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Yan J, Xia Q, Sun X, Yang P, Gao H, Pan Z, Gao J, Zhang L, Wang M, Wang K, Li C, Zhang X, Ju P, Zhu C. Dysregulation of interleukin-8 is involved in the onset and relapse of schizophrenia: An independent validation and meta-analysis. Prog Neuropsychopharmacol Biol Psychiatry 2024; 133:111018. [PMID: 38670447 DOI: 10.1016/j.pnpbp.2024.111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/30/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
As a major mental health disorder, symptoms of schizophrenia (SCZ) include delusions, reduced motivation, hallucinations, reduced motivation and a variety of cognitive disabilities. Many of these symptoms are now known to be associated with abnormal regulation of the immune system. Low blood levels of cytokines and chemokines have been suggested to be one of the underlying causes of SCZ. However, their biological roles at different stages of SCZ remain unclear. Our objective was to investigate expression patterns of cytokines and chemokines at different stages of onset and relapse in SCZ patients and to conduct an analysis of their relationship to disease progression. We also aimed to identify immune features associated with different disease trajectories in patients with SCZ. Gene set enrichment analysis (GSEA) was used to interrogate the GSE27383 dataset and identify key genes associated with inflammation. These results led us to recruit 36 healthy controls, 40 patients with first-episode psychosis (FEP), and 39 patients with SCZ relapse. Meso Scale Discovery technology was used to independently validate serum levels of 35 cytokines and chemokines. This was followed by a meta-analysis to gain a more comprehensive understanding of the role of interleukin-8 (IL-8/CXCL8) in SCZ. Analysis of the GSE27383 database revealed 3596 genes with distinct expression patterns. A significant portion of these genes were identified as inflammation-related and showed remarkable enrichment in three key pathways: IL-17, cytokine-cytokine receptor, and AGE-RAGE signaling in diabetic complications. We observed co-expression of CXCL8 and IL-16 within these three pathways. In a subsequent analysis of independently validated samples, a notable discrepancy was detected in the inflammatory status between individuals experiencing FEP and those in relapse. In particular, expression of CXCL8 demonstrated superior predictive capability in FEP and relapsed patients. Notably, results of the meta-analysis confirmed that Chinese and European populations were consistent with the overall results (Z = 4.60, P < 0.001; Z = 3.70, P < 0.001). However, in the American subgroup, there was no significant difference in CXCL8 levels between patients with SCZ compared to healthy controls (Z = 1.09, P = 0.277). Our findings suggest that the inflammatory response in patients with SCZ differs across the different stages, with CXCL8 emerging as a potential predictive factor. Collectively, our data suggest that CXCL8 has the potential to serve as a significant immunological signature of SCZ subtypes. Trial registration: The clinical registration number for this trial is ChiCTR2100045240 (Registration Date: 2021/04/09).
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Affiliation(s)
- Junwei Yan
- Brain Neurobiomedical Research Center, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Science and Education Department, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui 230022, China; Science and Education Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China
| | - Qingrong Xia
- Brain Neurobiomedical Research Center, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Science and Education Department, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui 230022, China; Science and Education Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China
| | - Xuejun Sun
- Lc-Bio Technology Co. Ltd, Hangzhou, Zhe Jiang 31000, China
| | - Pei Yang
- Lc-Bio Technology Co. Ltd, Hangzhou, Zhe Jiang 31000, China
| | - Hua Gao
- Psychiatry Department, Hefei Fourth People's Hospital, Hefei, Anhui 230022, China
| | - Zhongde Pan
- Psychiatry Department, Academy of Forensic Science, Shanghai 200061, China
| | - Jianliang Gao
- Psychiatry Department, Hefei Fourth People's Hospital, Hefei, Anhui 230022, China
| | - Loufeng Zhang
- Psychiatry Department, Hefei Fourth People's Hospital, Hefei, Anhui 230022, China
| | - Meiti Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai key Laboratory of Psychotic Disorders, Shanghai Institute of Traditional Chinese Medicine for Mental Health, Shanghai 201108, China
| | - Keming Wang
- Brain Neurobiomedical Research Center, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Science and Education Department, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui 230022, China; Science and Education Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China
| | - Chao Li
- Brain Neurobiomedical Research Center, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Science and Education Department, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui 230022, China; Science and Education Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China
| | - Xulai Zhang
- Geriatric Psychology Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China
| | - Peijun Ju
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai key Laboratory of Psychotic Disorders, Shanghai Institute of Traditional Chinese Medicine for Mental Health, Shanghai 201108, China.
| | - Cuizhen Zhu
- Brain Neurobiomedical Research Center, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230022, China; Science and Education Department, Hefei Fourth People's Hospital, Anhui Mental Health Center, Hefei, Anhui 230022, China; Science and Education Department, Anhui Clinical Center for Mental and Psychological Diseases, Hefei, Anhui 230022, China.
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Islam M, Behura SK. Molecular Regulation of Fetal Brain Development in Inbred and Congenic Mouse Strains Differing in Longevity. Genes (Basel) 2024; 15:604. [PMID: 38790233 PMCID: PMC11121069 DOI: 10.3390/genes15050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The objective of this study was to investigate gene regulation of the developing fetal brain from congenic or inbred mice strains that differed in longevity. Gene expression and alternative splice variants were analyzed in a genome-wide manner in the fetal brain of C57BL/6J mice (long-lived) in comparison to B6.Cg-Cav1tm1Mls/J (congenic, short-lived) and AKR/J (inbred, short-lived) mice on day(d) 12, 15, and 17 of gestation. The analysis showed a contrasting gene expression pattern during fetal brain development in these mice. Genes related to brain development, aging, and the regulation of alternative splicing were significantly differentially regulated in the fetal brain of the short-lived compared to long-lived mice during development from d15 and d17. A significantly reduced number of splice variants was observed on d15 compared to d12 or d17 in a strain-dependent manner. An epigenetic clock analysis of d15 fetal brain identified DNA methylations that were significantly associated with single-nucleotide polymorphic sites between AKR/J and C57BL/6J strains. These methylations were associated with genes that show epigenetic changes in an age-correlated manner in mice. Together, the finding of this study suggest that fetal brain development and longevity are epigenetically linked, supporting the emerging concept of the early-life origin of longevity.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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Gore S, Meche B, Shao D, Ginnett B, Zhou K, Azad RK. DiseaseNet: a transfer learning approach to noncommunicable disease classification. BMC Bioinformatics 2024; 25:107. [PMID: 38468193 PMCID: PMC10926612 DOI: 10.1186/s12859-024-05734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such as DNA methylation, have emerged as potential indicators for NCDs. These have previously been exploited in other contexts within the framework of neural network models that capture complex relationships within the data. Applications of neural networks have led to significant breakthroughs in various biological or biomedical fields but these have not yet been effectively applied to NCD modeling. This is, in part, due to limited datasets that are not amenable to building of robust neural network models. In this work, we leveraged a neural network trained on one class of NCDs, cancer, as the basis for a transfer learning approach to non-cancer NCD modeling. Our results demonstrate promising performance of the model in predicting three NCDs, namely, arthritis, asthma, and schizophrenia, for the respective blood samples, with an overall accuracy (f-measure) of 94.5%. Furthermore, a concept based explanation method called Testing with Concept Activation Vectors (TCAV) was used to investigate the importance of the sample sources and understand how future training datasets for multiple NCD models may be improved. Our findings highlight the effectiveness of transfer learning in developing accurate diagnostic and predictive models for NCDs.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Bailey Meche
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Danyang Shao
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Benjamin Ginnett
- Department of Engineering, Eastern Arizona College, Thatcher, AZ, USA
| | - Kelly Zhou
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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Wang F, Hu D, Lou X, Wang Y, Wang L, Zhang T, Yan Z, Meng N, Zou Y. BNIP3 and DAPK1 methylation in peripheral blood leucocytes are noninvasive biomarkers for gastric cancer. Gene 2024; 898:148109. [PMID: 38142898 DOI: 10.1016/j.gene.2023.148109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/26/2023]
Abstract
OBJECTIVE The objective of this study is to comprehensively investigate the potential value of BNIP3 and DAPK1 methylation in peripheral blood leukocytes as a non-invasive biomarker for the detection of gastric cancer (GC), prediction of chemotherapy efficacy, and prognosis assessment. PATIENTS AND METHODS Initially, multiple bioinformatic analyses were employed to explore the genetic landscape and biological effects of BNIP3 and DAPK1 in GC tissues. Subsequently, case-control and prospective follow-up studies were conducted to compare the differences in BNIP3 and DAPK1 methylation levels in peripheral blood leukocytes among GC patients and healthy controls, as well as between patients exhibiting sensitivity and resistance to platinum plus fluorouracil treatment, and between patients with varying survival outcomes of GC. Additionally, several predictive nomograms were constructed based on the identified CpG sites and relevant clinical parameters to forecast the occurrence of GC, chemotherapy efficacy, and prognosis. RESULTS The upregulation of BNIP3 and DAPK1 was found to be associated with the development and poorer survival outcomes of GC. Furthermore, the expression of BNIP3/DAPK1 exhibited an inverse relationship with their DNA methylation levels and demonstrated a positive correlation with immune cell infiltration, as well as the IC50 values of 5-Fluorouracil and Cisplatin in GC tissues. Increased infiltration of macrophages in the high-expression groups was observed to be linked to unfavorable GC survival. In the case-control and follow-up studies, lower methylation levels of BNIP3 and DAPK1 were identified in the peripheral leukocytes of GC patients compared to healthy controls. Hypomethylation was also associated with more aggressive subtypes, diminished chemotherapy efficacy, and poorer survival outcomes in GC. CONCLUSION The DNA methylation of BNIP3 and DAPK1 in peripheral blood leukocytes holds promise as a novel non-invasive biomarker for predicting the occurrence of GC, chemotherapy efficacy, and prognosis assessment.
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Affiliation(s)
- Fang Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai 2004332, China
| | - Xiaoqi Lou
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuhua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Linlin Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Tingyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Ziye Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Nana Meng
- Department of Quality Management Office, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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Zheng J, Womer FY, Tang L, Guo H, Zhang X, Tang Y, Wang F. Integrative omics analysis reveals epigenomic and transcriptomic signatures underlying brain structural deficits in major depressive disorder. Transl Psychiatry 2024; 14:17. [PMID: 38195555 PMCID: PMC10776753 DOI: 10.1038/s41398-023-02724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Several lines of evidence support the involvement of transcriptomic and epigenetic mechanisms in the brain structural deficits of major depressive disorder (MDD) separately. However, research in these two areas has remained isolated. In this study, we proposed an integrative strategy that combined neuroimaging, brain-wide gene expression, and peripheral DNA methylation data to investigate the genetic basis of gray matter abnormalities in MDD. The MRI T1-weighted images and Illumina 850 K DNA methylation microarrays were obtained from 269 patients and 416 healthy controls, and brain-wide transcriptomic data were collected from Allen Human Brain Atlas. The between-group differences in gray matter volume (GMV) and differentially methylated CpG positions (DMPs) were examined. The genes with their expression patterns spatially related to GMV changes and genes with DMPs were overlapped and selected. Using principal component regression, the associations between DMPs in overlapped genes and GMV across individual patients were investigated, and the region-specific correlations between methylation status and gene expression were examined. We found significant associations between the decreased GMV and DMPs methylation status in the anterior cingulate cortex, inferior frontal cortex, and fusiform face cortex regions. These DMPs genes were primarily enriched in the neurodevelopmental and synaptic transmission process. There was a significant negative correlation between DNA methylation and gene expression in genes associated with GMV changes of the frontal cortex in MDD. Our findings suggest that GMV abnormalities in MDD may have a transcriptomic and epigenetic basis. This imaging-transcriptomic-epigenetic integrative analysis provides spatial and biological links between cortical morphological deficits and peripheral epigenetic signatures in MDD.
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Affiliation(s)
- Junjie Zheng
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
| | - Fay Y Womer
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lili Tang
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
| | - Huiling Guo
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xizhe Zhang
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Yanqing Tang
- Department of Psychiatry, The First Hospital of China Medical University, Shenyang, China.
- Brain Function Research Section, The First Hospital of China Medical University, Shenyang, China.
- Department of Gerontology, The First Hospital of China Medical University, Shenyang, China.
- Shengjing Hospital of China Medical University, Shenyang, China.
| | - Fei Wang
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China.
- Department of Mental Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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Tang Y, Tan Y, Palaniyappan L, Yao Y, Luo Q, Li Y. Epigenetic profile of the immune system associated with symptom severity and treatment response in schizophrenia. J Psychiatry Neurosci 2024; 49:E45-E58. [PMID: 38359932 PMCID: PMC10890792 DOI: 10.1503/jpn.230099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Environmental modification of genetic information (epigenetics) is often invoked to explain interindividual differences in the phenotype of schizophrenia. In clinical practice, such variability is most prominent in the symptom profile and the treatment response. Epigenetic regulation of immune function is of particular interest, given the therapeutic relevance of this mechanism in schizophrenia. METHODS We analyzed the DNA methylation data of immune-relevant genes in patients with schizophrenia whose disease duration was less than 3 years, with previous lifetime antipsychotic treatment of no more than 2 weeks total. RESULTS A total of 441 patients met the inclusion criteria. Core symptoms were consistently associated with 206 methylation positions, many of which had previously been implicated in inflammatory responses. Of these, 24 methylation positions were located either in regulatory regions or near the CpG islands of 20 genes, including the SRC gene, which is a key player in glutamatergic signalling. These symptom-associated immune genes were enriched in neuronal development functions, such as neuronal migration and glutamatergic synapse. Compared with using only clinical information (including scores on the Positive and Negative Syndrome Scale), integrating methylation data into the model significantly improved the predictive ability (as indicated by area under the curve) for response to 8 weeks of antipsychotic treatment. LIMITATIONS We focused on a small number of methylation probes (immune-centred search) and lacked nutritional data and direct brain-based measures. CONCLUSION Epigenetic modifications of the immune system are associated with symptom severity at onset and subsequent treatment response in schizophrenia.
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Affiliation(s)
- Yuanhao Tang
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
| | - Yunlong Tan
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
| | - Lena Palaniyappan
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
| | - Yin Yao
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
| | - Qiang Luo
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
| | - Yanli Li
- From the National Clinical Research Center for Aging and Medicine at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science and School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China (Tang, Yao); the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Tan, Li); the Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Que. (Palaniyappan); Robarts Research Institute and Department of Medical Biophysics, Western University, London, Ont. (Palaniyappan); the Lawson Health Research Institute, London, Ont. (Palaniyappan); the MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China (Luo)
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Sint Jago SC, Bahabry R, Schreiber AM, Homola J, Ngyuen T, Meijia F, Allendorfer JB, Lubin FD. Aerobic exercise alters DNA hydroxymethylation levels in an experimental rodent model of temporal lobe epilepsy. Epilepsy Behav Rep 2023; 25:100642. [PMID: 38323091 PMCID: PMC10844942 DOI: 10.1016/j.ebr.2023.100642] [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: 10/17/2023] [Revised: 12/24/2023] [Accepted: 12/26/2023] [Indexed: 02/08/2024] Open
Abstract
The therapeutic potential of aerobic exercise in mitigating seizures and cognitive issues in temporal lobe epilepsy (TLE) is recognized, yet the underlying mechanisms are not well understood. Using a rodent TLE model induced by Kainic acid (KA), we investigated the impact of a single bout of exercise (i.e., acute) or 4 weeks of aerobic exercise (i.e., chronic). Blood was processed for epilepsy-associated serum markers, and DNA methylation (DNAme), and hippocampal area CA3 was assessed for gene expression levels for DNAme-associated enzymes. While acute aerobic exercise did not alter serum Brain-Derived Neurotrophic Factor (BDNF) or Interleukin-6 (IL-6), chronic exercise resulted in an exercise-specific decrease in serum BDNF and an increase in serum IL-6 levels in epileptic rats. Additionally, whole blood DNAme levels, specifically 5-hydroxymethylcytosine (5-hmC), decreased in epileptic animals following chronic exercise. Hippocampal CA3 5-hmC levels and ten-eleven translocation protein (TET1) expression mirrored these changes. Furthermore, immunohistochemistry analysis revealed that most 5-hmC changes in response to chronic exercise were neuron-specific within area CA3 of the hippocampus. Together, these findings suggest that DNAme mechanisms in the rodent model of TLE are responsive to chronic aerobic exercise, with emphasis on neuronal 5-hmC DNAme in the epileptic hippocampus.
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Affiliation(s)
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | | | - Julia Homola
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Tram Ngyuen
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Fernando Meijia
- Department of Neurobiology, University of Alabama at Birmingham, United States
| | - Jane B. Allendorfer
- Department of Neurobiology, University of Alabama at Birmingham, United States
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Farah D. Lubin
- Department of Neurobiology, University of Alabama at Birmingham, United States
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Strawn M, Safranski TJ, Behura SK. Does DNA methylation in the fetal brain leave an epigenetic memory in the blood? Gene 2023; 887:147788. [PMID: 37696423 DOI: 10.1016/j.gene.2023.147788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Epigenetic memory is an emerging concept that refers to the process in which epigenetic changes occurring early-in life can lead to long-term programs of gene regulation in time and space. By leveraging neural network regression modeling of DNA methylation data in pigs, we show that specific methylations in the adult blood can reliably predict methylation changes that occurred in the fetal brain. Genes associated with these methylations represented known markers of specific cell types of blood including bone marrow hematopoietic progenitor cells, and ependymal and oligodendrocyte cells of brain. This suggested that methylation changes that occurred in the developing brain were maintained as an epigenetic memory in the blood through the adult life.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Timothy J Safranski
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, United States; Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, United States.
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Reiner A, Bakulski KM, Fisher JD, Dou JF, Schneper L, Mitchell C, Notterman DA, Zawistowski M, Ware EB. Sex-specific DNA methylation in saliva from the multi-ethnic Future of Families and Child Wellbeing Study. Epigenetics 2023; 18:2222244. [PMID: 37300819 PMCID: PMC10259311 DOI: 10.1080/15592294.2023.2222244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The prevalence and severity of many diseases differs by sex, potentially due to sex-specific patterns in DNA methylation. Autosomal sex-specific differences in DNA methylation have been observed in cord blood and placental tissue but are not well studied in saliva or in diverse populations. We sought to characterize sex-specific DNA methylation on autosomal chromosomes in saliva samples from children in the Future of Families and Child Wellbeing Study, a multi-ethnic prospective birth cohort containing an oversampling of Black, Hispanic and low-income families. DNA methylation from saliva samples was analysed on 796 children (50.6% male) at both ages 9 and 15 with DNA methylation measured using the Illumina HumanMethylation 450k array. An epigenome-wide association analysis of the age 9 samples identified 8,430 sex-differentiated autosomal DNA methylation sites (P < 2.4 × 10-7), of which 76.2% had higher DNA methylation in female children. The strongest sex-difference was in the cg26921482 probe, in the AMDHD2 gene, with 30.6% higher DNA methylation in female compared to male children (P < 1 × 10-300). Treating the age 15 samples as an internal replication set, we observed highly consistent results between the ages 9 and 15 measurements, indicating stable and replicable sex-differentiation. Further, we directly compared our results to previously published DNA methylation sex differences in both cord blood and saliva and again found strong consistency. Our findings support widespread and robust sex-differential DNA methylation across age, human tissues, and populations. These findings help inform our understanding of potential biological processes contributing to sex differences in human physiology and disease.
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Affiliation(s)
- Allison Reiner
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonah D Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
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10
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Alberca CD, Papale LA, Madrid A, Alisch RS. Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism. Hum Mol Genet 2023; 32:3312-3322. [PMID: 37658766 DOI: 10.1093/hmg/ddad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.
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Affiliation(s)
- Carolina D Alberca
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Avenue, Madison, WI 53705, United States
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11
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Zhang S, Shi K, Lyu N, Zhang Y, Liang G, Zhang W, Wang X, Wen H, Wen L, Ma H, Wang J, Yu X, Guan L. Genome-wide DNA methylation analysis in families with multiple individuals diagnosed with schizophrenia and intellectual disability. World J Biol Psychiatry 2023; 24:741-753. [PMID: 37017099 DOI: 10.1080/15622975.2023.2198595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
OBJECTIVES Schizophrenia (SZ) and intellectual disability (ID) are both included in the continuum of neurodevelopmental disorders (NDDs). DNA methylation is known to be important in the occurrence of NDDs. The family study is conducive to eliminate the effects of relative epigenetic backgrounds, and to screen for differentially methylated positions (DMPs) and regions (DMRs) that are truly associated with NDDs. METHODS Four monozygotic twin families were recruited, and both twin individuals suffered from NDDs (either SZ, ID, or SZ plus ID). Genome-wide methylation analysis was performed in all samples and each family. DMPs and DMRs between NDD patients and unaffected individuals were identified. Functional and pathway enrichment analyses were performed on the annotated genes. RESULTS Two significant DMPs annotated to CYP2E1 were found in all samples. In Family One, 1476 DMPs mapped to 880 genes, and 162 DMRs overlapping with 153 unique genes were recognised. Our results suggested that the altered methylation levels of FYN, STAT3, RAC1, and NR4A2 were associated with the development of SZ and ID. Neurodevelopment and the immune system may participate in the occurrence of SZ and ID. CONCLUSIONS Our findings suggested that DNA methylation participated in the development of NDDs by affecting neurodevelopment and the immune system.
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Affiliation(s)
- Shengmin Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Kaiyu Shi
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nan Lyu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Beijing Anding Hospital, Beijing Key Laboratory of Mental Disorders, The National Clinical Research Centre for Mental Disorders, The Advanced Innovation Centre for Human Brain Protection, Capital Medical University, Beijing, China
| | - Yunshu Zhang
- The Sixth People's Hospital of Hebei Province, Hebei Mental Health Centre, Baoding, Hebei, China
| | | | - Wufang Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xijin Wang
- The First Psychiatric Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hong Wen
- The Third Hospital of Mianyang, Mianyang, Sichuan, China
| | - Liping Wen
- Zigong Mental Health Centre, Zigong, Sichuan, China
| | - Hong Ma
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jijun Wang
- Shanghai Mental Health Centre, Shanghai Jiaotong University School of Medicine, Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xin Yu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Lili Guan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
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12
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Eichenauer H, Ehlert U. The association between prenatal famine, DNA methylation and mental disorders: a systematic review and meta-analysis. Clin Epigenetics 2023; 15:152. [PMID: 37716973 PMCID: PMC10505322 DOI: 10.1186/s13148-023-01557-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Undernutrition in pregnant women is an unfavorable environmental condition that can affect the intrauterine development via epigenetic mechanisms and thus have long-lasting detrimental consequences for the mental health of the offspring later in life. One epigenetic mechanism that has been associated with mental disorders and undernutrition is alterations in DNA methylation. The effect of prenatal undernutrition on the mental health of adult offspring can be analyzed through quasi-experimental studies such as famine studies. The present systematic review and meta-analysis aims to analyze the association between prenatal famine exposure, DNA methylation, and mental disorders in adult offspring. We further investigate whether altered DNA methylation as a result of prenatal famine exposure is prospectively linked to mental disorders. METHODS We conducted a systematic search of the databases PubMed and PsycINFO to identify relevant records up to September 2022 on offspring whose mothers experienced famine directly before and/or during pregnancy, examining the impact of prenatal famine exposure on the offspring's DNA methylation and/or mental disorders or symptoms. RESULTS The systematic review showed that adults who were prenatally exposed to famine had an increased risk of schizophrenia and depression. Several studies reported an association between prenatal famine exposure and hyper- or hypomethylation of specific genes. The largest number of studies reported differences in DNA methylation of the IGF2 gene. Altered DNA methylation of the DUSP22 gene mediated the association between prenatal famine exposure and schizophrenia in adult offspring. Meta-analysis confirmed the increased risk of schizophrenia following prenatal famine exposure. For DNA methylation, meta-analysis was not suitable due to different microarrays/data processing approaches and/or unavailable data. CONCLUSION Prenatal famine exposure is associated with an increased risk of mental disorders and DNA methylation changes. The findings suggest that changes in DNA methylation of genes involved in neuronal, neuroendocrine, and immune processes may be a mechanism that promotes the development of mental disorders such as schizophrenia and depression in adult offspring. Such findings are crucial given that undernutrition has risen worldwide, increasing the risk of famine and thus also of negative effects on mental health.
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Affiliation(s)
- Heike Eichenauer
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland
| | - Ulrike Ehlert
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland.
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13
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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: 14] [Impact Index Per Article: 14.0] [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.
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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.
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14
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Jensen D, Chen J, Turner JA, Stephen JM, Wang YP, Wilson TW, Calhoun VD, Liu J. Epigenetic associations with adolescent grey matter maturation and cognitive development. Front Genet 2023; 14:1222619. [PMID: 37529779 PMCID: PMC10390095 DOI: 10.3389/fgene.2023.1222619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Introduction: Adolescence, a critical phase of human neurodevelopment, is marked by a tremendous reorganization of the brain and accompanied by improved cognitive performance. This development is driven in part by gene expression, which in turn is partly regulated by DNA methylation (DNAm). Methods: We collected brain imaging, cognitive assessments, and DNAm in a longitudinal cohort of approximately 200 typically developing participants, aged 9-14. This data, from three time points roughly 1 year apart, was used to explore the relationships between seven cytosine-phosphate-guanine (CpG) sites in genes highly expressed in brain tissues (GRIN2D, GABRB3, KCNC1, SLC12A9, CHD5, STXBP5, and NFASC), seven networks of grey matter (GM) volume change, and scores from seven cognitive tests. Results: The demethylation of the CpGs as well as the rates of change in DNAm were significantly related to improvements in total, crystalized, and fluid cognition scores, executive function, episodic memory, and processing speed, as well as several networks of GM volume increases and decreases that highlight typical patterns of brain maturation. Discussion: Our study provides a first look at the DNAm of genes involved in myelination, excitatory and inhibitory receptors, and connectivity, how they are related to the large-scale changes occurring in the brain structure as well as cognition during adolescence.
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Affiliation(s)
- Dawn Jensen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Jessica A. Turner
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Wexnar Medical Center, Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, United States
| | | | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, United States
| | - Tony W. Wilson
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE, United States
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
- The Mind Research Network, Albuquerque, NM, United States
- Psychology Department and Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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15
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Walton E, Baltramonaityte V, Calhoun V, Heijmans BT, Thompson PM, Cecil CAM. A systematic review of neuroimaging epigenetic research: calling for an increased focus on development. Mol Psychiatry 2023; 28:2839-2847. [PMID: 37185958 PMCID: PMC10615743 DOI: 10.1038/s41380-023-02067-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
Epigenetic mechanisms, such as DNA methylation (DNAm), have gained increasing attention as potential biomarkers and mechanisms underlying risk for neurodevelopmental, psychiatric and other brain-based disorders. Yet, surprisingly little is known about the extent to which DNAm is linked to individual differences in the brain itself, and how these associations may unfold across development - a time of life when many of these disorders emerge. Here, we systematically review evidence from the nascent field of Neuroimaging Epigenetics, combining structural or functional neuroimaging measures with DNAm, and the extent to which the developmental period (birth to adolescence) is represented in these studies. We identified 111 articles published between 2011-2021, out of which only a minority (21%) included samples under 18 years of age. Most studies were cross-sectional (85%), employed a candidate-gene approach (67%), and examined DNAm-brain associations in the context of health and behavioral outcomes (75%). Nearly half incorporated genetic data, and a fourth investigated environmental influences. Overall, studies support a link between peripheral DNAm and brain imaging measures, but there is little consistency in specific findings and it remains unclear whether DNAm markers present a cause, correlate or consequence of brain alterations. Overall, there is large heterogeneity in sample characteristics, peripheral tissue and brain outcome examined as well as the methods used. Sample sizes were generally low to moderate (median nall = 98, ndevelopmental = 80), and attempts at replication or meta-analysis were rare. Based on the strengths and weaknesses of existing studies, we propose three recommendations on how advance the field of Neuroimaging Epigenetics. We advocate for: (1) a greater focus on developmentally oriented research (i.e. pre-birth to adolescence); (2) the analysis of large, prospective, pediatric cohorts with repeated measures of DNAm and imaging to assess directionality; and (3) collaborative, interdisciplinary science to identify robust signals, triangulate findings and enhance translational potential.
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Affiliation(s)
- Esther Walton
- Department of Psychology, University of Bath, Bath, UK.
| | | | - Vince Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Dept. of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | - Charlotte A M Cecil
- Molecular Epidemiology, Dept. of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
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16
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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17
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Conole ELS, Vaher K, Cabez MB, Sullivan G, Stevenson AJ, Hall J, Murphy L, Thrippleton MJ, Quigley AJ, Bastin ME, Miron VE, Whalley HC, Marioni RE, Boardman JP, Cox SR. Immuno-epigenetic signature derived in saliva associates with the encephalopathy of prematurity and perinatal inflammatory disorders. Brain Behav Immun 2023; 110:322-338. [PMID: 36948324 DOI: 10.1016/j.bbi.2023.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Preterm birth is closely associated with a phenotype that includes brain dysmaturation and neurocognitive impairment, commonly termed Encephalopathy of Prematurity (EoP), of which systemic inflammation is considered a key driver. DNA methylation (DNAm) signatures of inflammation from peripheral blood associate with poor brain imaging outcomes in adult cohorts. However, the robustness of DNAm inflammatory scores in infancy, their relation to comorbidities of preterm birth characterised by inflammation, neonatal neuroimaging metrics of EoP, and saliva cross-tissue applicability are unknown. METHODS Using salivary DNAm from 258 neonates (n = 155 preterm, gestational age at birth 23.28 - 34.84 weeks, n = 103 term, gestational age at birth 37.00 - 42.14 weeks), we investigated the impact of a DNAm surrogate for C-reactive protein (DNAm CRP) on brain structure and other clinically defined inflammatory exposures. We assessed i) if DNAm CRP estimates varied between preterm infants at term equivalent age and term infants, ii) how DNAm CRP related to different types of inflammatory exposure (maternal, fetal and postnatal) and iii) whether elevated DNAm CRP associated with poorer measures of neonatal brain volume and white matter connectivity. RESULTS Higher DNAm CRP was linked to preterm status (-0.0107 ± 0.0008, compared with -0.0118 ± 0.0006 among term infants; p < 0.001), as well as perinatal inflammatory diseases, including histologic chorioamnionitis, sepsis, bronchopulmonary dysplasia, and necrotising enterocolitis (OR range |2.00 | to |4.71|, p < 0.01). Preterm infants with higher DNAm CRP scores had lower brain volume in deep grey matter, white matter, and hippocampi and amygdalae (β range |0.185| to |0.218|). No such associations were observed for term infants. Association magnitudes were largest for measures of white matter microstructure among preterms, where elevated epigenetic inflammation associated with poorer global measures of white matter integrity (β range |0.206| to |0.371|), independent of other confounding exposures. CONCLUSIONS Inflammatory-related DNAm captures the allostatic load of inflammatory burden in preterm infants. Such DNAm measures complement biological and clinical metrics when investigating the determinants of neurodevelopmental differences.
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Affiliation(s)
- Eleanor L S Conole
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Kadi Vaher
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Manuel Blesa Cabez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jill Hall
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael J Thrippleton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J Quigley
- Imaging Department, Royal Hospital for Children and Young People, Edinburgh, EH16 4TJ, UK
| | - Mark E Bastin
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James P Boardman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
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18
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Siecinski SK, Giamberardino SN, Spanos M, Hauser AC, Gibson JR, Chandrasekhar T, Trelles MDP, Rockhill CM, Palumbo ML, Cundiff AW, Montgomery A, Siper P, Minjarez M, Nowinski LA, Marler S, Kwee LC, Shuffrey LC, Alderman C, Weissman J, Zappone B, Mullett JE, Crosson H, Hong N, Luo S, She L, Bhapkar M, Dean R, Scheer A, Johnson JL, King BH, McDougle CJ, Sanders KB, Kim SJ, Kolevzon A, Veenstra-VanderWeele J, Hauser ER, Sikich L, Gregory SG. Genetic and epigenetic signatures associated with plasma oxytocin levels in children and adolescents with autism spectrum disorder. Autism Res 2023; 16:502-523. [PMID: 36609850 PMCID: PMC10023458 DOI: 10.1002/aur.2884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023]
Abstract
Oxytocin (OT), the brain's most abundant neuropeptide, plays an important role in social salience and motivation. Clinical trials of the efficacy of OT in autism spectrum disorder (ASD) have reported mixed results due in part to ASD's complex etiology. We investigated whether genetic and epigenetic variation contribute to variable endogenous OT levels that modulate sensitivity to OT therapy. To carry out this analysis, we integrated genome-wide profiles of DNA-methylation, transcriptional activity, and genetic variation with plasma OT levels in 290 participants with ASD enrolled in a randomized controlled trial of OT. Our analysis identified genetic variants with novel association with plasma OT, several of which reside in known ASD risk genes. We also show subtle but statistically significant association of plasma OT levels with peripheral transcriptional activity and DNA-methylation profiles across several annotated gene sets. These findings broaden our understanding of the effects of the peripheral oxytocin system and provide novel genetic candidates for future studies to decode the complex etiology of ASD and its interaction with OT signaling and OT-based interventions. LAY SUMMARY: Oxytocin (OT) is an abundant chemical produced by neurons that plays an important role in social interaction and motivation. We investigated whether genetic and epigenetic factors contribute to variable OT levels in the blood. To this, we integrated genetic, gene expression, and non-DNA regulated (epigenetic) signatures with blood OT levels in 290 participants with autism enrolled in an OT clinical trial. We identified genetic association with plasma OT, several of which reside in known autism risk genes. We also show statistically significant association of plasma OT levels with gene expression and epigenetic across several gene pathways. These findings broaden our understanding of the factors that influence OT levels in the blood for future studies to decode the complex presentation of autism and its interaction with OT and OT-based treatment.
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Affiliation(s)
- Stephen K Siecinski
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Marina Spanos
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Annalise C Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tara Chandrasekhar
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - M D Pilar Trelles
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol M Rockhill
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Michelle L Palumbo
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Paige Siper
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mendy Minjarez
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Lisa A Nowinski
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sarah Marler
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Lydia C Kwee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Cheryl Alderman
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jordana Weissman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke Zappone
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Jennifer E Mullett
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hope Crosson
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Natalie Hong
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Sheng Luo
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Lilin She
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Manjushri Bhapkar
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Russell Dean
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abby Scheer
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jacqueline L Johnson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryan H King
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Christopher J McDougle
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin B Sanders
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Soo-Jeong Kim
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Alexander Kolevzon
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Linmarie Sikich
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
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19
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Carlsen LN, Hansen CS, Kogelman LJA, Werge TM, Ullum H, Bybjerg-Grauholm J, Hansen TF, Jensen RH. DNA-methylation and immunological response in medication overuse headache. Cephalalgia 2023; 43:3331024221147482. [PMID: 36786322 DOI: 10.1177/03331024221147482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
OBJECTIVE To investigate whether medication-overuse headache patients have differential DNA-methylation pattern. METHODS We collected blood samples from 120 medication-overuse headache-patients, 57 controls (29 episodic migraine patients and 28 healthy controls) in a hypothesis-generating cross-sectional case-control pilot study; 100 of the medication-overuse headache-patients were followed for six months and samples were collected at two and six months for the longitudinal methylation analyses. Blood cell proportions of leucocytes (neutrophils, NK-cells, monocytes, CD8+ and CD4+ T-cells, and B-cells) and the neutrophile-lymphocyte ratio were estimated using methylation data as a measure for immunological analysis and a cell type-specific epigenome wide association study was conducted between medication-overuse headache-patients and controls, and longitudinally for reduction in headache days/month among medication-overuse headache-patients. RESULTS We found a higher neutrophile-lymphocyte ratio in medication-overuse headache-patients compared to controls, indicating a higher immunological response in medication-overuse headache-patients (false discovery rate (adjusted p-value)<0.001). Reduction in headache days/month (9.8; 95% CI 8.1-11.5) was associated with lower neutrophile-lymphocyte ratio (false discovery rate adjusted p-value = 0.041).Three genes (CORIN, CCKBR and CLDN9) were hypermethylated in specific cell types in medication-overuse headache-patients compared to controls. No methylation differences were associated with reduction in headache days in medication-overuse headache-patients after six months. CONCLUSION This pilot study was consistent with higher immunological response in medication-overuse headache-patients which decreased with a reduction in headache days in longitudinal analysis. medication-overuse headache-patients exhibited differential methylation in innate immune cells but did not exhibit longitudinal differences with alterations in headache days. Our study creates hypotheses for further biomarker searches.ClinicalTrials.gov Identifier: NCT02993289.
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Affiliation(s)
| | | | | | - Thomas Mears Werge
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Denmark
| | | | | | - Thomas Folkmann Hansen
- Danish Headache Center, Rigshospitalet, Denmark.,Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Denmark
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20
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Mediating effect of genome-wide DNA methylation on suicidal ideation induced by stressful events. Psychiatr Genet 2023; 33:26-33. [PMID: 36617744 DOI: 10.1097/ypg.0000000000000331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Schizophrenia is a debilitating disease that is associated with higher rates of death by unnatural causes including suicide. Exposure to stressful events is an important risk factor for suicidal ideation (SI); however, the mechanisms that link stress, SI, and suicide remain unclear. Epigenetic processes are involved in both vulnerability to suicidal behavior and stress. Therefore, we sought to study the relationship between epigenetic modifications and suicidal behavior and stress. METHODS This pilot study was conducted on 39 patients diagnosed with schizophrenia (54% men and age 45.5 ± 12.7). We analyzed the effects of (a) stress exposure and (b) the mediation of DNA methylation [via an epigenetic wide association study (EWAS) of more than 450 000 CpG sites across the genome] on SI severity. RESULTS The top CpG site mediating the effect of global stress exposure on SI was cg27660192 located in an intergenic region on chromosome 11, exerting a facilitating effect on worsening SI through DNA hypomethylation. CONCLUSION These preliminary results indicate that DNA methylation in peripheral tissues can shed light on the complex relationship between stress and SI in schizophrenia.
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21
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Gallardo VJ, Vila-Pueyo M, Pozo-Rosich P. The impact of epigenetic mechanisms in migraine: Current knowledge and future directions. Cephalalgia 2023; 43:3331024221145916. [PMID: 36759209 DOI: 10.1177/03331024221145916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
BACKGROUND Epigenetic mechanisms, including DNA methylation, microRNAs and histone modifications, may modulate the genetic expression in migraine and its interaction with internal and external factors, such as lifestyle and environmental changes. OBJECTIVE To summarize, contextualize and critically analyze the published literature on the current state of epigenetic mechanisms in migraine in a narrative review. FINDINGS The studies published to date have used different approaches and methodologies to determine the role of epigenetic mechanisms in migraine. Epigenetic changes seem to be involved in migraine and are increasing our knowledge of the disease. CONCLUSIONS Changes in DNA methylation, microRNA expression and histone modifications could be utilized as biomarkers that would be highly valuable for patient stratification, molecular diagnosis, and precision medicine in migraine.
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Affiliation(s)
- Víctor José Gallardo
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain
| | - Marta Vila-Pueyo
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain
| | - Patricia Pozo-Rosich
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain.,Headache Unit, Neurology Department, Vall d'Hebron University Hospital, Barcelona, Spain
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22
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Lu AKM, Hsieh S, Yang CT, Wang XY, Lin SH. DNA methylation signature of psychological resilience in young adults: Constructing a methylation risk score using a machine learning method. Front Genet 2023; 13:1046700. [PMID: 36712885 PMCID: PMC9877348 DOI: 10.3389/fgene.2022.1046700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Resilience is a process associated with the ability to recover from stress and adversity. We aimed to explore the resilience-associated DNA methylation signatures and evaluate the abilities of methylation risk scores to discriminate low resilience (LR) individuals. The study recruited 78 young adults and used Connor-Davidson Resilience Scale (CD-RISC) to divide them into low and high resilience groups. We randomly allocated all participants of two groups to the discovery and validation sets. We used the blood DNA of the subjects to conduct a genome-wide methylation scan and identify the significant methylation differences of CpG Sites in the discovery set. Moreover, the classification accuracy of the DNA methylation probes was confirmed in the validation set by real-time quantitative methylation-specific polymerase chain reaction. In the genome-wide methylation profiling between LR and HR individuals, seventeen significantly differentially methylated probes were detected. In the validation set, nine DNA methylation signatures within gene coding regions were selected for verification. Finally, three methylation probes [cg18565204 (AARS), cg17682313 (FBXW7), and cg07167608 (LINC01107)] were included in the final model of the methylation risk score for LR versus HR. These methylation risk score models of low resilience demonstrated satisfactory discrimination by logistic regression and support vector machine, with an AUC of 0.81 and 0.93, accuracy of 72.3% and 87.1%, sensitivity of 75%, and 87.5%, and specificity of 70% and 80%. Our findings suggest that methylation signatures can be utilized to identify individuals with LR and establish risk score models that may contribute to the field of psychology.
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Affiliation(s)
- Andrew Ke-Ming Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shulan Hsieh
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Ta Yang
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan,Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
| | - Xin-Yu Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Sheng-Hsiang Lin,
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23
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Sokolov AV, Manu DM, Nordberg DOT, Boström ADE, Jokinen J, Schiöth HB. Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression. Clin Epigenetics 2023; 15:1. [PMID: 36600305 PMCID: PMC9811786 DOI: 10.1186/s13148-022-01394-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Depression is a multifactorial disorder representing a significant public health burden. Previous studies have linked multiple single nucleotide polymorphisms with depressive phenotypes and suicidal behavior. MAD1L1 is a mitosis metaphase checkpoint protein that has been linked to depression in GWAS. Using a longitudinal EWAS approach in an adolescent cohort at two time points (n = 216 and n = 154), we identified differentially methylated sites that were associated with depression-related genetic variants in MAD1L1. Three methylation loci (cg02825527, cg18302629, and cg19624444) were consistently hypomethylated in the minor allele carriers, being cross-dependent on several SNPs. We further investigated whether DNA methylation at these CpGs is associated with depressive psychiatric phenotypes in independent cohorts. The first site (cg02825527) was hypomethylated in blood (exp(β) = 84.521, p value ~ 0.003) in participants with severe suicide attempts (n = 88). The same locus showed increased methylation in glial cells (exp(β) = 0.041, p value ~ 0.004) in the validation cohort, involving 29 depressed patients and 29 controls, and showed a trend for association with suicide (n = 40, p value ~ 0.089) and trend for association with depression treatment (n = 377, p value ~ 0.075). The second CpG (cg18302629) was significantly hypomethylated in depressed participants (exp(β) = 56.374, p value ~ 0.023) in glial cells, but did not show associations in the discovery cohorts. The last methylation site (cg19624444) was hypomethylated in the whole blood of severe suicide attempters; however, this association was at the borderline for statistical significance (p value ~ 0.061). This locus, however, showed a strong association with depression treatment in the validation cohort (exp(β) = 2.237, p value ~ 0.003) with 377 participants. The direction of associations between psychiatric phenotypes appeared to be different in the whole blood in comparison with brain samples for cg02825527 and cg19624444. The association analysis between methylation at cg18302629 and cg19624444 and MAD1L1 transcript levels in CD14+ cells shows a potential link between methylation at these CpGs and MAD1L1 expression. This study suggests evidence that methylation at MAD1L1 is important for psychiatric health as supported by several independent cohorts.
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Affiliation(s)
- Aleksandr V. Sokolov
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Diana-Maria Manu
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Didi O. T. Nordberg
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Adrian D. E. Boström
- grid.12650.300000 0001 1034 3451Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden ,grid.4714.60000 0004 1937 0626Department of Women’s and Children’s Health/Neuropediatrics, Karolinska Institutet, Stockholm, Sweden
| | - Jussi Jokinen
- grid.12650.300000 0001 1034 3451Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden ,grid.4714.60000 0004 1937 0626Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Helgi B. Schiöth
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
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24
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Du H, Ma J, Zhou W, Li M, Huai C, Shen L, Wu H, Zhao X, Zhang N, Gao S, Wang Q, He L, Wu X, Qin S, Zhao M. Methylome-wide association study of different responses to risperidone in schizophrenia. Front Pharmacol 2022; 13:1078464. [PMID: 36618913 PMCID: PMC9815458 DOI: 10.3389/fphar.2022.1078464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Accumulating evidence shows that DNA methylation plays a role in antipsychotic response. However, the mechanisms by which DNA methylation changes are associated with antipsychotic responses remain largely unknown. Methods: We performed a methylome-wide association study (MWAS) to evaluate the association between DNA methylation and the response to risperidone in schizophrenia. Genomic DNA methylation patterns were assessed using the Agilent Human DNA Methylation Microarray. Results: We identified numerous differentially methylated positions (DMPs) and regions (DMRs) associated with antipsychotic response. CYP46A1, SPATS2, and ATP6V1E1 had the most significant DMPs, with p values of 2.50 × 10-6, 3.53 × 10-6, and 5.71 × 10-6, respectively. The top-ranked DMR was located on chromosome 7, corresponding to the PTPRN2 gene with a Šidák-corrected p-value of 9.04 × 10-13. Additionally, a significant enrichment of synaptic function and neurotransmitters was found in the differentially methylated genes after gene ontology and pathway analysis. Conclusion: The identified DMP- and DMR-overlapping genes associated with antipsychotic response are related to synaptic function and neurotransmitters. These findings may improve understanding of the mechanisms underlying antipsychotic response and guide the choice of antipsychotic in schizophrenia.
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Affiliation(s)
- Huihui Du
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jingsong Ma
- School o f Engineering, Westlake University, Hangzhou, Zhejiang, China,Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xianglong Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Na Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Songyin Gao
- Zhumadian Psychiatric Hospital, Zhumadian, China
| | - Qi Wang
- Hebei Mental Health Center, Hebei Sixth People’s Hospital, Baoding, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xuming Wu
- Nantong Fourth People’s Hospital, Nantong, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
| | - Mingzhe Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China,Affiliated Mental Health Center and Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
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25
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Younesian S, Yousefi AM, Momeny M, Ghaffari SH, Bashash D. The DNA Methylation in Neurological Diseases. Cells 2022; 11:3439. [PMID: 36359835 PMCID: PMC9657829 DOI: 10.3390/cells11213439] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is critical for the normal development and functioning of the human brain, such as the proliferation and differentiation of neural stem cells, synaptic plasticity, neuronal reparation, learning, and memory. Despite the physical stability of DNA and methylated DNA compared to other epigenetic modifications, some DNA methylation-based biomarkers have translated into clinical practice. Increasing reports indicate a strong association between DNA methylation profiles and various clinical outcomes in neurological diseases, making DNA methylation profiles valuable as novel clinical markers. In this review, we aim to discuss the latest evidence concerning DNA methylation alterations in the development of neurodegenerative, neurodevelopmental, and neuropsychiatric diseases. We also highlighted the relationship of DNA methylation alterations with the disease progression and outcome in many neurological diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and autism.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
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26
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Kalyakulina A, Yusipov I, Bacalini MG, Franceschi C, Vedunova M, Ivanchenko M. Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI. Gigascience 2022; 11:giac097. [PMID: 36259657 PMCID: PMC9718659 DOI: 10.1093/gigascience/giac097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND DNA methylation has a significant effect on gene expression and can be associated with various diseases. Meta-analysis of available DNA methylation datasets requires development of a specific workflow for joint data processing. RESULTS We propose a comprehensive approach of combined DNA methylation datasets to classify controls and patients. The solution includes data harmonization, construction of machine learning classification models, dimensionality reduction of models, imputation of missing values, and explanation of model predictions by explainable artificial intelligence (XAI) algorithms. We show that harmonization can improve classification accuracy by up to 20% when preprocessing methods of the training and test datasets are different. The best accuracy results were obtained with tree ensembles, reaching above 95% for Parkinson's disease. Dimensionality reduction can substantially decrease the number of features, without detriment to the classification accuracy. The best imputation methods achieve almost the same classification accuracy for data with missing values as for the original data. XAI approaches have allowed us to explain model predictions from both populational and individual perspectives. CONCLUSIONS We propose a methodologically valid and comprehensive approach to the classification of healthy individuals and patients with various diseases based on whole-blood DNA methylation data using Parkinson's disease and schizophrenia as examples. The proposed algorithm works better for the former pathology, characterized by a complex set of symptoms. It allows to solve data harmonization problems for meta-analysis of many different datasets, impute missing values, and build classification models of small dimensionality.
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Affiliation(s)
- Alena Kalyakulina
- Correspondence author. Alena Kalyakulina, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Gagarin avenue 22, Nizhny Novgorod 603022, Russia. E-mail:
| | | | | | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, 603022 Nizhny Novgorod, Russia
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Kho SH, Yee JY, Puang SJ, Han L, Chiang C, Rapisarda A, Goh WWB, Lee J, Sng JCG. DNA methylation levels of RELN promoter region in ultra-high risk, first episode and chronic schizophrenia cohorts of schizophrenia. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:81. [PMID: 36216926 PMCID: PMC9550813 DOI: 10.1038/s41537-022-00278-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
The essential role of the Reelin gene (RELN) during brain development makes it a prominent candidate in human epigenetic studies of Schizophrenia. Previous literature has reported differing levels of DNA methylation (DNAm) in patients with psychosis. Therefore, this study aimed to (1) examine and compare RELN DNAm levels in subjects at different stages of psychosis cross-sectionally, (2) analyse the effect of antipsychotics (AP) on DNAm, and (3) evaluate the effectiveness and applicability of RELN promoter DNAm as a possible biological-based marker for symptom severity in psychosis.. The study cohort consisted of 56 healthy controls, 87 ultra-high risk (UHR) individuals, 26 first-episode (FE) psychosis individuals and 30 chronic schizophrenia (CS) individuals. The Positive and Negative Syndrome Scale (PANSS) was used to assess Schizophrenia severity. After pyrosequencing selected CpG sites of peripheral blood, the Average mean DNAm levels were compared amongst the 4 subgroups. Our results showed differing levels of DNAm, with UHR having the lowest (7.72 ± 0.19) while the CS had the highest levels (HC: 8.78 ± 0.35; FE: 7.75 ± 0.37; CS: 8.82 ± 0.48). Significantly higher Average mean DNAm levels were found in CS subjects on AP (9.12 ± 0.61) compared to UHR without medication (UHR(-)) (7.39 ± 0.18). A significant association was also observed between the Average mean DNAm of FE and PANSS Negative symptom factor (R2 = 0.237, ß = -0.401, *p = 0.033). In conclusion, our findings suggested different levels of DNAm for subjects at different stages of psychosis. Those subjects that took AP have different DNAm levels. There were significant associations between FE DNAm and Negative PANSS scores. With more future experiments and on larger cohorts, there may be potential use of DNAm of the RELN gene as one of the genes for the biological-based marker for symptom severity in psychosis.
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Affiliation(s)
- Sok-Hong Kho
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Jie Yin Yee
- Research Division, Institute of Mental Health, Singapore, Singapore
| | - Shu Juan Puang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Luke Han
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Christine Chiang
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Attilio Rapisarda
- Research Division, Institute of Mental Health, Singapore, Singapore
- Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Wilson Wen Bin Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jimmy Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Research Division, Institute of Mental Health, Singapore, Singapore
- Department of Psychosis, Institute of Mental Health, Singapore, Singapore
| | - Judy Chia Ghee Sng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Barbu MC, Harris M, Shen X, Aleks S, Green C, Amador C, Walker R, Morris S, Adams M, Sandu A, McNeil C, Waiter G, Evans K, Campbell A, Wardlaw J, Steele D, Murray A, Porteous D, McIntosh A, Whalley H. Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study. Epigenetics 2022; 17:1143-1158. [PMID: 34738878 PMCID: PMC9542280 DOI: 10.1080/15592294.2021.1997404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023] Open
Abstract
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores.We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two assessments, (i) at baseline recruitment, ~6 years prior to MRI assessment (N = 672) and (ii) concurrent with MRI assessment (N=565). Four CpGs at baseline were associated with global cerebral white matter, total grey matter, and whole-brain volume (Bonferroni p≤7.41×10-8, βrange = -1.46x10-6 to 9.59 × 10-7). These CpGs were annotated to genes implicated in brain-related traits, including psychiatric disorders, development, and ageing. We did not find significant associations in the meta-analysis of the EWAS of the two sets concurrent with imaging at the corrected level.These findings reveal global brain structural changes associated with DNAm measured ~6 years previously, indicating a potential role of early DNAm modifications in brain structure. Although concurrent DNAm was not associated with global brain structure, the nominally significant findings identified here present a rationale for future investigation of associations between DNA methylation and structural brain phenotypes in larger population-based samples.
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Affiliation(s)
- Miruna Carmen Barbu
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Mat Harris
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Stolicyn Aleks
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Claire Green
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Carmen Amador
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Rosie Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Stewart Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Mark Adams
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca Sandu
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Christopher McNeil
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Gordon Waiter
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Kathryn Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Archie Campbell
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Douglas Steele
- Imaging Science and Technology, School of Medicine, University of Dundee, DundeeUK
| | - Alison Murray
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - David Porteous
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Andrew McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Heather Whalley
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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Xiao L, Cheng H, Cai H, Wei Y, Zan G, Feng X, Liu C, Li L, Huang L, Wang F, Chen X, Zou Y, Yang X. Associations of Heavy Metals with Activities of Daily Living Disability: An Epigenome-Wide View of DNA Methylation and Mediation Analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:87009. [PMID: 36036794 PMCID: PMC9423034 DOI: 10.1289/ehp10602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 07/07/2022] [Accepted: 08/15/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exposure to heavy metals has been reported to be associated with multiple diseases. However, direct associations and potential mechanisms of heavy metals with physical disability remain unclear. OBJECTIVES We aimed to quantify associations of heavy metals with physical disability and further explore the potential mechanisms of DNA methylation on the genome scale. METHODS A cross-sectional study of 4,391 older adults was conducted and activities of daily living (ADL) disability were identified using a 14-item scale questionnaire including basic and instrumental activities to assess the presence of disability (yes or no) rated on a scale of dependence. Odds ratios (ORs) and 95% confidence intervals (CI) were estimated to quantify associations between heavy metals and ADL disability prevalence using multivariate logistic regression and Bayesian kernel machine regression (BKMR) models. Whole blood-derived DNA methylation was measured using the HumanMethylationEPIC BeadChip array. An ADL disability-related epigenome-wide DNA methylation association study (EWAS) was performed among 212 sex-matched ADL disability cases and controls, and mediation analysis was further applied to explore potential mediators of DNA methylation. RESULTS Each 1-standard deviation (SD) higher difference in log10-transformed manganese, copper, arsenic, and cadmium level was significantly associated with a 14% (95% CI: 1.05, 1.24), 16% (95% CI:1.07, 1.26), 22% (95% CI:1.13, 1.33), and 15% (95% CI:1.06, 1.26) higher odds of ADL disability, which remained significant in the multiple-metal and BKMR models. A total of 85 differential DNA methylation sites were identified to be associated with ADL disability prevalence, among which methylation level at cg220000984 and cg23012519 (annotated to IRGM and PKP3) mediated 31.0% and 31.2% of manganese-associated ADL disability prevalence, cg06723863 (annotated to ESRP2) mediated 32.4% of copper-associated ADL disability prevalence, cg24433124 (nearest to IER3) mediated 15.8% of arsenic-associated ADL disability prevalence, and cg07905190 and cg17485717 (annotated to FREM1 and TCP11L1) mediated 21.5% and 30.5% of cadmium-associated ADL disability prevalence (all p<0.05). DISCUSSION Our findings suggested that heavy metals contributed to higher prevalence of ADL disability and that locus-specific DNA methylation are partial mediators, providing potential biomarkers for further cellular mechanism studies. https://doi.org/10.1289/EHP10602.
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Affiliation(s)
- Lili Xiao
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Hong Cheng
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Haiqing Cai
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yue Wei
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Gaohui Zan
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiuming Feng
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Chaoqun Liu
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Longman Li
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Lulu Huang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Fei Wang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xing Chen
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yunfeng Zou
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaobo Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
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31
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Elevated BICD2 DNA methylation in blood of major depressive disorder patients and reduction of depressive-like behaviors in hippocampal Bicd2-knockdown mice. Proc Natl Acad Sci U S A 2022; 119:e2201967119. [PMID: 35858435 PMCID: PMC9335189 DOI: 10.1073/pnas.2201967119] [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] [Indexed: 11/18/2022] Open
Abstract
Major depressive disorder (MDD) is a prevalent and devastating mental illness. To date, the diagnosis of MDD is largely dependent on clinical interviews and questionnaires and still lacks a reliable biomarker. DNA methylation has a stable and reversible nature and is likely associated with the course and therapeutic efficacy of complex diseases, which may play an important role in the etiology of a disease. Here, we identified and validated a DNA methylation biomarker for MDD from four independent cohorts of the Chinese Han population. First, we integrated the analysis of the DNA methylation microarray (n = 80) and RNA expression microarray data (n = 40) and identified BICD2 as the top-ranked gene. In the replication phase, we employed the Sequenom MassARRAY method to confirm the DNA hypermethylation change in a large sample size (n = 1,346) and used the methylation-sensitive restriction enzymes and a quantitative PCR approach (MSE-qPCR) and qPCR method to confirm the correlation between DNA hypermethylation and mRNA down-regulation of BICD2 (n = 60). The results were replicated in the peripheral blood of mice with depressive-like behaviors, while in the hippocampus of mice, Bicd2 showed DNA hypomethylation and mRNA/protein up-regulation. Hippocampal Bicd2 knockdown demonstrates antidepressant action in the chronic unpredictable mild stress (CUMS) mouse model of depression, which may be mediated by increased BDNF expression. Our study identified a potential DNA methylation biomarker and investigated its functional implications, which could be exploited to improve the diagnosis and treatment of MDD.
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32
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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33
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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23: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.
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Effect of Prenatal Opioid Exposure on the Human Placental Methylome. Biomedicines 2022; 10:biomedicines10051150. [PMID: 35625888 PMCID: PMC9138340 DOI: 10.3390/biomedicines10051150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Prenatal exposure to addictive drugs can lead to placental epigenetic modifications, but a methylome-wide evaluation of placental DNA methylation changes after prenatal opioid exposure has not yet been performed. Placental tissue samples were collected at delivery from 19 opioid-exposed and 20 unexposed control full-term pregnancies. Placental DNA methylomes were profiled using the Illumina Infinium HumanMethylationEPIC BeadChip. Differentially methylated CpG sites associated with opioid exposure were identified with a linear model using the ‘limma’ R package. To identify differentially methylated regions (DMRs) spanning multiple CpG sites, the ‘DMRcate’ R package was used. The functions of genes mapped by differentially methylated CpG sites and DMRs were further annotated using Enrichr. Differentially methylated CpGs (n = 684, unadjusted p < 0.005 and |∆β| ≥ 0.05) were mapped to 258 genes (including PLD1, MGAM, and ALCS2). Differentially methylated regions (n = 199) were located in 174 genes (including KCNMA1). Enrichment analysis of the top differentially methylated CpG sites and regions indicated disrupted epigenetic regulation of genes involved in synaptic structure, chemical synaptic transmission, and nervous system development. Our findings imply that placental epigenetic changes due to prenatal opioid exposure could result in placental dysfunction, leading to abnormal fetal brain development and the symptoms of opioid withdrawal in neonates.
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35
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Caramaschi D, Neumann A, Cardenas A, Tindula G, Alemany S, Zillich L, Pesce G, Lahti JMT, Havdahl A, Mulder R, Felix JF, Tiemeier H, Sirignano L, Frank J, Witt SH, Rietschel M, Deuschle M, Huen K, Eskenazi B, Send TS, Ferrer M, Gilles M, de Agostini M, Baïz N, Rifas-Shiman SL, Kvist T, Czamara D, Tuominen ST, Relton CL, Rai D, London SJ, Räikkönen K, Holland N, Annesi-Maesano I, Streit F, Hivert MF, Oken E, Sunyer J, Cecil CAM, Sharp G. Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills. Mol Psychiatry 2022; 27:2126-2135. [PMID: 35145228 PMCID: PMC9126809 DOI: 10.1038/s41380-022-01441-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Cognitive skills are a strong predictor of a wide range of later life outcomes. Genetic and epigenetic associations across the genome explain some of the variation in general cognitive abilities in the general population and it is plausible that epigenetic associations might arise from prenatal environmental exposures and/or genetic variation early in life. We investigated the association between cord blood DNA methylation at birth and cognitive skills assessed in children from eight pregnancy cohorts within the Pregnancy And Childhood Epigenetics (PACE) Consortium across overall (total N = 2196), verbal (total N = 2206) and non-verbal cognitive scores (total N = 3300). The associations at single CpG sites were weak for all of the cognitive domains investigated. One region near DUSP22 on chromosome 6 was associated with non-verbal cognition in a model adjusted for maternal IQ. We conclude that there is little evidence to support the idea that variation in cord blood DNA methylation at single CpG sites is associated with cognitive skills and further studies are needed to confirm the association at DUSP22.
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Affiliation(s)
- Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK.
- Department of Psychology, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Silvia Alemany
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Giancarlo Pesce
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Jari M T Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alexandra Havdahl
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
- Department of Mental Disorders, Norwegian Institute of Public Health and Nic Waals Institute of Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Rosa Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Michael Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA
| | - Tabea Sarah Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Muriel Ferrer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Maria Gilles
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maria de Agostini
- Inserm, Centre for Research in Epidemiology and StatisticS (CRESS), Research Team on Early Life Origins of Health (EAROH), Villejuif, France
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Samuli T Tuominen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | - Dheeraj Rai
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
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Kim B, Sasaki A, Murphy K, Matthews SG. DNA methylation signatures in human neonatal blood following maternal antenatal corticosteroid treatment. Transl Psychiatry 2022; 12:132. [PMID: 35354798 PMCID: PMC8967826 DOI: 10.1038/s41398-022-01902-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
Antenatal corticosteroids (ACS) are used to treat women at risk of preterm birth to improve neonatal survival. Though affected children may be at long-term risk of neurobehavioural disorders, the driving mechanisms remain unknown. Animal studies have shown that ACS exposure can lead to overlapping changes in DNA methylation between the blood and the brain, identifying gene pathways for neurodevelopment, which highlights the potential to examine peripheral blood as a surrogate for inaccessible human brain tissue. We hypothesized that differential methylation will be identified in blood of term-born neonates following ACS. Mother-infant dyads that received ACS were retrospectively identified through the Ontario Birth Study at Sinai Health Complex and matched to untreated controls for maternal age, BMI, parity and foetal sex (n = 14/group). Genome-wide methylation differences were examined at single-nucleotide resolution in DNA extracted from dried bloodspot cards using reduced representative bisulfite sequencing approaches. 505 differentially methylated CpG sites (DMCs) were identified, wherein 231 were hypermethylated and 274 were hypomethylated. These sites were annotated to 219 genes, of which USP48, SH3PXD2A, NTM, CAMK2N2, MAP6D1 were five of the top ten genes with known neurological function. Collectively, the set of hypermethylated genes were enriched for pathways of transcription regulation, while pathways of proteasome activity were enriched among the set of hypomethylated genes. This study is the first to identify DNA methylation changes in human neonatal blood following ACS. Understanding the epigenetic changes that occur in response to ACS will support future investigations to delineate the effects of prenatal glucocorticoid exposure on human development.
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Affiliation(s)
- Bona Kim
- Department of Physiology, University of Toronto, Toronto, ON, Canada. .,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
| | - Aya Sasaki
- grid.17063.330000 0001 2157 2938Department of Physiology, University of Toronto, Toronto, ON Canada ,grid.250674.20000 0004 0626 6184Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada
| | - Kellie Murphy
- grid.17063.330000 0001 2157 2938Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada
| | - Stephen G. Matthews
- grid.17063.330000 0001 2157 2938Department of Physiology, University of Toronto, Toronto, ON Canada ,grid.250674.20000 0004 0626 6184Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada
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Ngwa JS, Nwulia E, Ntekim O, Bedada FB, Kwabi-Addo B, Nadarajah S, Johnson S, Southerland WM, Kwagyan J, Obisesan TO. Aerobic Exercise Training-Induced Changes on DNA Methylation in Mild Cognitively Impaired Elderly African Americans: Gene, Exercise, and Memory Study - GEMS-I. Front Mol Neurosci 2022; 14:752403. [PMID: 35110995 PMCID: PMC8802631 DOI: 10.3389/fnmol.2021.752403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND DNA methylation at CpG sites is a vital epigenetic modification of the human genome affecting gene expression, and potentially, health outcomes. However, evidence is just budding on the effects of aerobic exercise-induced adaptation on DNA methylation in older mild cognitively impaired (MCI) elderly African American (AAs). Therefore, we examined the effects of a 6-month aerobic exercise-intervention on genome-wide DNA methylation in elderly AA MCI volunteers. DESIGN Elderly AA volunteers confirmed MCI assigned into a 6-month program of aerobic exercise (eleven participants) underwent a 40-min supervised-training 3-times/week and controls (eight participants) performed stretch training. Participants had maximal oxygen consumption (VO2max) test and Genome-wide methylation levels at CpG sites using the Infinium HumanMethylation450 BeadChip assay at baseline and after a 6-month exercise program. We computed false discovery rates (FDR) using Sidak to account for multiplicity of tests and performed quantitative real-time polymerase chain-reaction (qRT-PCR) to confirm the effects of DNA methylations on expression levels of the top 5 genes among the aerobic participants. CpG sites identified from aerobic-exercise participants were similarly analyzed by the stretch group to quantify the effects of exercise-induced methylation changes among the group of stretch participants. RESULTS Eleven MCI participants (aerobic: 73% females; mean age 72.3 ± 6.6 years) and eight MCI participants (stretch: 75% female; mean age 70.6 ± 6.7 years) completed the training. Aerobic exercise-training was associated with increases in VO2max and with global hypo- and hypermethylation changes. The most notable finding was CpG hypomethylation within the body of the VPS52 gene (P = 5.4 × 10-26), a Golgi-associated protein, involved in intracellular protein trafficking including amyloid precursor protein. qRT-PCR confirmed a nearly twofold increased expression of VPS52. Other top findings with FDR q-value < 10-5, include hypomethylations of SCARB1 (8.8 × 10-25), ARTN (6.1 × 10-25), NR1H2 (2.1 × 10-18) and PPP2R5D (9.8 × 10-18). CONCLUSION We conclude that genome-wide DNA methylation patterns is associated with exercise training-induced methylation changes. Identification of methylation changes around genes previously shown to interact with amyloid biology, intracellular protein trafficking, and lipoprotein regulations provide further support to the likely protective effect of exercise in MCI. Future studies in larger samples are needed to confirm our findings.
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Affiliation(s)
- Julius S. Ngwa
- Division of Cardiovascular Medicine, Department of Internal Medicine, Howard University, Washington, DC, United States
| | - Evaristus Nwulia
- Department of Psychiatry and Behavioral Sciences, Howard University, Washington, DC, United States
| | - Oyonumo Ntekim
- Department of Nutritional Sciences, Howard University, Washington, DC, United States
| | - Fikru B. Bedada
- Department of Clinical Laboratory Sciences, Howard University, Washington, DC, United States
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University, Washington, DC, United States
| | - Sheeba Nadarajah
- Division of Nursing, Howard University, Washington, DC, United States,School of Nursing and Allied Health Sciences, Howard University, Washington, DC, United States,Department of Medicine, Howard University, Washington, DC, United States
| | - Steven Johnson
- Division of Geriatrics, Department of Medicine and Clinical/Translational Science Program, Howard University Hospital, Washington, DC, United States
| | - William M. Southerland
- Department of Biochemistry and Molecular Biology, Howard University, Washington, DC, United States
| | - John Kwagyan
- Georgetown-Howard U Center for Clinical and Translation Science (GHUCCTS), Howard University Hospital, Washington, DC, United States
| | - Thomas O. Obisesan
- Division of Geriatrics, Department of Medicine and Clinical/Translational Science Program, Howard University Hospital, Washington, DC, United States,*Correspondence: Thomas O. Obisesan,
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Coto-Vílchez C, Martínez-Magaña JJ, Mora-Villalobos L, Valerio D, Genis-Mendoza AD, Silverman JM, Nicolini H, Raventós H, Chavarria-Soley G. Genome-wide DNA methylation profiling in nonagenarians suggests an effect of PM20D1 in late onset Alzheimer's disease. CNS Spectr 2021; 28:1-27. [PMID: 34911598 DOI: 10.1017/s109285292100105x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractBackgroundThe aim of this study is to identify differentially methylated regions (DMRs) in the genomes of a sample of cognitively healthy individuals and a sample of individuals with LOAD, all of them nonagenarians from Costa Rica.MethodsIn this study, we compared whole blood DNA methylation profiles of 32 individuals: 21 cognitively healthy and 11 with LOAD, using the Infinium MethylationEPIC BeadChip. First, we calculated the epigenetic age of the participants based on Horvath’s epigenetic clock. DMRcate and Bumphunter were used to identify DMRs. After in silico and knowledge-based filtering of the DMRs, we performed a methylation quantitative loci (mQTL) analysis (rs708727 and rs960603).ResultsOn average, the epigenetic age was 73 years in both groups, which represents a difference of over 20 years between epigenetic and chronological age in both affected and unaffected individuals. Methylation analysis revealed 11 DMRs between groups, which contain six genes and two pseudogenes. These genes are involved in cell cycle regulation, embryogenesis, synthesis of ceramides, and migration of interneurons to the cerebral cortex. One of the six genes is PM20D1, for which altered expression has been reported in LOAD. After genotyping previously reported mQTL SNPs for the gene, we found that average methylation in the PM20D1 DMR differs between genotypes for rs708727, but not for rs960603.ConclusionsThis work supports the possible role of PM20D1 in protection against AD, by showing differential methylation in blood of affected and unaffected nonagenarians. Our results also support the influence of genetic factors on PM20D1 methylation levels.
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Cerutti J, Lussier AA, Zhu Y, Liu J, Dunn EC. Associations between indicators of socioeconomic position and DNA methylation: a scoping review. Clin Epigenetics 2021; 13:221. [PMID: 34906220 PMCID: PMC8672601 DOI: 10.1186/s13148-021-01189-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Socioeconomic position (SEP) is a major determinant of health across the life course. Yet, little is known about the biological mechanisms explaining this relationship. One possibility widely pursued in the scientific literature is that SEP becomes biologically embedded through epigenetic processes such as DNA methylation (DNAm), wherein the socioeconomic environment causes no alteration in the DNA sequence but modifies gene activity in ways that shape health. METHODS To understand the evidence supporting a potential SEP-DNAm link, we performed a scoping review of published empirical findings on the association between SEP assessed from prenatal development to adulthood and DNAm measured across the life course, with an emphasis on exploring how the developmental timing, duration, and type of SEP exposure influenced DNAm. RESULTS Across the 37 identified studies, we found that: (1) SEP-related DNAm signatures varied across the timing, duration, and type of SEP indicator; (2) however, longitudinal studies examining repeated SEP and DNAm measures are generally lacking; and (3) prior studies are conceptually and methodologically diverse, limiting the interpretability of findings across studies with respect to these three SEP features. CONCLUSIONS Given the complex relationship between SEP and DNAm across the lifespan, these findings underscore the importance of analyzing SEP features, including timing, duration, and type. To guide future research, we highlight additional research gaps and propose four recommendations to further unravel the relationship between SEP and DNAm.
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Affiliation(s)
- Janine Cerutti
- Department of Pscyhology, University of Vermont, 2 Colchester Ave, Burlington, VT, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
| | - Alexandre A Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiwen Zhu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiaxuan Liu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Erin C Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Dada O, Qian J, Al-Chalabi N, Kolla NJ, Graff A, Zai C, Gerretsen P, De Luca V. Epigenetic studies in suicidal ideation and behavior. Psychiatr Genet 2021; 31:205-215. [PMID: 34694247 DOI: 10.1097/ypg.0000000000000298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Most psychiatric disorders are associated with an elevated risk of suicide. Suicidal behavior is the product of the interaction of many risk factors, such as genetics and environmental factors. Hence, epigenetics research may help to understand the mechanisms leading to suicidal ideation and behavior. This review will discuss epigenetic studies in both suicidal ideation and behavior. Epigenetic modifications are likely to be important in both suicidal ideation and behavior. Most of the reviewed studies found significant epigenetic modifications linked with suicidal behavior rather than ideation. Although sizable research has been carried out on this topic, most studies have been done on small-scale samples, and future research is required in larger samples with better clinical characterization of suicide phenotypes to investigate these epigenetic modifications further.
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Martins J, Czamara D, Sauer S, Rex-Haffner M, Dittrich K, Dörr P, de Punder K, Overfeld J, Knop A, Dammering F, Entringer S, Winter SM, Buss C, Heim C, Binder EB. Childhood adversity correlates with stable changes in DNA methylation trajectories in children and converges with epigenetic signatures of prenatal stress. Neurobiol Stress 2021; 15:100336. [PMID: 34095363 PMCID: PMC8163992 DOI: 10.1016/j.ynstr.2021.100336] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022] Open
Abstract
Childhood maltreatment (CM) is an established major risk factor for a number of negative health outcomes later in life. While epigenetic mechanisms, such as DNA methylation (DNAm), have been proposed as a means of embedding this environmental risk factor, little is known about its timing and trajectory, especially in very young children. It is also not clear whether additional environmental adversities, often experienced by these children, converge on similar DNAm changes. Here, we calculated a cumulative adversity score, which additionally to CM includes socioeconomic status (SES), other life events, parental psychopathology and epigenetic biomarkers of prenatal smoking and alcohol consumption. We investigated the effects of CM alone as well as the adversity score on longitudinal DNAm trajectories in the Berlin Longitudinal Child Study. This is a cohort of 173 children aged 3-5 years at baseline of whom 86 were exposed to CM. These children were followed-up for 2 years with extensive psychometric and biological assessments as well as saliva collection at 5 time points providing genome-wide DNAm levels. Overall, only a few DNAm patterns were stable over this timeframe, but less than 10 DNAm regions showed significant changes. At baseline, neither CM nor the adversity score associated with DNAm changes. However, in 6 differentially methylated regions (DMRs), CM and the adversity score significantly moderated DNAm trajectories over time. A number of these DMRs have previously been associated with adverse prenatal exposures. In our study, children exposed to CM also presented with epigenetic signatures indicative of increased prenatal exposure to tobacco and alcohol, as compared to non-CM exposed children. These epigenetic signatures of prenatal exposure strongly correlate with DNAm regions associated with CM and the adversity score. Finally, weighted correlation network analysis revealed a module of CpGs exclusively associated with CM. While our study identifies DNAm loci specifically associated with CM, especially within long non-coding RNAs, the majority of associations were found with the adversity score with convergent association with indicators of adverse prenatal exposures. This study highlights the importance of mapping not only of the epigenome but also the exposome and extending the observational timeframe to well before birth.
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Affiliation(s)
- Jade Martins
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Susann Sauer
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Katja Dittrich
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Peggy Dörr
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Karin de Punder
- Natura Foundation, Research and Development, Numansdrop, 3281, NC, Netherlands
| | - Judith Overfeld
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Andrea Knop
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Felix Dammering
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Sonja Entringer
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Sibylle M. Winter
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Claudia Buss
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Christine Heim
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- Dept. of Biobehavioral Health, College of Health & Human Development, The Pennsylvania State University, University Park, PA, USA
| | - Elisabeth B. Binder
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30329, USA
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Longley MJ, Lee J, Jung J, Lohoff FW. Epigenetics of alcohol use disorder-A review of recent advances in DNA methylation profiling. Addict Biol 2021; 26:e13006. [PMID: 33538087 PMCID: PMC8596445 DOI: 10.1111/adb.13006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) is a major contributor to morbidity and mortality worldwide. Although there is a heritable component, the etiology of AUD is complex and can involve environmental exposures like trauma and can be associated with many different patterns of alcohol consumption. Epigenetic modifications, which can mediate the influence of genetic variants and environmental variables on gene expression, have emerged as an important area of AUD research. Over the past decade, the number of studies investigating AUD and DNA methylation, a form of epigenetic modification, has grown rapidly. Yet we are still far from understanding how DNA methylation contributes to or reflects aspects of AUD. In this paper, we reviewed studies of DNA methylation and AUD and discussed how the field has evolved. We found that global DNA and candidate DNA methylation studies did not produce replicable results. To assess whether findings of epigenome-wide association studies (EWAS) were replicated, we aggregated significant findings across studies and identified 184 genes and 15 gene ontological pathways that were differentially methylated in at least two studies and four genes and three gene ontological pathways that were differentially methylated in three studies. These genes and pathways repeatedly found enrichment of immune processes, which is in line with recent developments suggesting that the immune system may be altered in AUD. Finally, we assess the current limitations of studies of DNA methylation and AUD and make recommendations on how to design future studies to resolve outstanding questions.
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Affiliation(s)
- Martha J. Longley
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
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Danoff JS, Connelly JJ, Morris JP, Perkeybile AM. An epigenetic rheostat of experience: DNA methylation of OXTR as a mechanism of early life allostasis. COMPREHENSIVE PSYCHONEUROENDOCRINOLOGY 2021; 8:100098. [PMID: 35757665 PMCID: PMC9216658 DOI: 10.1016/j.cpnec.2021.100098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023] Open
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Smyth LJ, Cruise SM, Tang J, Young I, McGuinness B, Kee F, McKnight AJ. An investigation into DNA methylation patterns associated with risk preference in older individuals. Epigenetics 2021; 17:1159-1172. [PMID: 34696705 PMCID: PMC9542846 DOI: 10.1080/15592294.2021.1992910] [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] [Indexed: 11/17/2022] Open
Abstract
Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile. Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs. Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10−5) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p<9x10−8) following covariate adjustment. Protein-coding genes NWD1 and LRP1 were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions. Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.
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Affiliation(s)
- Laura J Smyth
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Sharon M Cruise
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Jianjun Tang
- School of Agricultural Economics and Rural Development, Renmin University of China, Beijing, China
| | - Ian Young
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Bernadette McGuinness
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Frank Kee
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University Belfast, Northern Ireland, UK
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Magwai T, Shangase KB, Oginga FO, Chiliza B, Mpofana T, Xulu KR. DNA Methylation and Schizophrenia: Current Literature and Future Perspective. Cells 2021; 10:2890. [PMID: 34831111 PMCID: PMC8616184 DOI: 10.3390/cells10112890] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Schizophrenia is a neuropsychiatric disorder characterized by dissociation of thoughts, idea, identity, and emotions. It has no central pathophysiological mechanism and precise diagnostic markers. Despite its high heritability, there are also environmental factors implicated in the development of schizophrenia. Epigenetic factors are thought to mediate the effects of environmental factors in the development of the disorder. Epigenetic modifications like DNA methylation are a risk factor for schizophrenia. Targeted gene approach studies attempted to find candidate gene methylation, but the results are contradictory. Genome-wide methylation studies are insufficient in literature and the available data do not cover different populations like the African populations. The current genome-wide studies have limitations related to the sample and methods used. Studies are required to control for these limitations. Integration of DNA methylation, gene expression, and their effects are important in the understanding of the development of schizophrenia and search for biomarkers. There are currently no precise and functional biomarkers for the disorder. Several epigenetic markers have been reported to be common in functional and peripheral tissue. This makes the peripheral tissue epigenetic changes a surrogate of functional tissue, suggesting common epigenetic alteration can be used as biomarkers of schizophrenia in peripheral tissue.
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Affiliation(s)
- Thabo Magwai
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
- National Health Laboratory Service, Department of Chemical Pathology, University of Kwa-Zulu Natal, Durban 4085, South Africa
| | - Khanyiso Bright Shangase
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Fredrick Otieno Oginga
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Bonginkosi Chiliza
- Department of Psychiatry, Nelson R Mandela School of Medicine, University of Kwa-Zulu Natal, Durban 4001, South Africa;
| | - Thabisile Mpofana
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Khethelo Richman Xulu
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
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Prenatal Particulate Matter Exposure Is Associated with Saliva DNA Methylation at Age 15: Applying Cumulative DNA Methylation Scores as an Exposure Biomarker. TOXICS 2021; 9:toxics9100262. [PMID: 34678958 PMCID: PMC8538839 DOI: 10.3390/toxics9100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022]
Abstract
Exposure in utero to particulate matter (PM2.5 and PM10) is associated with maladaptive health outcomes. Although exposure to prenatal PM2.5 and PM10 has cord blood DNA methylation signatures at birth, signature persistence into childhood and saliva cross-tissue applicability has not been tested. In the Fragile Families and Child Wellbeing Study, a United States 20-city birth cohort, average residential PM2.5 and PM10 during the three months prior to birth was estimated using air quality monitors with inverse distance weighting. Saliva DNA methylation at ages 9 (n = 749) and 15 (n = 793) was measured using the Illumina HumanMethylation 450 k BeadArray. Cumulative DNA methylation scores for particulate matter were estimated by weighting participant DNA methylation at each site by independent meta-analysis effect estimates and standardizing the sums. Using a mixed-effects regression analysis, we tested the associations between cumulative DNA methylation scores at ages 9 and 15 and PM exposure during pregnancy, adjusted for child sex, age, race/ethnicity, maternal income-to-needs ratio, nonmartial birth status, and saliva cell-type proportions. Our study sample was 50.5% male, 56.3% non-Hispanic Black, and 19.8% Hispanic, with a median income-to-needs ratio of 1.4. Mean exposure levels for PM2.5 were 27.9 μg/m3/day (standard deviation: 7.0; 23.7% of observations exceeded safety standards) and for PM10 were 15.0 μg/m3/day (standard deviation: 3.1). An interquartile range increase in PM2.5 exposure (10.73 μg/m3/day) was associated with a −0.0287 standard deviation lower cumulative DNA methylation score for PM2.5 (95% CI: −0.0732, 0.0158, p = 0.20) across all participants. An interquartile range increase in PM10 exposure (3.20 μg/m3/day) was associated with a −0.1472 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.3038, 0.0095, p = 0.06) across all participants. The PM10 findings were driven by the age 15 subset where an interquartile range increase in PM10 exposure was associated with a −0.024 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.043, −0.005, p = 0.012). Findings were robust to adjustment for PM exposure at ages 1 and 3. In utero PM10-associated DNA methylation differences were identified at age 15 in saliva. Benchmarking the timing and cell-type generalizability is critical for epigenetic exposure biomarker assessment.
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Wong LM, Phoon LQ, Wei LK. Epigenetics Modifications in Large-Artery Atherosclerosis: A Systematic Review. J Stroke Cerebrovasc Dis 2021; 30:106033. [PMID: 34598837 DOI: 10.1016/j.jstrokecerebrovasdis.2021.106033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/15/2021] [Accepted: 08/01/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES In recent years, the evidence of the relationship between epigenetics and acute ischemic stroke (AIS) were accumulating, however, the epigenetic characteristics that directs specifically towards the aetiology of large-artery atherosclerosis (LAA) remain ambiguous. The aim of this study was to highlight the overall evidence concerning the epigenetic mechanisms associated with the occurrence of LAA. MATERIALS AND METHODS Studies that involve investigations related to epigenetic markers (DNA methylation and RNA modifications) and LAA were retrieved from eleven scientific publication databases. The studies were screened through the pre-set inclusion and exclusion criteria prior to the NOS evaluation. RESULTS Eligible studies (n=25) were evaluated. Of which, six reported on DNA methylation and 19 studies assessed RNA modifications (16 on miRNAs, two on lncRNAs, and one study on circRNA). Hypomethylation of MTRNR2L8 and ERα promoters; microRNAs (miR-7-2-3p, miR-16, miR-34a-5p, miR-126, miR-143, miR-200b, miR-223, miR-503, miR-1908, miR-146a rs2910164 C/G, miR-149 rs2292832 T/C, miR-200b rs7549819 T/C, miR-34a rs2666433); lncRNA of ZFAS1; and circRNA of hsa_circRNA_102488 were associated with LAA significantly. CONCLUSION Current systematic review highlighted hypomethylation of miRNAs and lncRNA might be the potential biomarkers for LAA.
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Affiliation(s)
- Li Min Wong
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Bandar Barat, Kampar, Perak 31900, Malaysia
| | - Lee Quen Phoon
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Bandar Barat, Kampar, Perak 31900, Malaysia
| | - Loo Keat Wei
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Bandar Barat, Kampar, Perak 31900, Malaysia.
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Liu Z, Chen W, Zhang Z, Wang J, Yang YK, Hai L, Wei Y, Qiao J, Sun Y. Whole-Genome Methylation Analysis Revealed ART-Specific DNA Methylation Pattern of Neuro- and Immune-System Pathways in Chinese Human Neonates. Front Genet 2021; 12:696840. [PMID: 34589113 PMCID: PMC8473827 DOI: 10.3389/fgene.2021.696840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022] Open
Abstract
The DNA methylation of human offspring can change due to the use of assisted reproductive technology (ART). In order to find the differentially methylated regions (DMRs) in ART newborns, cord blood maternal cell contamination and parent DNA methylation background, which will add noise to the real difference, must be removed. We analyzed newborns’ heel blood from six families to identify the DMRs between ART and natural pregnancy newborns, and the genetic model of methylation was explored, meanwhile we analyzed 32 samples of umbilical cord blood of infants born with ART and those of normal pregnancy to confirm which differences are consistent with cord blood data. The DNA methylation level was lower in ART-assisted offspring at the whole genome-wide level. Differentially methylated sites, DMRs, and cord blood differentially expressed genes were enriched in the important pathways of the immune system and nervous system, the genetic patterns of DNA methylation could be changed in the ART group. A total of three imprinted genes and 28 housekeeping genes which were involved in the nervous and immune systems were significant different between the two groups, six of them were detected both in heel blood and cord blood. We concluded that there is an ART-specific DNA methylation pattern involved in neuro- and immune-system pathways of human ART neonates, providing an epigenetic basis for the potential long-term health risks in ART-conceived neonates.
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Affiliation(s)
- Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences and Peking Union Medical College, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Wei Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zilong Zhang
- University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China.,Tianjin Novogene Bioinformatic Technology Co., Ltd.,, Tianjin, China
| | - Junyun Wang
- University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Yi-Kun Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yuan Wei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academic of Medical Sciences and Peking Union Medical College, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
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Ramos-Rosales DF, Vazquez-Alaniz F, Urtiz-Estrada N, Ramirez-Valles EG, Mendez-Hernádez EM, Salas-Leal AC, Barraza-Salas M. Epigenetic marks in suicide: a review. Psychiatr Genet 2021; 31:145-161. [PMID: 34412082 DOI: 10.1097/ypg.0000000000000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Suicide is a complex phenomenon and a global public health problem that involves several biological factors that could contribute to the pathophysiology of suicide. There is evidence that epigenetic factors influence some psychiatric disorders, suggesting a predisposition to suicide or suicidal behavior. Here, we review studies of molecular mechanisms of suicide in an epigenetic perspective in the postmortem brain of suicide completers and peripheral blood cells of suicide attempters. Besides, we include studies of gene-specific DNA methylation, epigenome-wide association, histone modification, and interfering RNAs as epigenetic factors. This review provides an overview of the epigenetic mechanisms described in different biological systems related to suicide, contributing to an understanding of the genetic regulation in suicide. We conclude that epigenetic marks are potential biomarkers in suicide, and they could become attractive therapeutic targets due to their reversibility and importance in regulating gene expression.
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Affiliation(s)
| | - Fernando Vazquez-Alaniz
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango
- Hospital General 450. Servicios de Salud de Durango
| | | | | | - Edna M Mendez-Hernádez
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - Alma C Salas-Leal
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
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Chalfun G, Reis MM, de Oliveira MBG, de Araújo Brasil A, Dos Santos Salú M, da Cunha AJLA, Prata-Barbosa A, de Magalhães-Barbosa MC. Perinatal stress and methylation of the NR3C1 gene in newborns: systematic review. Epigenetics 2021; 17:1003-1019. [PMID: 34519616 DOI: 10.1080/15592294.2021.1980691] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Adverse experiences in the perinatal period have been associated with the methylation of the human glucocorticoid receptor gene (NR3C1) and long-term diseases. We conducted a systematic review on the association between adversities in the perinatal period and DNA methylation in the 1 F region of the NR3C1 gene in newborns. We explored the MEDLINE, Web of Science, Scopus, Scielo, and Lilacs databases without time or language limitations. Two independent reviewers performed the selection of articles and data extraction. A third participated in the methodological quality assessment and consensus meetings at all stages. Finally, ten studies were selected. Methodological quality was considered moderate in six and low in four. Methylation changes were reported in 41 of the 47 CpG sites of exon 1 F. Six studies addressed maternal conditions during pregnancy: two reported methylation changes at the same sites (CpG 10, 13, 20, 21 and 47), and four at one or more sites from CpG 35 to 39. Four studies addressed neonatal parameters and morbidities: methylation changes at the same sites 4, 8, 10, 16, 25, and 35 were reported in two. Hypermethylation associated with stressful conditions prevailed. Hypomethylation was more often associated with protective conditions (maternal-foetal attachment during pregnancy, breast milk intake, higher birth weight or Apgar). In conclusion, methylation changes in several sites of the 1 F region of the NR3C1 gene in newborns and very young infants were associated with perinatal stress, but more robust and comparable results are needed to corroborate site-specific associations.
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Affiliation(s)
- Georgia Chalfun
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil.,Federal University of Rio de Janeiro (Ufrj), Rio De Janeiro, RJ, Brazil
| | - Marcelo Martins Reis
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil
| | | | - Aline de Araújo Brasil
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil
| | - Margarida Dos Santos Salú
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil
| | - Antônio José Ledo Alves da Cunha
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil.,Federal University of Rio de Janeiro (Ufrj), Rio De Janeiro, RJ, Brazil
| | - Arnaldo Prata-Barbosa
- Department of Pediatrics, D'Or Institute for Research and Education (Idor), Rio de Janeiro, RJ, Brazil.,Federal University of Rio de Janeiro (Ufrj), Rio De Janeiro, RJ, Brazil
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