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Zwolińska W, Bilska K, Tarhonska K, Reszka E, Skibińska M, Pytlińska N, Słopień A, Dmitrzak-Węglarz M. Biomarkers of Depression among Adolescent Girls: BDNF and Epigenetics. Int J Mol Sci 2024; 25:3281. [PMID: 38542252 PMCID: PMC10970207 DOI: 10.3390/ijms25063281] [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: 02/02/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Alterations in brain-derived neurotrophic factor (BDNF) expression have been suggested to mediate the influence of environmental factors on the emergence of depression through epigenetic modifications. However, research on this subject in the developmental population is lacking and the pathophysiology of adolescent depression remains unclear. We aimed to investigate the alterations in BDNF expression and global DNA methylation in depression among adolescent girls. Thirty female inpatients with the initial diagnosis of depression were assessed before and after the period of antidepressant treatment and compared with thirty age-matched healthy controls. The assessment involved BDNF and proBDNF serum levels, the BDNF gene exon IV promoter methylation, and global DNA methylation. The methylation level in the BDNF gene exon IV promoter was significantly lower in the studied group compared with the control and correlated negatively with the severity of depression. The test distinguished the studied group from the controls with a sensitivity of 37% and specificity of 90%. The differences were no longer present after the period of antidepressant treatment. No differences in the global DNA methylation, BDNF, and proBDNF levels were found. We concluded that decreased methylation in the BDNF exon IV promoter could be considered as a biomarker of a depression state among adolescent girls.
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Affiliation(s)
- Weronika Zwolińska
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Karolina Bilska
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
| | - Kateryna Tarhonska
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-348 Łódź, Poland; (K.T.); (E.R.)
| | - Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-348 Łódź, Poland; (K.T.); (E.R.)
| | - Maria Skibińska
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
| | - Natalia Pytlińska
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Agnieszka Słopień
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Monika Dmitrzak-Węglarz
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
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Castillo-Navarrete JL, Bustos C, Guzman-Castillo A, Vicente B. Increased academic stress is associated with decreased plasma BDNF in Chilean college students. PeerJ 2023; 11:e16357. [PMID: 37941931 PMCID: PMC10629390 DOI: 10.7717/peerj.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction Academic stress (AS) is a prevalent challenge faced by university students, potentially affecting molecular indicators such as brain-derived neurotrophic factor (BDNF) and global DNA methylation (G-DNA-M). These indicators could illuminate the physiological ramifications of academic stress. Study Design and Methods This research followed a quantitative, non-experimental, longitudinal panel design spanning two academic semesters, observing phenomena in their natural context. Students from the Medical Technology program at Universidad de Concepción, Chile were involved, with assessments at the beginning and during heightened academic stress periods. Sample Of the total participants, 63.0% were females, with an average age of 21.14 years at baseline, and 36.92% were males, averaging 21.36 years. By the study's conclusion, female participants averaged 21.95 years, and males 22.13 years. Results Significant differences were observed between initial and final assessments for the SISCO-II Inventory of Academic Stress and Beck Depression Inventory-II, notably in stressor scores, and physical, and psychological reactions. Gender differences emerged in the final physical and psychological reactions. No significant changes were detected between the two assessments in plasma BDNF or G-DNA-M values. A refined predictive model showcased that, on average, there was a 3.56% decrease in females' plasma BDNF at the final assessment and a 17.14% decrease in males. In the sample, the G-DNA-M percentage at the final assessment increased by 15.06% from the baseline for females and 18.96% for males. Conclusions The study underscores the physiological impact of academic stress on university students, evidenced by changes in markers like BDNF and G-DNA-M. These findings offer an in-depth understanding of the intricate mechanisms regulating academic stress responses and highlight the need for interventions tailored to mitigate its physiological and psychological effects.
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Affiliation(s)
- Juan-Luis Castillo-Navarrete
- Departamento Tecnología Médica, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- PhD Programme in Mental Health, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Programa de Neurociencia, Psiquiatría y Salud Mental, NEPSAM, Universidad de Concepción, Concepción, Chile
| | - Claudio Bustos
- PhD Programme in Mental Health, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Programa de Neurociencia, Psiquiatría y Salud Mental, NEPSAM, Universidad de Concepción, Concepción, Chile
- Departamento de Psicología, Facultad de Ciencias Sociales, Universidad de Concepción, Chile, Chile
| | - Alejandra Guzman-Castillo
- PhD Programme in Mental Health, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Programa de Neurociencia, Psiquiatría y Salud Mental, NEPSAM, Universidad de Concepción, Concepción, Chile
- Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Benjamin Vicente
- PhD Programme in Mental Health, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
- Programa de Neurociencia, Psiquiatría y Salud Mental, NEPSAM, Universidad de Concepción, Concepción, Chile
- Departamento de Psiquiatría y Salud Mental, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
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Xia M, Yan R, Wang W, Kong A, Zhang M, Miao Z, Ge W, Wan B, Xu X. The Tet2–Upf1 complex modulates mRNA stability under stress conditions. Front Genet 2023; 14:1158954. [PMID: 37091805 PMCID: PMC10117899 DOI: 10.3389/fgene.2023.1158954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Introduction: Environmental stress promotes epigenetic alterations that impact gene expression and subsequently participate in the pathological processes of the disorder. Among epigenetic regulations, ten–eleven Translocation (Tet) enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA and RNA and function as critical players in the pathogenesis of diseases. Our previous results showed that chronic stress increases the expression of cytoplasmic Tet2 in the hippocampus of mice exposed to chronic mild stress (CMS). Whether the cytoplasmic Tet2 alters RNA 5hmC modification in chronic stress-related processes remains largely unknown.Methods: To explore the role of cytoplasmic Tet2 under CMS conditions, we established CMS mice model and detected the expression of RNA 5hmC by dot blot. We verified the interaction of Tet2 and its interacting protein by co-immunoprecipitation combined with mass spectrometry and screened downstream target genes by cluster analysis of Tet2 and upstream frameshift 1 (Upf1) interacting RNA. The expression of protein was detected by Western blot and the expression of the screened target genes was detected by qRT-PCR.Results: In this study, we found that increased cytoplasmic Tet2 expression under CMS conditions leads to increase in total RNA 5hmC modification. Tet2 interacted with the key non-sense-mediated mRNA decay (NMD) factor Upf1, regulated the stability of stress-related genes such as Unc5b mRNA, and might thereby affect neurodevelopment.Discussion: In summary, this study revealed that Tet2-mediated RNA 5hmC modification is involved in stress-related mRNA stability regulation and may serve as a potential therapeutic target for chronic stress-related diseases such as depression.
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Affiliation(s)
- Meiling Xia
- Departments of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Rui Yan
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Wenjuan Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Anqi Kong
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Meng Zhang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Wei Ge
- Institute of Neuroscience, Soochow University, Suzhou, China
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
| | - Xingshun Xu
- Departments of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
- *Correspondence: Wei Ge, ; Bo Wan, ; Xingshun Xu,
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4
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New Insights into TETs in Psychiatric Disorders. Int J Mol Sci 2022; 23:ijms23094909. [PMID: 35563298 PMCID: PMC9103987 DOI: 10.3390/ijms23094909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022] Open
Abstract
Psychiatric disorders are complex and heterogeneous disorders arising from the interaction of multiple factors based on neurobiology, genetics, culture, and life experience. Increasing evidence indicates that sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Over the past decade, the critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Here, we review the progress of studies designed to provide a better understanding of how profiles of TET proteins and 5hmC are powerful mechanisms by which to explain neuronal plasticity and long-term behaviors, and impact transcriptional programs operative in the brain that contribute to psychiatric disorders.
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Zeng D, He S, Zhao N, Hu M, Gao J, Yu Y, Huang J, Shen Y, Li H. Promoter Hypomethylation of miR-124 Gene Is Associated With Major Depressive Disorder. Front Mol Neurosci 2022; 14:771103. [PMID: 34992522 PMCID: PMC8724533 DOI: 10.3389/fnmol.2021.771103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Based on our previous studies and other evidence, miR-124 is an important biomarker and therapeutic target for major depressive disorder (MDD). The aim of this study was to clarify the role of miR-124 methylation in MDD and antidepressant effects from the perspective of epigenetics. MethylTarget™ was used to detect methylation levels of the three miR-124 precursor genes (MIR124-1, MIR124-2, and MIR124-3) in 33 pre- and post-treatment MDD patients and 33 healthy controls. A total of 11 cytosine-phosphate-guanine (CpG) islands in the three miR-124 precursor genes, including 222 CpG sites, were detected. All CpG islands were hypomethylated in MDD patients when compared to healthy controls and seven CpG regions were still identified with a statistically significant difference after Bonferroni correction. In addition, 137 of 222 CpG sites were found a statistical difference between MDD patients and controls, and 40 CpG sites were still statistically significant after Bonferroni correction. After performing the LASSO regression model, seven biomarkers with differential methylation among 40 CpG sites were identified. Mean methylation score was lower in MDD patients (z = -5.84, p = 5.16E-9). The AUC value reached 0.917 (95% CI: 0.854-0.981) to discriminate MDD and controls. No changes in methylation of the three miR-124 precursor genes were found in MDD patients following antidepressant treatment. The methylation of miR-124 could be a promising diagnostic biomarker for MDD.
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Affiliation(s)
- Duan Zeng
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shen He
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Zhao
- Department of Psychiatry, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Manji Hu
- Department of Psychiatry, Shanghai Pudong New Area Mental Health Center, School of Medicine, Tongji University, Shanghai, China
| | - Jie Gao
- Yingbo Community Health Service Center, Shanghai, China
| | - Yimin Yu
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Clinical Research Center for Mental Health, Shanghai, China
| | - Jingjing Huang
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Clinical Research Center for Mental Health, Shanghai, China
| | - Yifeng Shen
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Clinical Research Center for Mental Health, Shanghai, China
| | - Huafang Li
- Department of Psychiatry, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Clinical Research Center for Mental Health, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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6
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Kawatake-Kuno A, Murai T, Uchida S. The Molecular Basis of Depression: Implications of Sex-Related Differences in Epigenetic Regulation. Front Mol Neurosci 2021; 14:708004. [PMID: 34276306 PMCID: PMC8282210 DOI: 10.3389/fnmol.2021.708004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of disability worldwide. Although the etiology and pathophysiology of MDD remain poorly understood, aberrant neuroplasticity mediated by the epigenetic dysregulation of gene expression within the brain, which may occur due to genetic and environmental factors, may increase the risk of this disorder. Evidence has also been reported for sex-related differences in the pathophysiology of MDD, with female patients showing a greater severity of symptoms, higher degree of functional impairment, and more atypical depressive symptoms. Males and females also differ in their responsiveness to antidepressants. These clinical findings suggest that sex-dependent molecular and neural mechanisms may underlie the development of depression and the actions of antidepressant medications. This review discusses recent advances regarding the role of epigenetics in stress and depression. The first section presents a brief introduction of the basic mechanisms of epigenetic regulation, including histone modifications, DNA methylation, and non-coding RNAs. The second section reviews their contributions to neural plasticity, the risk of depression, and resilience against depression, with a particular focus on epigenetic modulators that have causal relationships with stress and depression in both clinical and animal studies. The third section highlights studies exploring sex-dependent epigenetic alterations associated with susceptibility to stress and depression. Finally, we discuss future directions to understand the etiology and pathophysiology of MDD, which would contribute to optimized and personalized therapy.
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Affiliation(s)
- Ayako Kawatake-Kuno
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshiya Murai
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shusaku Uchida
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
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7
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Xie Y, Xiao L, Chen L, Zheng Y, Zhang C, Wang G. Integrated Analysis of Methylomic and Transcriptomic Data to Identify Potential Diagnostic Biomarkers for Major Depressive Disorder. Genes (Basel) 2021; 12:genes12020178. [PMID: 33513891 PMCID: PMC7912210 DOI: 10.3390/genes12020178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Major depressive disorder (MDD) is a mental illness with high incidence and complex etiology, that poses a serious threat to human health and increases the socioeconomic burden. Currently, high-accuracy biomarkers for MDD diagnosis are urgently needed. This paper aims to identify novel blood-based diagnostic biomarkers for MDD. Whole blood DNA methylation data and gene expression data from the Gene Expression Omnibus database are downloaded. Then, differentially expressed/methylated genes (DEGs/DMGs) are identified. In addition, we made a systematic analysis of the DNA methylation on 5′-C-phosphate-G-3′ (CpGs) in all of the gene regions, as well as different gene regions, and then we defined a “dominant” region. Subsequently, integrated analysis is employed to identify the robust MDD-related blood biomarkers. Finally, a gene expression classifier and a methylation classifier are constructed using the random forest algorithm and the leave-one-out cross-validation method. Our results demonstrate that DEGs are mainly involved in the inflammatory response-associated pathways, while DMGs are primarily concentrated in the neurodevelopment- and neuroplasticity-associated pathways. Our integrated analysis identified 46 hypo-methylated and up-regulated (hypo-up) genes and 71 hyper-methylated and down-regulated (hyper-down) genes. One gene expression classifier and two DNA methylation classifiers, based on the CpGs in all of the regions or in the dominant regions are constructed. The gene expression classifier possessed the best predictive ability, followed by the DNA methylation classifiers, based on the CpGs in both the dominant regions and all of the regions. In summary, the integrated analysis of DNA methylation and gene expression has identified 46 hypo-up genes and 71 hyper-down genes, which could be used as diagnostic biomarkers for MDD.
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Affiliation(s)
- Yinping Xie
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Y.X.); (Y.Z.)
| | - Ling Xiao
- Institute of Neuropsychiatry, Renmin Hospital, Wuhan University, Wuhan 430060, China;
| | - Lijuan Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yage Zheng
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Y.X.); (Y.Z.)
| | - Caixia Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China;
| | - Gaohua Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan 430060, China; (Y.X.); (Y.Z.)
- Institute of Neuropsychiatry, Renmin Hospital, Wuhan University, Wuhan 430060, China;
- Correspondence: ; Tel.: +86-27-88041911
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8
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The neuroendocrine modulation of global DNA methylation in neuropsychiatric disorders. Mol Psychiatry 2021; 26:66-69. [PMID: 33099577 DOI: 10.1038/s41380-020-00924-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 01/03/2023]
Abstract
There is an increasing body of knowledge on the influence of differential DNA methylation of specific genomic regions in psychiatric disorders. However, fewer studies have addressed global DNA methylation (GMe) levels. GMe is an estimative of biological functioning that is regulated by pervasive mechanisms able to capture the big picture of metabolic and environmental influences upon gene expression. In the present perspective article, we highlighted evidence for the relationships between cortisol and sex hormones and GMe in psychiatric disorders. We argue that the far-reaching effects of cortisol and sexual hormones on GMe may lie on the pathways linking stress and mental health. Further research on these endocrine-epigenetic links may help to explain the role of environmental stress as well as sex differences in the prevalence of psychiatric disorders.
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9
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Mo J, Liang Z, Lu M, Wang H. Protonation-Suppression-Free LC-MS/MS Analysis for Profiling of DNA Cytosine Modifications in Adult Mice. Anal Chem 2020; 92:7430-7436. [PMID: 32353227 DOI: 10.1021/acs.analchem.0c00962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA cytosine modifications are important epigenetic marks. To elucidate their roles by a large scale of comparative studies, it is important to quantify the abundance of DNA cytosine modifications accurately. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a golden option. The performance of LC-MS/MS is heavily dependent on the ionization or protonation of target analytes. Initially, we found that two factors, DNA hydrolysate buffer and residual coeluted nucleosides, might greatly suppress the protonation of 5-(hydroxymethyl)-2'-deoxycytidine (5hmdC). Surprisingly, ammonium bicarbonate can eliminate the suppression caused by both factors. Mechanistically, ammonium bicarbonate increases the protonation capacity in the gas phase and facilitates proton transfer to the target nucleosides. Benefiting from these findings, we developed a suppression-free, sensitive, and robust ultrahigh-performance LC-MS/MS assay for massive detection of three DNA cytosine modifications, including 5-methyl-2'-deoxycytidine (5mdC), 5hmdC, and 5-formyl-2'-deoxycytidine (5fdC). In 30 consecutive analyses, the relative standard deviation (RSD) of the 5hmdC and 5fdC peak areas is 2.0% and 3.2%, respectively. In this case, no stable isotope-labeled standard is required for internal calibration. We further performed a comprehensive profiling of DNA cytosine modifications in 26 tissues of age-different C57BL/6N mice. Interestingly, we found that only liver 5hmdC abundance increases with the increasing age of adult mice, suggesting that liver 5hmdC might be a potential indicator of age in adulthood.
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Affiliation(s)
- Jiezhen Mo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiling Lu
- Greater China Market Division, Agilent Technologies, Beijing 100102, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China
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10
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Peedicayil J. Identification of Biomarkers in Neuropsychiatric Disorders Based on Systems Biology and Epigenetics. Front Genet 2019; 10:985. [PMID: 31681422 PMCID: PMC6801306 DOI: 10.3389/fgene.2019.00985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
Clinically useful biomarkers are available for some neuropsychiatric disorders like fragile X syndrome, Rett syndrome, and Huntington’s disease. Despite many decades of research on the pathogenesis of neuropsychiatric disorders like schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD), the exact pathogenesis of these disorders remains unclear, and there are no clinically useful biomarkers for these disorders. However, there is increasing evidence that abnormal epigenetic mechanisms of gene expression contribute to the pathogenesis of SZ, BD, and MDD. Both systems (or network) biology and epigenetics (a component of systems biology) attempt to make sense of biological systems that are highly dynamic and multi-compartmental. This article suggests that systems biology, emphasizing the epigenetic component of systems biology, could help identify clinically useful biomarkers in neuropsychiatric disorders like SZ, BD, and MDD.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India
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11
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Abstract
OBJECTIVE Depression is associated with various environmental risk factors such as stress, childhood maltreatment experiences, and stressful life events. Current approaches to assess the pathophysiology of depression, such as epigenetics and gene-environment (GxE) interactions, have been widely leveraged to determine plausible markers, genes, and variants for the risk of developing depression. METHODS We focus on the most recent developments for genomic research in epigenetics and GxE interactions. RESULTS In this review, we first survey a variety of association studies regarding depression with consideration of GxE interactions. We then illustrate evidence of epigenetic mechanisms such as DNA methylation, microRNAs, and histone modifications to influence depression in terms of animal models and human studies. Finally, we highlight their limitations and future directions. CONCLUSION In light of emerging technologies in artificial intelligence and machine learning, future research in epigenetics and GxE interactions promises to achieve novel innovations that may lead to disease prevention and future potential therapeutic treatments for depression.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA , USA.,Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
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12
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What do DNA methylation studies tell us about depression? A systematic review. Transl Psychiatry 2019; 9:68. [PMID: 30718449 PMCID: PMC6362194 DOI: 10.1038/s41398-019-0412-y] [Citation(s) in RCA: 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.
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In Vivo and In Vitro Neuronal Plasticity Modulation by Epigenetic Regulators. J Mol Neurosci 2018; 65:301-311. [PMID: 29931501 DOI: 10.1007/s12031-018-1101-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/12/2018] [Indexed: 10/28/2022]
Abstract
Prenatal stress (PS) induces molecular changes that alter neural connectivity, increasing the risk for neuropsychiatric disorders. Here we analyzed -in the hippocampus of adult rats exposed to PS- the epigenetic signature mediating the PS-induced neuroplasticity changes. Furthermore, using cultured hippocampal neurons, we investigated the effects on neuroplasticity of an epigenetic modulator. PS induced significant modifications in the mRNA levels of stress-related transcription factor MEF2A, SUV39H1 histone methyltransferase, and TET1 hydroxylase, indicating that PS modifies gene expression through chromatin remodeling. In in vitro analysis, histone acetylation inhibition with apicidin increased filopodium density, suggesting that the external regulation of acetylation levels might modulate neuronal morphology. These results offer a way to enhance neural connectivity that could be considered to revert PS effects.
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Dmitrzak-Weglarz M, Reszka E. Pathophysiology of Depression: Molecular Regulation of Melatonin Homeostasis - Current Status. Neuropsychobiology 2018; 76:117-129. [PMID: 29898451 DOI: 10.1159/000489470] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/19/2018] [Indexed: 12/29/2022]
Abstract
Circadian rhythm alterations resulting in disturbed sleep and disturbed melatonin secretion are flagship features of depression. Melatonin, known as a hormone of darkness, is secreted by the pineal gland located near to the center of the brain between the two hemispheres. Melatonin has an antidepressant effect by maintaining the body's circadian rhythm, by regulating the pattern of expression of the clock genes in the suprachiasmatic nucleus (SCN) and modifying the key genes of serotoninergic neurotransmission that are linked with a depressive mood. Melatonin is produced via the metabolism of serotonin in two steps which are catalyzed by serotonin N-acetyltransferase (SNAT) and acetylserotonin-O-methyltransferase (ASMT). Serotonin, SNAT, and ASMT are key melatonin level regulation factors. Melatonin acts mainly on the MT1 and MT2 receptors, which are present in the SCN, to regulate physiological and neuroendocrine functions including circadian entrainment, referred to as a chronobiotic effect. Although melatonin has been known about and refereed to for almost 50 years, the relationship between melatonin and depression is still not clear. In this review, we summarize current knowledge about the genetic and epigenetic regulation of enzymes involved in melatonin synthesis and metabolism as potential features of depression pathophysiology and treatment. Confirmation that melatonin metabolism in peripheral blood partially reflects a disorder in the brain could be a breakthrough in the standardization of measurements of melatonin level for the development of treatment standards, finding new therapeutic targets, and elaborating simple noninvasive clinical tests.
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Affiliation(s)
- Monika Dmitrzak-Weglarz
- Department of Psychiatric Genetics, Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Edyta Reszka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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Maulik U, Sen S, Mallik S, Bandyopadhyay S. Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus. BMC Genet 2018; 19:9. [PMID: 29357837 PMCID: PMC5776763 DOI: 10.1186/s12863-017-0574-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/29/2017] [Indexed: 01/09/2023] Open
Abstract
Background Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection. Results First of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis. Thereafter, we utilize weighted topological overlap matrix (TOM) measure and average linkage clustering consecutively on these genesets for intra- and inter-species study.We identify co-methylated and multi-stage co-methylated gene modules by using dynamic tree cut, for intra-and inter-species cases, respectively. Each module is represented by individual color in the dendrogram. Gene Ontology and KEGG pathway based analysis are then performed to identify biological functionalities of the identified modules. Finally, top ten regulator TFs and targeter miRNAs that are associated with the maximum number of gene modules, are determined for both intra-and inter-species analysis. Conclusions The novel TFs and miRNAs obtained from the analysis are: MYST3 and ZNF771 as TFs (for human intra-species analysis), BAZ2B, RCOR3 and ATF1 as TFs (for rhesus intra-species analysis), and mml-miR-768-3p and mml-miR-561 as miRs (for rhesus intra-species analysis); and MYST3 and ZNF771 as miRs(for inter-species study). Furthermore, the genes/TFs/miRNAs that are already found to be liable for several brain-related dreadful diseases as well as rare neglected diseases (e.g., wolf Hirschhorn syndrome, Joubarts Syndrome, Huntington’s disease, Simian Immunodeficiency Virus(SIV) mediated enchaphilits, Parkinsons Disease, Bipolar disorder and Schizophenia etc.) are mentioned. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0574-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India.
| | - Sagnik Sen
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
| | - Saurav Mallik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
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17
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Forster VJ, McDonnell A, Theobald R, McKay JA. Effect of methotrexate/vitamin B 12 on DNA methylation as a potential factor in leukemia treatment-related neurotoxicity. Epigenomics 2017; 9:1205-1218. [PMID: 28809129 PMCID: PMC5638018 DOI: 10.2217/epi-2016-0165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Methotrexate (MTX) is administered to treat childhood acute lymphoblastic leukemia (ALL). It acts by inhibiting dihydrofolate reductase which reduces methyltetrahydrofolate, a key component in one carbon metabolism, thus reducing cell proliferation. Further perturbations to one carbon metabolism, such as reduced vitamin B12 levels via the use of nitrous oxide for sedation during childhood ALL treatment, may increase neurotoxicity risk. With B12 as an enzymatic cofactor, methyltetrahydrofolate is essential to produce methionine, which is critical for DNA methylation. We investigated global and gene specific DNA methylation in neuronal cell lines in response to MTX treatment and vitamin B12 concentration individually, and in combination. Results: MTX treatment alone significantly increased LINE-1 methylation in SH-SY5Y (p = 0.040) and DAOY (p < 0.001), and increased FKBP5 methylation in MO3.13 cells (p = 0.009). Conclusion: We conclude that altered DNA methylation of brain/central nervous system cells could be one mechanism involved in MTX treatment-related neurotoxicities and neurocognitive late effects in ALL survivors.
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Affiliation(s)
- Victoria J Forster
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Alex McDonnell
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Theobald
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Jill A McKay
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
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Shi DQ, Ali I, Tang J, Yang WC. New Insights into 5hmC DNA Modification: Generation, Distribution and Function. Front Genet 2017; 8:100. [PMID: 28769976 PMCID: PMC5515870 DOI: 10.3389/fgene.2017.00100] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/05/2017] [Indexed: 01/10/2023] Open
Abstract
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals. Here, we review recent advances on the generation, distribution, and function of 5hmC modification in mammals and discuss its potential roles in plants.
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Affiliation(s)
- Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Iftikhar Ali
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Jun Tang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijing, China
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Discovery and replication of a peripheral tissue DNA methylation biosignature to augment a suicide prediction model. Clin Epigenetics 2016; 8:113. [PMID: 27822318 PMCID: PMC5093988 DOI: 10.1186/s13148-016-0279-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/20/2016] [Indexed: 12/25/2022] Open
Abstract
Background Suicide is the second leading cause of death among adolescents in the USA, and rates are rising. Methods to identify individuals at risk are essential for implementing prevention strategies, and the development of a biomarker can potentially improve prediction of suicidal behaviors. Prediction of our previously reported SKA2 biomarker for suicide and PTSD is substantially improved by questionnaires assessing perceived stress or anxiety and is therefore reliant on psychological assessment. However, such stress-related states may also leave a biosignature that could equally improve suicide prediction. In genome-wide DNA methylation data, we observed significant overlap between waking cortisol-associated and suicide-associated DNA methylation in blood and the brain, respectively. Results Using a custom bioinformatic brain to blood discovery algorithm, we derived a DNA methylation biosignature that interacts with SKA2 methylation to improve the prediction of suicidal ideation in our existing suicide prediction model across both blood and saliva data sets. This biosignature was independently validated in the Grady Trauma Project cohort and interacted with HPA axis metrics in the same cohort. The biosignature showed a relationship with immune status by its correlation with myeloid-derived cell proportions in all data sets and with IL-6 measures in a prospective postpartum depression cohort. Three probes showed significant correlations with the biosignature: cg08469255 (DDR1), cg22029879 (ARHGEF10), and cg24437859 (SHP1), of which SHP1 methylation correlated with immune measures. Conclusions We conclude that this biosignature interacts with SKA2 methylation to improve suicide prediction and may represent a biological state of immune and HPA axis modulation that mediates suicidal behavior. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0279-1) contains supplementary material, which is available to authorized users.
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