in major depressive disorder and its implication on diagnosis and therapeutic response. J Affect Disord 2021; 286:80-86. [PMID: 33714174 DOI: 10.1016/j.jad.2021.02.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/01/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a serious and common psychiatric disorder with a high prevalence in the population. Although great advances have been made, its pathogenesis is still unclear and a validated biomarker for diagnosis or therapeutic response remains unidentified. This review aims at summarizing the functional role of miRNAs in MDD pathogenesis and their potential as biomarkers for MDD diagnosis and antidepressant response. METHODS We performed a bibliographic research on the main databases (PubMed, Google Scholar and Web of Science) using the terms "microRNAs", "major depressive disorder", "synaptic plasticity", "biomarker", "antidepressant treatment", in order to find studies that propose the role of microRNAs in MDD pathogenesis and their potential as biomarkers for MDD diagnosis and antidepressant response. RESULTS microRNAs (miRNAs), a class of small noncoding RNAs, act as key regulators of synaptic plasticity in MDD pathogenesis. Growing researches provide the evidence for peripheral miRNAs as potential biomarkers for MDD diagnosis and antidepressant response. These results suggest that targeting miRNAs directly could be therapeutically beneficial for MDD and miRNAs are potential biomarkers of MDD and its treatment. LIMITATIONS The role of miRNAs in MDD pathogenesis needs further investigation. Whether miRNAs in peripheral tissues truly represent brain-derived miRNAs is still unclear at the present time. Moreover, only a few blood miRNAs alterations are consistent across studies. CONCLUSIONS Overall, miRNAs act key regulators of synaptic plasticity in MDD pathogenesis and hold significant promise as biomarkers or therapeutic targets for MDD, but further research is still needed.
Collapse
|
7
|
Distinct epigenetic signatures between adult-onset and late-onset depression. Sci Rep 2021; 11:2296. [PMID: 33504850 PMCID: PMC7840753 DOI: 10.1038/s41598-021-81758-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
The heterogeneity of major depressive disorder (MDD) is attributed to the fact that diagnostic criteria (e.g., DSM-5) are only based on clinical symptoms. The discovery of blood biomarkers has the potential to change the diagnosis of MDD. The purpose of this study was to identify blood biomarkers of DNA methylation by strategically subtyping patients with MDD by onset age. We analyzed genome-wide DNA methylation of patients with adult-onset depression (AOD; age ≥ 50 years, age at depression onset < 50 years; N = 10) and late-onset depression (LOD; age ≥ 50 years, age at depression onset ≥ 50 years; N = 25) in comparison to that of 30 healthy subjects. The methylation profile of the AOD group was not only different from that of the LOD group but also more homogenous. Six identified methylation CpG sites were validated by pyrosequencing and amplicon bisulfite sequencing as potential markers for AOD in a second set of independent patients with AOD and healthy control subjects (N = 11). The combination of three specific methylation markers achieved the highest accuracy (sensitivity, 64%; specificity, 91%; accuracy, 77%). Taken together, our findings suggest that DNA methylation markers are more suitable for AOD than for LOD patients.
Collapse
|
8
|
Tsamou M, Vrijens K, Wang C, Winckelmans E, Neven KY, Madhloum N, de Kok TM, Nawrot TS. Genome-wide microRNA expression analysis in human placenta reveals sex-specific patterns: an ENVIR ONAGE birth cohort study. Epigenetics 2020; 16:373-388. [PMID: 32892695 PMCID: PMC7993149 DOI: 10.1080/15592294.2020.1803467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
There is an increasing interest in microRNAs (miRNAs) as they are of utmost importance in gene regulation at the posttranscriptional level. Sex-related susceptibility for non-communicable diseases later in life could originate in early life. Until now, no data on sex-specific miRNA expression are available for the placenta. Therefore, we investigated the difference by sex of newborn's miRNA expression in human placental tissue. Within the ENVIRONAGE birth cohort, miRNA and mRNA expression profiling was performed in 60 placentae (50% boys) using Agilent (8 × 60 K) microarrays. The distribution of chromosome locations was studied and pathway analysis of the identified sex-specific miRNAs in the placenta was carried out. Of the total 2558 miRNAs on the array, 597 miRNAs were expressed in over 70% of the samples and were included for further analyses. A total of 142 miRNAs were significantly (FDR<0.05) associated with the newborn's sex. In newborn girls, 76 miRNAs had higher expression (hsa-miR-361-5p as most significant) and 66 miRNAs had lower expression (hsa-miR-4646-5p as most significant) than in newborn boys. In the same study population, placental differentially expressed genes by sex were also identified using a whole genome approach. The placental gene expression revealed 27 differentially expressed genes by comparing girls to boys. Ultimately, we studied the miRNA-RNA interactome and identified 14 miRNA-mRNA interactions as sex-specific. Sex differences in placental m(i)RNA expression may reveal sex-specific patterns already present during pregnancy, which may influence physiological conditions in early or later life. These molecular processes might play a role in sex-specific disease susceptibility in later life.
Collapse
Affiliation(s)
- Maria Tsamou
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Karen Vrijens
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Ellen Winckelmans
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Kristof Y Neven
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Narjes Madhloum
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Theo M de Kok
- Department of Toxicogenomics, GROW Institute of Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Tim S Nawrot
- Center for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Public Health, Environment & Health Unit, Leuven University (KU Leuven), Leuven, Belgium
| |
Collapse
|
9
|
Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
Collapse
Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
| |
Collapse
|
10
|
Humphreys KL, Moore SR, Davis EG, MacIsaac JL, Lin DTS, Kobor MS, Gotlib IH. DNA methylation of HPA-axis genes and the onset of major depressive disorder in adolescent girls: a prospective analysis. Transl Psychiatry 2019; 9:245. [PMID: 31582756 PMCID: PMC6776528 DOI: 10.1038/s41398-019-0582-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/11/2019] [Indexed: 12/28/2022] Open
Abstract
The stress response system is disrupted in individuals with major depressive disorder (MDD) as well as in those at elevated risk for developing MDD. We examined whether DNA methylation (DNAm) levels of CpG sites within HPA-axis genes predict the onset of MDD. Seventy-seven girls, approximately half (n = 37) of whom were at familial risk for MDD, were followed longitudinally. Saliva samples were taken in adolescence (M age = 13.06 years [SD = 1.52]) when participants had no current or past MDD diagnosis. Diagnostic interviews were administered approximately every 18 months until the first onset of MDD or early adulthood (M age of last follow-up = 19.23 years [SD = 2.69]). We quantified DNAm in saliva samples using the Illumina EPIC chip and examined CpG sites within six key HPA-axis genes (NR3C1, NR3C2, CRH, CRHR1, CRHR2, FKBP5) alongside 59 genotypes for tagging SNPs capturing cis genetic variability. DNAm levels within CpG sites in NR3C1, CRH, CRHR1, and CRHR2 were associated with risk for MDD across adolescence and young adulthood. To rule out the possibility that findings were merely due to the contribution of genetic variability, we re-analyzed the data controlling for cis genetic variation within these candidate genes. Importantly, methylation levels in these CpG sites continued to significantly predict the onset of MDD, suggesting that variation in the epigenome, independent of proximal genetic variants, prospectively predicts the onset of MDD. These findings suggest that variation in the HPA axis at the level of the methylome may predict the development of MDD.
Collapse
Affiliation(s)
- Kathryn L. Humphreys
- 0000 0001 2264 7217grid.152326.1Department of Psychology and Human Development, Vanderbilt University, Nashville, TN USA
| | - Sarah R. Moore
- 0000 0001 2288 9830grid.17091.3eBC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Elena Goetz Davis
- 0000000419368956grid.168010.eDepartment of Psychology, Stanford University, Stanford, USA
| | - Julie L. MacIsaac
- 0000 0001 2288 9830grid.17091.3eBC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
| | - David T. S. Lin
- 0000 0001 2288 9830grid.17091.3eBC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Michael S. Kobor
- 0000 0001 2288 9830grid.17091.3eBC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Ian H. Gotlib
- 0000000419368956grid.168010.eDepartment of Psychology, Stanford University, Stanford, USA
| |
Collapse
|
11
|
What do DNA methylation studies tell us about depression? A systematic review. Transl Psychiatry 2019; 9:68. [PMID: 30718449 PMCID: PMC6362194 DOI: 10.1038/s41398-019-0412-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 11/09/2022] Open
Abstract
There has been a limited number of systematic reviews conducted to summarize the overview of the relationship between DNA methylation and depression, and to critically appraise the roles of major study characteristics in the accuracy of study findings. This systematic review aims to critically appraise the impact of study characteristics on the association between DNA methylation and depression, and summarize the overview of this association. Electronic databases and gray literatures until December 2017 were searched for English-language studies with standard diagnostic criteria of depression. A total of 67 studies were included in this review along with a summary of their study characteristics. We grouped the findings into etiological and treatment studies. Majority of these selected studies were recently published and from developed countries. Whole blood samples were the most studied common tissues. Bisulfite conversion, along with pyrosequencing, was widely used to test the DNA methylation level across all the studies. High heterogeneity existed among the studies in terms of experimental and statistical methodologies and study designs. As recommended by the Cochrane guideline, a systematic review without meta-analysis should be undertaken. This review has, in general, found that DNA methylation modifications were associated with depression. Subgroup analyses showed that most studies found BDNF and SLC6A4 hypermethylations to be associated with MDD or depression in general. In contrast, studies on NR3C1, OXTR, and other genes, which were tested by only few studies, reported mixed findings. More longitudinal studies using standardized experimental and laboratory methodologies are needed in future studies to enable more systematical comparisons and quantitative synthesis.
Collapse
|
12
|
Fries GR, Zhang W, Benevenuto D, Quevedo J. MicroRNAs in Major Depressive Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:175-190. [PMID: 30747423 DOI: 10.1007/978-3-030-05542-4_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Major depressive disorder (MDD) is a severe and chronic psychiatric disorder with a high prevalence in the population. Although our understanding of its pathophysiological mechanisms has significantly increased over the years, available treatments still present several limitations and are not effective to all MDD patients. Epigenetic mechanisms have recently been suggested to play key roles in MDD pathogenesis and treatment, including the effects of small noncoding RNAs known as microRNAs (miRNAs). miRNAs can modulate gene expression posttranscriptionally by interfering with the stability and translation of messenger RNA molecules and are also known to cross-talk with other epigenetic mechanisms. In this review, we will summarize and discuss recent findings of alterations in miRNAs in tissues of patients with MDD and evidence of treatment-induced effects in these molecules.
Collapse
Affiliation(s)
- Gabriel R Fries
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Wei Zhang
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Deborah Benevenuto
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil.
| |
Collapse
|
13
|
Ciuculete DM, Boström AE, Tuunainen AK, Sohrabi F, Kular L, Jagodic M, Voisin S, Mwinyi J, Schiöth HB. Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents. J Psychiatr Res 2018; 102:44-51. [PMID: 29604450 DOI: 10.1016/j.jpsychires.2018.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022]
Abstract
Generalized anxiety disorder (GAD) is highly prevalent among adolescents. An early detection of individuals at risk may prevent later psychiatric condition. Genome-wide studies investigating single nucleotide polymorphisms (SNPs) concluded that a focus on epigenetic mechanisms, which mediate the impact of environmental factors, could more efficiently help the understanding of GAD pathogenesis. We investigated the relationship between epigenetic shifts in blood and the risk to develop GAD, evaluated by the Development and Well-Being Assessment (DAWBA) score, in 221 otherwise healthy adolescents. Our analysis focused specifically on methylation sites showing high inter-individual variation but low tissue-specific variation, in order to infer a potential correlation between results obtained in blood and brain. Two statistical methods were applied, 1) a linear model with limma and 2) a likelihood test followed by Bonferroni correction. Methylation findings were validated in a cohort of 160 adults applying logistic models against the outcome variable "anxiety treatment obtained in the past" and studied in a third cohort with regards to associated expression changes measured in monocytes. One CpG site showed 1% increased methylation in adolescents at high risk of GAD (cg16333992, padj. = 0.028, estimate = 3.22), as confirmed in the second cohort (p = 0.031, estimate = 1.32). The identified and validated CpG site is located within the STK32B promoter region and its methylation level was positively associated with gene expression. Gene ontology analysis revealed that STK32B is involved in stress response and defense response. Our results provide evidence that shifts in DNA methylation are associated with a modulated risk profile for GAD in adolescence.
Collapse
Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden.
| | - Adrian E Boström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Anna-Kaisa Tuunainen
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Farah Sohrabi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Sarah Voisin
- Institute of Sport, Exercise and Active Living, Victoria University, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| |
Collapse
|
14
|
Peedicayil J, Kumar A. Epigenetic Drugs for Mood Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:151-174. [PMID: 29933949 DOI: 10.1016/bs.pmbts.2018.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is increasing evidence that changes in epigenetic mechanisms of gene expression are involved in the pathogenesis of mood disorders. Such evidence stems from studies conducted on postmortem brain tissues and peripheral cells or tissues of patients with mood disorders. This article describes and discusses the epigenetic changes in the mood disorders (major depressive disorder and bipolar disorder) found to date. The article also describes and discusses preclinical drug trials of epigenetic drugs for treating mood disorders. In addition, nonrandomized and randomized controlled trials of nutritional drugs with effects on epigenetic mechanisms of gene expression in patients with major depressive disorder and bipolar disorder are discussed. Trials of epigenetic drugs and nutritional drugs with epigenetic effects are showing promising results for the treatment of mood disorders. Thus, epigenetic drugs and nutritional drugs with epigenetic effects could be useful in the treatment of patients with these disorders.
Collapse
|
15
|
An epigenome-wide methylation study of healthy individuals with or without depressive symptoms. J Hum Genet 2018; 63:319-326. [PMID: 29305581 DOI: 10.1038/s10038-017-0382-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/29/2017] [Accepted: 10/11/2017] [Indexed: 12/23/2022]
Abstract
Major depressive disorder is a common psychiatric disorder that is thought to be triggered by both genetic and environmental factors. Depressive symptoms are an important public health problem and contribute to vulnerability to major depression. Although a substantial number of genetic and epigenetic studies have been performed to date, the detailed etiology of depression remains unclear and there are no validated biomarkers. DNA methylation is one of the major epigenetic modifications that play diverse roles in the etiology of complex diseases. In this study, we performed an epigenome-wide association study (EWAS) of DNA methylation on subjects with (N = 20) or without (N = 27) depressive symptoms in order to examine whether different levels of DNA methylation were associated with depressive tendencies. Employing methylation-array technology, a total of 363,887 methylation sites across the genomes were investigated and several candidate CpG sites associated with depressive symptoms were identified, especially annotated to genes linked to a G-protein coupled receptor protein signaling pathway. These data provide a strong impetus for validation studies using a larger cohort and support the possibility that G-protein coupled receptor protein signaling pathways are involved in the pathogenesis of depression.
Collapse
|