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Zhang P, Lu Y, Li Y, Wang K, An H, Tan Y. Genome-wide DNA methylation analysis in schizophrenia with tardive dyskinesia: a preliminary study. Genes Genomics 2023; 45:1317-1328. [PMID: 37414911 DOI: 10.1007/s13258-023-01414-5] [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: 09/25/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Tardive dyskinesia (TD) develops in 20-30% of schizophrenia patients and up to 50% in patients > 50 years old. DNA methylation may play an important role in the development of TD. OBJECTIVE DNA methylation analyses in schizophrenia with TD. METHODS We conducted a genome-wide DNA methylation analysis in schizophrenia with TD using methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-Seq) in a Chinese sample including five schizophrenia patients with TD and five without TD (NTD), and five healthy controls. The results were expressed as the log2FC, fold change of normalized tags between two groups within the differentially methylated region (DMR). For validation, the pyrosequencing was used to quantify DNA methylation levels of several methylated genes in an independent sample (n = 30). RESULTS Through genome-wide MeDIP-Seq analysis, we identified 116 genes that were significantly differentially methylated in promotor regions in comparison of TD group with NTD group including 66 hypermethylated genes (top 4 genes are GABRR1, VANGL2, ZNF534, and ZNF746) and 50 hypomethylated genes (top 4 genes are DERL3, GSTA4, KNCN, and LRRK1). Part of these genes (such as DERL3, DLGAP2, GABRR1, KLRG2, LRRK1, VANGL2, and ZP3) were previously reported to be associated with methylation in schizophrenia. Gene Ontology enrichment and KEGG pathway analyses identified several pathways. So far, we have confirmed the methylation of 3 genes (ARMC6, WDR75, and ZP3) in schizophrenia with TD using pyrosequencing. CONCLUSIONS This study identified number of methylated genes and pathways for TD and will provide potential biomarkers for TD and serve as a resource for replication in other populations.
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Affiliation(s)
- Ping Zhang
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA
| | - Yanli Li
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Office 6419, Post Office Box 9600, Morgantown, WV, 26506, USA.
| | - Huimei An
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China
| | - Yunlong Tan
- Beijing HuiLongGuan Hospital, Peking University HuiLongGuan Clinical Medical School, Beijing, 100096, China.
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2
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Fu S, Debes JD, Boonstra A. DNA methylation markers in the detection of hepatocellular carcinoma. Eur J Cancer 2023; 191:112960. [PMID: 37473464 DOI: 10.1016/j.ejca.2023.112960] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and has a poor prognosis. Epigenetic modification has been shown to be deregulated during HCC development by dramatically impacting the differentiation, proliferation, and function of cells. One important epigenetic modification is DNA methylation during which methyl groups are added to cytosines without changing the DNA sequence itself. Studies found that methylated DNA markers can be specific for detection of HCC. On the basis of these findings, the utility of methylated DNA markers as novel biomarkers for early-stage HCC has been measured in blood, and indeed superior sensitivity and specificity have been found in several studies when compared to current surveillance methods. However, a variety of factors currently limit the immediate application of these exciting biomarkers. In this review, we provide a detailed rationalisation of the approach and basis for the use of methylation biomarkers for HCC detection and summarise recent studies on methylated DNA markers in HCC focusing on the importance of the aetiological cause of liver disease in the mechanisms leading to cancer.
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Affiliation(s)
- Siyu Fu
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - José D Debes
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - André Boonstra
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands.
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3
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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing. J Hum Genet 2022; 67:711-720. [PMID: 36167771 DOI: 10.1038/s10038-022-01083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/01/2022] [Accepted: 09/11/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Kabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone modification enzymes. Although KS is considered a single gene disorder, its symptoms vary widely. Recently, disease-specific DNA methylation patterns, or episignatures, have been recognized and used as a diagnostic tool for KS. Because of various crosstalk mechanisms between histone modifications and DNA methylation, DNA methylation analysis may have high potential for investigations into the pathogenesis of KS. RESULTS In this study, we investigated altered CpG-methylation sites that were specific to KS to find important genes associated with the various phenotypes or pathogenesis of KS. Whole genome bisulfite sequencing (WGBS) was performed to select target CpG islands, and enzymatic conversion technology was applied after hybridization capture to confirm KS-specific episignatures of 130 selected differently methylated target regions (DMTRs) in DNA samples from the 65 participants, 31 patients with KS and 34 unaffected individuals, in this study. We identified 26 candidate genes in 22 DMTRs that may be associated with KS. Our results indicate that disease-specific methylation sites can be identified from a small number of WGBS samples, and hybridization capture followed by enzymatic methylation sequencing can simultaneously test the sites. CONCLUSIONS Although DNA methylation can be tissue-specific, our results suggest that methylation profiling of DNA extracted from peripheral blood may be a powerful approach to study the pathogenesis of diseases.
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Ramasamy D, Rao AKDM, Balaiah M, Vittal Rangan A, Sundersingh S, Veluswami S, Thangarajan R, Mani S. Locus-Specific Enrichment Analysis of 5-Hydroxymethylcytosine Reveals Novel Genes Associated with Breast Carcinogenesis. Cells 2022; 11:cells11192939. [PMID: 36230901 PMCID: PMC9562672 DOI: 10.3390/cells11192939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Highlights Abstract An imbalance in DNA methylation is a hallmark epigenetic alteration in cancer. The conversion of 5-methylcytosine (5-mC) to 5-hydroxymethyl cytosine (5-hmC), which causes the imbalance, results in aberrant gene expression. The precise functional role of 5-hydroxymethylcytosine in breast cancer remains elusive. In this study, we describe the landscape of 5-mC and 5-hmC and their association with breast cancer development. We found a distinguishable global loss of 5-hmC in the localized and invasive types of breast cancer that strongly correlate with TET expression. Genome-wide analysis revealed a unique 5-mC and 5-hmC signature in breast cancer. The differentially methylated regions (DMRs) were primarily concentrated in the proximal regulatory regions such as the promoters and UTRs, while the differentially hydroxymethylated regions (DhMRs) were densely packed in the distal regulatory regions, such as the intergenic regions (>−5 kb from TSSs). Our results indicate 4809 DMRs and 4841 DhMRs associated with breast cancer. Validation of nine 5-hmC enriched loci in a distinct set of breast cancer and normal samples positively correlated with their corresponding gene expression. The novel 5-hmC candidates such as TXNL1, and CNIH3 implicate a pro-oncogenic role in breast cancer. Overall, these results provide new insights into the loci-specific accumulation of 5-mC and 5-hmC, which are aberrantly methylated and demethylated in breast cancer.
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Affiliation(s)
- Deepa Ramasamy
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | | | - Meenakumari Balaiah
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Arvinden Vittal Rangan
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Shirley Sundersingh
- Department of Oncopathology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Sridevi Veluswami
- Department of Surgical Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Rajkumar Thangarajan
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), 38, Sardar Patel Road, Chennai 600036, Tamilnadu, India
- Correspondence: ; Tel.: +91-44-22350131 (ext. 196)
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Garcia-Manteiga JM, Clarelli F, Bonfiglio S, Mascia E, Giannese F, Barbiera G, Guaschino C, Sorosina M, Santoro S, Protti A, Martinelli V, Cittaro D, Lazarevic D, Stupka E, Filippi M, Esposito F, Martinelli-Boneschi F. Identification of differential DNA methylation associated with multiple sclerosis: A family-based study. J Neuroimmunol 2021; 356:577600. [PMID: 33991750 DOI: 10.1016/j.jneuroim.2021.577600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Multiple Sclerosis (MS) is caused by a still unknown interplay between genetic and environmental factors. Epigenetics, including DNA methylation, represents a model for environmental factors to influence MS risk. Twenty-six affected and 26 unaffected relatives from 8 MS multiplex families were analysed in a multicentric Italian study using MeDIP-Seq, followed by technical validation and biological replication in two additional families of differentially methylated regions (DMRs) using SeqCap Epi Choice Enrichment kit (Roche®). Associations from MeDIP-Seq across families were combined with aggregation statistics, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypo-methylated regions, which point to NTM and BAI3 genes, and to 2 hyper-methylated regions in PIK3R1 and CAPN13. These 4 novel regions contain genes of potential interest that need to be tested in larger cohorts of patients.
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Affiliation(s)
- J M Garcia-Manteiga
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - F Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - S Bonfiglio
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - E Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - F Giannese
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - G Barbiera
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - C Guaschino
- Department of Neurology, Sant'Antonio Abate Hospital, Gallarate, Italy
| | - M Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - S Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy
| | - A Protti
- Ospedale Niguarda, Department of Neurology, Milan, Italy
| | - V Martinelli
- Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - D Cittaro
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - D Lazarevic
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - E Stupka
- Centre for Omics Sciences, San Raffaele Scientific Institute IRCCS, Milan, Italy
| | - M Filippi
- Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 48, 20132 Milan, Italy; Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Neurophysiology Unit, IRCCS San Raffaele Scientific Institute, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy; Neurology Unit, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Italy; Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy; Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy.
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6
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Danstrup CS, Marcussen M, Pedersen IS, Jacobsen H, Dybkær K, Gaihede M. DNA methylation biomarkers in peripheral blood of patients with head and neck squamous cell carcinomas. A systematic review. PLoS One 2020; 15:e0244101. [PMID: 33332423 PMCID: PMC7746174 DOI: 10.1371/journal.pone.0244101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinomas (HNSCC) are often diagnosed in advanced stages. In search of new diagnostic tools, focus has shifted towards the biological properties of the HNSCC, and the number of different biomarkers under investigation is rapidly growing. OBJECTIVES The objective was to review the current literature regarding aberrantly methylated DNA found in peripheral blood plasma or serum in patients with HNSCC and to evaluate the diagnostic accuracy of these changes. METHODS The inclusion criteria were clinical studies involving patients with verified HNSCC that reported findings of aberrantly methylated DNA in peripheral blood serum or plasma. We systematically searched PubMed, OVID Embase and Cochrane Library. In addition to the search, we performed forward and backward chaining in references and Web of Science. The protocol was registered in PROSPERO: CRD42019135406. Two authors independently extracted data. The quality and the risk of bias of the included studies were assessed by the QUADAS-2 tool. RESULTS A total of 1,743 studies were found eligible for screening, while ultimately seven studies were included. All studies were found to have methodological weaknesses, mainly concerning patient selection bias. The best individual marker of HNSCC was Septin 9 in plasma with a sensitivity of 57% and a specificity of 95%. CONCLUSIONS None of the aberrantly methylated genes found in the retrieved studies are applicable as single diagnostic markers for HNSCC and the best gene-panels still lack diagnostic accuracy. Future studies may benefit from newer sequencing techniques but validation studies with well-designed cohorts are also needed in the process of developing epigenetic based diagnostic tests for HNSCC.
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Affiliation(s)
- Christian Sander Danstrup
- Department of Otorhinolaryngology–Head & Neck Surgery and Audiology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Mette Marcussen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Henrik Jacobsen
- Department of Otorhinolaryngology–Head & Neck Surgery and Audiology, Aalborg University Hospital, Aalborg, Denmark
| | - Karen Dybkær
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otorhinolaryngology–Head & Neck Surgery and Audiology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Leal A, Sidransky D, Brait M. Tissue and Cell-Free DNA-Based Epigenomic Approaches for Cancer Detection. Clin Chem 2020; 66:105-116. [PMID: 31843869 DOI: 10.1373/clinchem.2019.303594] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/01/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Over 9 million people die of cancer each year worldwide, reflecting the unmet need for effective biomarkers for both cancer diagnosis and prognosis. Cancer diagnosis is complex because the majority of malignant tumors present with long periods of latency and lack of clinical presentation at early stages. During carcinogenesis, premalignant cells experience changes in their epigenetic landscapes, such as differential DNA methylation, histone modifications, nucleosome positioning, and higher orders of chromatin changes that confer growth advantage and contribute to determining the biologic phenotype of human cancers. CONTENT Recent progress in microarray platforms and next-generation sequencing approaches has allowed the characterization of abnormal epigenetic patterns genome wide in a large number of cancer cases. The sizable amount of processed data also comes with challenges regarding data management and assessment for effective biomarker exploration to be further applied in prospective clinical trials. Epigenetics-based single or panel tests of genes are being explored for clinical management to fulfill unmet needs in oncology. The advance of these tests to the clinical routine will depend on rigorous, extensive, and independent validation in well-annotated cohort of patients and commercial development of clinical routine-friendly and adequate procedures. SUMMARY In this review we discuss the analytic validation of tissue and cell-free DNA-based epigenomic approaches for early cancer detection, diagnosis, and treatment monitoring and the clinical utility of candidate epigenetic alterations applied to colorectal, glioblastoma, breast, prostate, bladder, and lung cancer management.
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Affiliation(s)
- Alessandro Leal
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Sidransky
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mariana Brait
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
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Thomas M, Coope A, Falkenberg C, Dunlop BW, Czamara D, Provencal N, Craighead WE, Mayberg HS, Nemeroff CB, Binder EB, Nieratschker V. Investigation of MORC1 DNA methylation as biomarker of early life stress and depressive symptoms. J Psychiatr Res 2020; 120:154-162. [PMID: 31683097 PMCID: PMC6866669 DOI: 10.1016/j.jpsychires.2019.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 12/28/2022]
Abstract
Early life stress (ELS) is associated with an increased risk of depression and this association may be mediated by epigenetic mechanisms. A previous epigenome-wide DNA methylation (DNAm) study investigating human newborns and two animal models of ELS suggested that the epigenetic regulator MORC1 is differentially methylated following ELS. The ELS-induced DNAm alterations were long-lasting in the animal models. However, whether this finding is also transferable to humans experiencing ELS in childhood was not investigated. Further, MORC1 may provide a link between ELS and adult depression, as MORC1 DNAm and genetic variants were found to be associated with depressive symptoms in humans. In the present study, we investigated the validity of MORC1 DNAm as a biomarker of ELS in humans and its role in linking ELS to depression later in life by studying childhood maltreatment. We analyzed whole blood MORC1 DNAm in an adult cohort (N = 151) that was characterized for both the presence of depressive symptoms and childhood maltreatment. Further, we investigated the association between MORC1 DNAm, depressive symptoms and childhood maltreatment in two additional cohorts (N = 299, N = 310). Overall, our data do not indicate an association of MORC1 DNAm with childhood maltreatment. An association of MORC1 DNAm with depressive symptoms was present in all cohorts, but was inconsistent in the specific CpG sites associated and the direction of effect (Tuebingen cohort: standardized β = 0.16, unstandardized β = 0.01, 95% CI [-0.0004, -0.0179], p = 0.061, PReDICT cohort: standardized β = -0.12, unstandardized β = -0.01, 95% CI [-0.0258, -0.0003], p = 0.045), Grady cohort: standardized β = 0.16, unstandardized β = 0.008, 95% CI [0.0019, 0.0143], p = 0.01). Our study thus suggests that peripheral MORC1 DNAm cannot serve as biomarker of childhood maltreatment in adults, but does provide further indication for the association of MORC1 DNAm with depressive symptoms.
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Affiliation(s)
- Mara Thomas
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72070, Tübingen, Germany; Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany.
| | - Andressa Coope
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada,BC Children’s Hospital Research Institute, 938 W 28th Ave, Vancouver, British Columbia V5Z 4H4, Canada
| | - Carolin Falkenberg
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72070 Tübingen, Germany
| | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park, Atlanta, Georgia 30329, USA
| | - Darina Czamara
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park, Atlanta, Georgia 30329, USA,Department of Translational Research in Psychiatriy, Max-Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Nadine Provencal
- Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada,BC Children’s Hospital Research Institute, 938 W 28th Ave, Vancouver, British Columbia V5Z 4H4, Canada
| | - W. Edward Craighead
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park, Atlanta, Georgia 30329, USA
| | - Helen S. Mayberg
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park, Atlanta, Georgia 30329, USA,Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy PI, New York, NY 10029, USA
| | - Charles B. Nemeroff
- Department of Psychiatry, Dell Medical School, University of Texas at Austin, 1601 Trinity St, Austin, Texas 78712, USA
| | - Elisabeth B. Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park, Atlanta, Georgia 30329, USA,Department of Translational Research in Psychiatriy, Max-Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Vanessa Nieratschker
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72070 Tübingen, Germany
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9
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Schuster J, Uzun A, Stablia J, Schorl C, Mori M, Padbury JF. Effect of prematurity on genome wide methylation in the placenta. BMC MEDICAL GENETICS 2019; 20:116. [PMID: 31253109 PMCID: PMC6599230 DOI: 10.1186/s12881-019-0835-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Abstract
Background Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns. Despite decades of research, the molecular mechanism underlying its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The “fetal origins” hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility. Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages. We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs). Results Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p < 0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p < 0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth. Conclusion These studies form the basis for future studies on the epigenetics of preterm birth, “fetal programming” and the impact of environment exposures on this important clinical challenge. Electronic supplementary material The online version of this article (10.1186/s12881-019-0835-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Schuster
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Alper Uzun
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA
| | - Joan Stablia
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, 02906, USA
| | - Mari Mori
- Pediatrics and Genetics, Hasbro Children's Hospital, Providence, Rhode Island, 02905, USA
| | - James F Padbury
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA. .,, Providence, USA.
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10
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Zeng H, He B, Yi C. Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem 2019; 20:1898-1905. [PMID: 30809902 DOI: 10.1002/cbic.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/19/2022]
Abstract
Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Bo He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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11
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Williams KE, Jawale RM, Schneider SS, Otis CN, Pentecost BT, Arcaro KF. DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence. J Cell Biochem 2018; 120:738-755. [DOI: 10.1002/jcb.27431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/12/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Kristin E. Williams
- Department of Molecular and Cellular Biology University of Massachusetts –Amherst Amherst Massachusetts
| | - Rahul M. Jawale
- Department of Pathology Baystate Medical Center Springfield Massachusetts
| | - Sallie S. Schneider
- Biospecimen Resource and Molecular Analysis Facility Baystate Medical Center Springfield Massachusetts
| | | | - Brian T. Pentecost
- Division of Translational Medicine Wadsworth Center, New York State Department of Health Albany New York
| | - Kathleen F. Arcaro
- Department of Veterinary and Animal Sciences University of Massachusetts – Amherst Amherst Massachusetts
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12
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Wei J, Li G, Zhang J, Zhou Y, Dang S, Chen H, Wu Q, Liu M. Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer. Oncotarget 2018; 7:62547-62558. [PMID: 27566576 PMCID: PMC5308745 DOI: 10.18632/oncotarget.11534] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
DNA methylation was regarded as the promising biomarker for rectal cancer diagnosis. However, the optimal methylation biomarkers with ideal diagnostic performance for rectal cancer are still limited. To identify new molecular markers for rectal cancer, we mapped DNA methylation and transcriptomic profiles in the six rectal cancer and paired normal samples. Further analysis revealed the hypermethylated probes in cancer prone to be located in gene promoter. Meanwhile, transcriptome analysis presented 773 low-expressed and 1,161 over-expressed genes in rectal cancer. Correction analysis identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels, including 10 known colorectal cancer related genes. From the other 26 novel marker genes, GFRA1 and GSTM2 were selected for further analysis on the basis of their biological functions. Further experiment analysis confirmed their methylation and expression status in a larger number (44) of rectal cancer samples, and ROC curves showed higher AUC than SEPT9, which has been used as a biomarker in rectal cancer. Our data suggests that aberrant DNA methylation of contiguous CpG sites in methylation array may be potential diagnostic markers of rectal cancer.
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Affiliation(s)
- Jiufeng Wei
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Jinning Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Yuhui Zhou
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Shuwei Dang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, P.R. China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China.,Bio-Bank of Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
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13
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Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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14
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Arathimos R, Suderman M, Sharp GC, Burrows K, Granell R, Tilling K, Gaunt TR, Henderson J, Ring S, Richmond RC, Relton CL. Epigenome-wide association study of asthma and wheeze in childhood and adolescence. Clin Epigenetics 2017; 9:112. [PMID: 29046734 PMCID: PMC5640901 DOI: 10.1186/s13148-017-0414-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis. METHODS Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx. 1000 participants. We used Mendelian randomization (MR), a method of causal inference that uses genetic variants as instrumental variables, to infer the direction of association between DNA methylation and asthma. RESULTS We identified 302 CpGs associated with current asthma status (FDR-adjusted P value < 0.05) and 445 with current wheeze status at 7.5 years, with substantial overlap between the two. Genes annotated to the 302 associated CpGs were enriched for pathways related to movement of cellular/subcellular components, locomotion, interleukin-4 production and eosinophil migration. All associations attenuated when adjusted for eosinophil and neutrophil cell count estimates. At 16.5 years, two sites were associated with current asthma after adjustment for cell counts. The CpGs mapped to the AP2A2 and IL5RA genes, with a - 2.32 [95% CI - 1.47, - 3.18] and - 2.49 [95% CI - 1.56, - 3.43] difference in percentage methylation in asthma cases respectively. Two-sample bi-directional MR indicated a causal effect of asthma on DNA methylation at several CpG sites at 7.5 years. However, associations did not persist after adjustment for multiple testing. There was no evidence of a causal effect of asthma on DNA methylation at either of the two CpG sites at 16.5 years. CONCLUSION The majority of observed associations are driven by higher eosinophil cell counts in asthma cases, acting as an intermediate phenotype, with important implications for future studies of DNA methylation in atopic diseases.
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Affiliation(s)
- Ryan Arathimos
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Matthew Suderman
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Gemma C. Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Kate Tilling
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Tom R. Gaunt
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Susan Ring
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Rebecca C. Richmond
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
| | - Caroline L. Relton
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, BS8 2BN UK
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15
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Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res 2017; 45:e77. [PMID: 28126923 PMCID: PMC5605247 DOI: 10.1093/nar/gkx026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/20/2017] [Indexed: 01/03/2023] Open
Abstract
Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population.
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Affiliation(s)
- Lin Han
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Haiying Zhu
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Sadie L Marjani
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Xiaoyuan Zi
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.,Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
| | - Jennifer Yang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jasper Han
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Rafael Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Sherman M Weissman
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xinghua Pan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangzhou, China.,Guangdong Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou 510515, Guangdong, China
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16
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Zhang R, Liu L, Yao Y, Fei F, Wang F, Yang Q, Gui Y, Wang X. High Resolution Imaging of DNA Methylation Dynamics using a Zebrafish Reporter. Sci Rep 2017; 7:5430. [PMID: 28710355 PMCID: PMC5511286 DOI: 10.1038/s41598-017-05648-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/01/2017] [Indexed: 12/17/2022] Open
Abstract
As one of the major epigenetic modifications, DNA methylation is constantly regulated during embryonic development, cell lineage commitment, and pathological processes. To facilitate real-time observation of DNA methylation, we generated a transgenic zebrafish reporter of DNA methylation (zebraRDM) via knockin of an mCherry-fused methyl-CpG binding domain (MBD) probe driven by the bactin2 promoter. The probe colocalized with heterochromatin, and its intensity was positively correlated with 5 mC immunostaining at a subcellular resolution in early embryos. Biochemical assays indicated that cells with stronger fluorescence maintained a higher level of DNA methylation, and time-lapse imaging at the blastula stage showed that the level of DNA methylation was transiently strengthened during mitosis. By crossing zebraRDM with other fluorescent transgenic lines, we demonstrate that the reporter can visually distinguish different cell lineages in organs like the heart. Our zebraRDM reporter therefore serves as a convenient and powerful tool for high-resolution investigation of methylation dynamics in live animals.
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Affiliation(s)
- Ranran Zhang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Lian Liu
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yuxiao Yao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Fei Fei
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Feng Wang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Qian Yang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yonghao Gui
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Xu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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17
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Radhakrishnan S, Literman R, Mizoguchi B, Valenzuela N. MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination. Epigenetics Chromatin 2017; 10:28. [PMID: 28533820 PMCID: PMC5438563 DOI: 10.1186/s13072-017-0136-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis. Results Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation. Conclusions Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Robert Literman
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Beatriz Mizoguchi
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
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18
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Devall M, Smith RG, Jeffries A, Hannon E, Davies MN, Schalkwyk L, Mill J, Weedon M, Lunnon K. Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue. Clin Epigenetics 2017; 9:47. [PMID: 28473874 PMCID: PMC5415779 DOI: 10.1186/s13148-017-0337-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 03/30/2017] [Indexed: 12/22/2022] Open
Abstract
Background DNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. Mitochondrial DNA methylation is a phenomenon that is receiving ever-increasing interest, particularly in diseases characterized by mitochondrial dysfunction; however, most studies have been limited to the investigation of specific target regions. Analyses spanning the entire mitochondrial genome have been limited, potentially due to the amount of input DNA required. Further, mitochondrial genetic studies have been previously confounded by nuclear-mitochondrial pseudogenes. Methylated DNA Immunoprecipitation Sequencing is a technique widely used to profile DNA methylation across the nuclear genome; however, reads mapped to mitochondrial DNA are often discarded. Here, we have developed an approach to control for nuclear-mitochondrial pseudogenes within Methylated DNA Immunoprecipitation Sequencing data. We highlight the utility of this approach in identifying differences in mitochondrial DNA methylation across regions of the human brain and pre-mortem blood. Results We were able to correlate mitochondrial DNA methylation patterns between the cortex, cerebellum and blood. We identified 74 nominally significant differentially methylated regions (p < 0.05) in the mitochondrial genome, between anatomically separate cortical regions and the cerebellum in matched samples (N = 3 matched donors). Further analysis identified eight significant differentially methylated regions between the total cortex and cerebellum after correcting for multiple testing. Using unsupervised hierarchical clustering analysis of the mitochondrial DNA methylome, we were able to identify tissue-specific patterns of mitochondrial DNA methylation between blood, cerebellum and cortex. Conclusions Our study represents a comprehensive analysis of the mitochondrial methylome using pre-existing Methylated DNA Immunoprecipitation Sequencing data to identify brain region-specific patterns of mitochondrial DNA methylation.
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Affiliation(s)
- Matthew Devall
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Rebecca G Smith
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Aaron Jeffries
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Eilis Hannon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Matthew N Davies
- Department of Twin Research & Genetic Epidemiology, King's College London, Lambeth Palace Road, London, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Michael Weedon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Katie Lunnon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
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19
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Han X, Wang J, Sun Y. Circulating Tumor DNA as Biomarkers for Cancer Detection. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:59-72. [PMID: 28392479 PMCID: PMC5414889 DOI: 10.1016/j.gpb.2016.12.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022]
Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
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Affiliation(s)
- Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyun Wang
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingli Sun
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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20
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Agrawal K, Das V, Otmar M, Krečmerová M, Džubák P, Hajdúch M. Cell-based DNA demethylation detection system for screening of epigenetic drugs in 2D, 3D, and xenograft models. Cytometry A 2016; 91:133-143. [DOI: 10.1002/cyto.a.23004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 09/01/2016] [Accepted: 10/05/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Khushboo Agrawal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University; Hněvotínská 5 77900 Olomouc Czech Republic
| | - Viswanath Das
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University; Hněvotínská 5 77900 Olomouc Czech Republic
| | - Miroslav Otmar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i, Flemingovo náměstí 2 16610 Prague 6 Czech Republic
| | - Marcela Krečmerová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic; v.v.i, Flemingovo náměstí 2 16610 Prague 6 Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University; Hněvotínská 5 77900 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University; Hněvotínská 5 77900 Olomouc Czech Republic
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21
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Jadhav RR, Wang YV, Hsu YT, Liu J, Garcia D, Lai Z, Huang THM, Jin VX. Methyl-binding DNA capture Sequencing for Patient Tissues. J Vis Exp 2016. [PMID: 27842364 DOI: 10.3791/54131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Methylation is one of the essential epigenetic modifications to the DNA, which is responsible for the precise regulation of genes required for stable development and differentiation of different tissue types. Dysregulation of this process is often the hallmark of various diseases like cancer. Here, we outline one of the recent sequencing techniques, Methyl-Binding DNA Capture sequencing (MBDCap-seq), used to quantify methylation in various normal and disease tissues for large patient cohorts. We describe a detailed protocol of this affinity enrichment approach along with a bioinformatics pipeline to achieve optimal quantification. This technique has been used to sequence hundreds of patients across various cancer types as a part of the 1,000 methylome project (Cancer Methylome System).
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Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Yao V Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Joseph Liu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio
| | - Tim H M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio;
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22
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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Viuff ACF, Pedersen LH, Kyng K, Staunstrup NH, Børglum A, Henriksen TB. Antidepressant medication during pregnancy and epigenetic changes in umbilical cord blood: a systematic review. Clin Epigenetics 2016; 8:94. [PMID: 27610205 PMCID: PMC5015265 DOI: 10.1186/s13148-016-0262-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/30/2016] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Epigenetic mechanisms are important for the regulation of gene expression and differentiation in the fetus and the newborn child. Symptoms of maternal depression and antidepressant use affects up to 20 % of pregnant women, and may lead to epigenetic changes with life-long impact on child health. The aim of this review is to investigate whether there is an association between exposure to maternal antidepressants during pregnancy and epigenetic changes in the newborn. MATERIAL AND METHODS Systematic literature searches were performed in MEDLINE and EMBASE combining MeSH terms covering epigenetic changes, use of antidepressant medication, pregnancy and newborns. A keyword search was also performed. We included studies on pregnant women and their children where there was a history of maternal depressed mood or anxiety, a reported use of antidepressant medication, and measurements of epigenetic changes in umbilical cord blood. Studies using genome-wide or candidate-based epigenetic analyses were included. Citations and references from the included articles were investigated to locate further relevant articles. The completeness of reporting as well as the risk of bias and confounding was assessed. RESULTS Six studies were included. They all investigated methylation changes. Genome-wide methylation changes were examined in 184 children and methylation status in specific genes was examined in 96 children exposed to antidepressant medication. Three of the studies found an association between use of antidepressant medication during pregnancy and methylation status at various CpG sites measured in cord blood of the newborn. One of these studies found an association in African-Americans, but not Caucasians. The remaining three studies found associations between maternal mood and epigenetic changes in umbilical cord blood but no association between epigenetic changes and maternal use of antidepressant medication. CONCLUSION The included studies have not established a clear association between use of antidepressant medication during pregnancy and epigenetic changes in the cord blood. Future studies using newer, more wide-ranging epigenetic methods could discover possible new differentially methylated sites. Larger sample sizes and good validity of exposures are warranted in order to adjust for level of maternal depression, other maternal illness, maternal use of other types of medication, and maternal ethnicity. PROSPERO registration number: CRD42015026575.
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Affiliation(s)
- Anne-Cathrine F. Viuff
- Perinatal Epidemiology Research Unit, Pediatric Department, Aarhus University Hospital Skejby, Aarhus, Denmark
| | - Lars Henning Pedersen
- Department of Obstetrics and Gynecology, Aarhus University Hospital Skejby, Aarhus, Denmark
| | - Kasper Kyng
- Perinatal Epidemiology Research Unit, Pediatric Department, Aarhus University Hospital Skejby, Aarhus, Denmark
| | - Nicklas Heine Staunstrup
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Risskov, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, University of Aarhus, Aarhus C, 8000 Denmark
- Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark
| | - Anders Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Risskov, Denmark
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, University of Aarhus, Aarhus C, 8000 Denmark
| | - Tine Brink Henriksen
- Perinatal Epidemiology Research Unit, Pediatric Department, Aarhus University Hospital Skejby, Aarhus, Denmark
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24
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Yang Y, Ma ZH, Li XG, Zhang WF, Wan J, Du LJ, Li GJ, Yang GK, Lu P. Iodine-125 irradiation inhibits invasion of gastric cancer cells by reactivating microRNA-181c expression. Oncol Lett 2016; 12:2789-2795. [PMID: 27698859 DOI: 10.3892/ol.2016.5033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/07/2016] [Indexed: 02/06/2023] Open
Abstract
Iodine-125 (125I) seed implantation has been widely used for the treatment of unresectable advanced tumors. However, the molecular mechanisms underlying the tumor-suppressive effects of 125I irradiation have not been fully elucidated. The present study demonstrated that 125I irradiation suppresses cell viability and inhibits cell invasiveness of gastric cancer KATO-III and MKN45 cells. Further mechanistic analysis suggested the involvement of microRNA (miR)-181c in the inhibitory effects induced by 125I irradiation. Methylated DNA immunoprecipitation coupled with quantitative-polymerase chain reaction demonstrated that treatment with 125I irradiation, at the dose of 4 Gy, induced promoter demethylation of the miR-181c gene in KATO-III and MKN45 cells. Following irradiation, the expression of miR-181c was significantly increased, which may be attributed to the demethylation caused by 125I irradiation. In addition, upregulation of miR-181c by administration of miR-181c mimics decreased cell invasion, suggesting the role of miR-181c as a tumor suppressor. More importantly, the tumor-suppressive effects of 125I irradiation were significantly compromised by the introduction of miR-181c inhibitors. Overall, these results reveal that 125I irradiation inhibits invasiveness of gastric cancer cells by reactivating miR-181c at the epigenetic level, thereby providing important molecular evidence for the anticancer effects of 125I irradiation.
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Affiliation(s)
- Yong Yang
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Zhen-Huan Ma
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Xiao-Gang Li
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Abdominal Surgery Centre, The Health and Family Planning Commission of Yunnan Kunming, Kunming, Yunnan 650021, P.R. China
| | - Wan-Fu Zhang
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Abdominal Surgery Centre, The Health and Family Planning Commission of Yunnan Kunming, Kunming, Yunnan 650021, P.R. China
| | - Jia Wan
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Ling-Juan Du
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Guo-Jian Li
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Guo-Kai Yang
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
| | - Ping Lu
- Department of General Surgery, The Second People's Hospital of Yunnan, Kunming, Yunnan 650021, P.R. China; Department of Vascular Surgery, Fourth Affiliated Hospital to Kunming Medical University, Kunming, Yunnan 650021, P.R. China; Vascular Surgery Centre in Yunnan, Kunming, Yunnan 650021, P.R. China
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25
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Staunstrup NH, Starnawska A, Nyegaard M, Christiansen L, Nielsen AL, Børglum A, Mors O. Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots. Clin Epigenetics 2016; 8:81. [PMID: 27462375 PMCID: PMC4960904 DOI: 10.1186/s13148-016-0242-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed. RESULTS Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample. CONCLUSIONS In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.
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Affiliation(s)
- Nicklas H Staunstrup
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anna Starnawska
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Lene Christiansen
- Department of Public Health, University of Southern Denmark, Odense C, 5000 Denmark
| | - Anders L Nielsen
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
| | - Anders Børglum
- Department of Biomedicine, University of Aarhus, Aarhus C, 8000 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark ; Center for Integrative Sequencing, iSEQ, AU, Aarhus C, Denmark
| | - Ole Mors
- Translational Neuropsychiatric Unit, Aarhus University Hospital, Risskov, 8240 Denmark ; Research Department P, Aarhus University Hospital, Risskov, 8240 Denmark ; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus C, Denmark
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26
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Discovery and Validation of Hypermethylated Markers for Colorectal Cancer. DISEASE MARKERS 2016; 2016:2192853. [PMID: 27493446 PMCID: PMC4963574 DOI: 10.1155/2016/2192853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 12/31/2022]
Abstract
Colorectal carcinoma (CRC) is one of the most prevalent malignant tumors worldwide. Screening and early diagnosis are critical for the clinical management of this disease. DNA methylation changes have been regarded as promising biomarkers for CRC diagnosis. Here, we map DNA methylation profiling on CRC in six CRCs and paired normal samples using a 450 K bead array. Further analysis confirms the methylation status of candidates in two data sets from the Gene Expression Omnibus. Receiver operating characteristic (ROC) curves are calculated to determine the diagnostic performances. We identify 1549 differentially methylated regions (DMRs) showing differences in methylation between CRC and normal tissue. Two genes (ADD2 and AKR1B1), related to the DMRs, are selected for further validation. ROC curves show that the areas under the curves of ADD2 and AKR1B1 are higher than that of SEPT9, which has been clinically used as a screening biomarker of CRC. Our data suggests that aberrant DNA methylation of ADD2 and AKR1B1 could be potential screening markers of CRC.
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27
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Yong WS, Hsu FM, Chen PY. Profiling genome-wide DNA methylation. Epigenetics Chromatin 2016; 9:26. [PMID: 27358654 PMCID: PMC4926291 DOI: 10.1186/s13072-016-0075-3] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/17/2016] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.
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Affiliation(s)
- Wai-Shin Yong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - Fei-Man Hsu
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561 Japan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC
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28
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Fries GR, Li Q, McAlpin B, Rein T, Walss-Bass C, Soares JC, Quevedo J. The role of DNA methylation in the pathophysiology and treatment of bipolar disorder. Neurosci Biobehav Rev 2016; 68:474-488. [PMID: 27328785 DOI: 10.1016/j.neubiorev.2016.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/03/2016] [Accepted: 06/12/2016] [Indexed: 12/31/2022]
Abstract
Bipolar disorder (BD) is a multifactorial illness thought to result from an interaction between genetic susceptibility and environmental stimuli. Epigenetic mechanisms, including DNA methylation, can modulate gene expression in response to the environment, and therefore might account for part of the heritability reported for BD. This paper aims to review evidence of the potential role of DNA methylation in the pathophysiology and treatment of BD. In summary, several studies suggest that alterations in DNA methylation may play an important role in the dysregulation of gene expression in BD, and some actually suggest their potential use as biomarkers to improve diagnosis, prognosis, and assessment of response to treatment. This is also supported by reports of alterations in the levels of DNA methyltransferases in patients and in the mechanism of action of classical mood stabilizers. In this sense, targeting specific alterations in DNA methylation represents exciting new treatment possibilities for BD, and the 'plastic' characteristic of DNA methylation accounts for a promising possibility of restoring environment-induced modifications in patients.
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Affiliation(s)
- Gabriel R Fries
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA.
| | - Qiongzhen Li
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Blake McAlpin
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA
| | - Theo Rein
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstraße 2-10, 80804, Munich, Germany
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Jair C Soares
- Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), 1941 East Rd, 77054, Houston, TX, USA; Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA; Laboratory of Neurosciences, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
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29
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Jeong HM, Lee S, Chae H, Kim R, Kwon MJ, Oh E, Choi YL, Kim S, Shin YK. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics 2016; 8:1061-77. [PMID: 27266718 DOI: 10.2217/epi-2016-0038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIMS We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. RESULTS MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. CONCLUSION MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.
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Affiliation(s)
- Hae Min Jeong
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sangseon Lee
- School of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea
| | - Heejoon Chae
- Computer Science Department, School of Informatics & Computing, Indiana University, Bloomington, IN, USA
| | - RyongNam Kim
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
| | - Ensel Oh
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics & Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Kim
- Department of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Young Kee Shin
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.,The Center for Anti-Cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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30
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Gokhman D, Meshorer E, Carmel L. Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics. Trends Ecol Evol 2016; 31:290-300. [DOI: 10.1016/j.tree.2016.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 01/08/2023]
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31
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Devall M, Roubroeks J, Mill J, Weedon M, Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett 2016; 625:47-55. [PMID: 26876477 DOI: 10.1016/j.neulet.2016.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
The field of mitochondrial epigenetics has received increased attention in recent years and changes in mitochondrial DNA (mtDNA) methylation has been implicated in a number of diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis. However, current publications have been limited by the use of global or targeted methods of measuring DNA methylation. In this review, we discuss current findings in mitochondrial epigenetics as well as its potential role as a regulator of mitochondria within the brain. Finally, we summarize the current technologies best suited to capturing mtDNA methylation, and how a move towards whole epigenome sequencing of mtDNA may help to advance our current understanding of the field.
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Affiliation(s)
- Matthew Devall
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Janou Roubroeks
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, The Netherlands
| | - Jonathan Mill
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, De Crespigny Park, London, UK
| | - Michael Weedon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK.
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32
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
Next-generation sequencing (NGS) approaches are highly applicable to clinical studies. We review recent advances in sequencing technologies, as well as their benefits and tradeoffs, to provide an overview of clinical genomics from study design to computational analysis. Sequencing technologies enable genomic, transcriptomic, and epigenomic evaluations. Studies that use a combination of whole genome, exome, mRNA, and bisulfite sequencing are now feasible due to decreasing sequencing costs. Single-molecule sequencing increases read length, with the MinIONTM nanopore sequencer, which offers a uniquely portable option at a lower cost. Many of the published comparisons we review here address the challenges associated with different sequencing methods. Overall, NGS techniques, coupled with continually improving analysis algorithms, are useful for clinical studies in many realms, including cancer, chronic illness, and neurobiology. We, and others in the field, anticipate the clinical use of NGS approaches will continue to grow, especially as we shift into an era of precision medicine.
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Affiliation(s)
- Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Alexa B.R. McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York. Feil Family Brain and Mind Research Institute, New York, New York
| | - Jeffrey P. Greenfield
- Department of Neurological Surgery, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, New York
| | - Sheng Li
- Department of Neurological Surgery, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, New York
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Sanchez-Mut JV, Gräff J. Epigenetic Alterations in Alzheimer's Disease. Front Behav Neurosci 2015; 9:347. [PMID: 26734709 PMCID: PMC4681781 DOI: 10.3389/fnbeh.2015.00347] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is the major cause of dementia in Western societies. It progresses asymptomatically during decades before being belatedly diagnosed when therapeutic strategies have become unviable. Although several genetic alterations have been associated with AD, the vast majority of AD cases do not show strong genetic underpinnings and are thus considered a consequence of non-genetic factors. Epigenetic mechanisms allow for the integration of long-lasting non-genetic inputs on specific genetic backgrounds, and recently, a growing number of epigenetic alterations in AD have been described. For instance, an accumulation of dysregulated epigenetic mechanisms in aging, the predominant risk factor of AD, might facilitate the onset of the disease. Likewise, mutations in several enzymes of the epigenetic machinery have been associated with neurodegenerative processes that are altered in AD such as impaired learning and memory formation. Genome-wide and locus-specific epigenetic alterations have also been reported, and several epigenetically dysregulated genes validated by independent groups. From these studies, a picture emerges of AD as being associated with DNA hypermethylation and histone deacetylation, suggesting a general repressed chromatin state and epigenetically reduced plasticity in AD. Here we review these recent findings and discuss several technical and methodological considerations that are imperative for their correct interpretation. We also pay particular focus on potential implementations and theoretical frameworks that we expect will help to better direct future studies aimed to unravel the epigenetic participation in AD.
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Affiliation(s)
- Jose V Sanchez-Mut
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Johannes Gräff
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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Differential DNA methylation of microRNAs within promoters, intergenic and intragenic regions of type 2 diabetic, pre-diabetic and non-diabetic individuals. Clin Biochem 2015; 49:433-438. [PMID: 26656639 DOI: 10.1016/j.clinbiochem.2015.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Accumulating evidence supports the role of epigenetic modifications, and in particular DNA methylation and non-coding RNAs in the pathophysiology of type 2 diabetes. Alterations in methylation patterns within promoter regions are linked with aberrant transcription and pathological gene expression; however the role of methylation within non-promoter regions is not yet fully elucidated. DESIGN AND METHODS We performed whole genome methylated DNA immunoprecipitation sequencing (MeDIP-Seq) in peripheral-blood-derived DNA from age-gender-body mass index (BMI)-ethnicity matched type 2 diabetic, pre-diabetic and non-diabetic individuals. RESULTS The density of methylation normalized to the average length of the promoter, intergenic and intragenic regions and to CpG count was 3.17, 9.80 and 0.09 for the promoter, intergenic and intragenic regions, respectively. Methylation within these regions varied according to glucose tolerance status and was associated with hypermethylation rather than hypomethylation. MicroRNA-DNA methylation peaks accounted for 4.8% of the total number of peaks detected. Differential DNA methylation of these microRNA peaks was observed during dysglycemia, with the promoter, intergenic and intragenic regions accounting for 2%, 95% and 3% respectively, of the differentially methylated microRNA peaks. CONCLUSION Genome-wide DNA methylation varied according to glucose tolerance. Methylation within non-promoter regions accounted for the majority of differentially methylated peaks identified, thus highlighting the importance of DNA methylation within these non-promoter regions in the pathogenesis of type 2 diabetes. This study suggests that DNA methylation within intergenic regions is a mechanism regulating microRNAs, another increasingly important epigenetic factor, during type 2 diabetes.
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Bhasin JM, Lee BH, Matkin L, Taylor MG, Hu B, Xu Y, Magi-Galluzzi C, Klein EA, Ting AH. Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing Indolent from Aggressive Prostate Cancer. Cell Rep 2015; 13:2135-46. [PMID: 26628371 DOI: 10.1016/j.celrep.2015.10.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/10/2015] [Accepted: 10/28/2015] [Indexed: 01/12/2023] Open
Abstract
A critical need in understanding the biology of prostate cancer is characterizing the molecular differences between indolent and aggressive cases. Because DNA methylation can capture the regulatory state of tumors, we analyzed differential methylation patterns genome-wide among benign prostatic tissue and low-grade and high-grade prostate cancer and found extensive, focal hypermethylation regions unique to high-grade disease. These hypermethylation regions occurred not only in the promoters of genes but also in gene bodies and at intergenic regions that are enriched for DNA-protein binding sites. Integration with existing RNA-sequencing (RNA-seq) and survival data revealed regions where DNA methylation correlates with reduced gene expression associated with poor outcome. Regions specific to aggressive disease are proximal to genes with distinct functions from regions shared by indolent and aggressive disease. Our compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer.
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Affiliation(s)
- Jeffrey M Bhasin
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Byron H Lee
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lars Matkin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Margaret G Taylor
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bo Hu
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Cristina Magi-Galluzzi
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Angela H Ting
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Zhang Y, Wang H, Zhou D, Moody L, Lezmi S, Chen H, Pan YX. High-fat diet caused widespread epigenomic differences on hepatic methylome in rat. Physiol Genomics 2015. [DOI: 10.1152/physiolgenomics.00110.2014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A high-fat (HF) diet is associated with progression of liver diseases. To illustrate genome-wide landscape of DNA methylation in liver of rats fed either a control or HF diet, two enrichment-based methods, namely methyl-DNA immunoprecipitation assay with high-throughput sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq), were performed in our study. Rats fed with the HF diet exhibited an increased body weight and liver fat accumulation compared with that of the control group when they were 12 wk of age. Genome-wide analysis of differentially methylated regions (DMRs) showed that 12,494 DMRs induced by HF diet were hypomethylated and 6,404 were hypermethylated. DMRs with gene annotations [differentially methylated genes (DMGs)] were further analyzed to show gene-specific methylation profile. There were 88, 2,680, and 95 hypomethylated DMGs identified with changes in DNA methylation in the promoter, intragenic and downstream regions, respectively, compared with fewer hypermethylated DMGs (45, 1,623, and 50 in the respective regions). Some of these genes also contained an ACGT cis-acting motif whose DNA methylation status may affect gene expression. Pathway analysis showed that these DMGs were involved in critical hepatic signaling networks related to hepatic development. Therefore, HF diet had global impacts on DNA methylation profile in the liver of rats, leading to differential expression of genes in hepatic pathways that may involve in functional changes in liver development.
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Affiliation(s)
- Yukun Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Huan Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Dan Zhou
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Stéphane Lezmi
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Hong Chen
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yuan-Xiang Pan
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois; and
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Devall M, Mill J, Lunnon K. The mitochondrial epigenome: a role in Alzheimer's disease? Epigenomics 2015; 6:665-75. [PMID: 25531259 DOI: 10.2217/epi.14.50] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Considerable evidence suggests that mitochondrial dysfunction occurs early in Alzheimer's disease, both in affected brain regions and in leukocytes, potentially precipitating neurodegeneration through increased oxidative stress. Epigenetic processes are emerging as a dynamic mechanism through which environmental signals may contribute to cellular changes, leading to neuropathology and disease. Until recently, little attention was given to the mitochondrial epigenome itself, as preliminary studies indicated an absence of DNA modifications. However, recent research has demonstrated that epigenetic changes to the mitochondrial genome do occur, potentially playing an important role in several disorders characterized by mitochondrial dysfunction. This review explores the potential role of mitochondrial epigenetic dysfunction in Alzheimer's disease etiology and discusses some technical issues pertinent to the study of these processes.
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Affiliation(s)
- Matthew Devall
- University of Exeter Medical School, RILD Level 4, Barrack Road, Exeter, Devon, UK
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Walker DL, Bhagwate AV, Baheti S, Smalley RL, Hilker CA, Sun Z, Cunningham JM. DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip. Epigenomics 2015; 7:1287-302. [PMID: 26192535 DOI: 10.2217/epi.15.64] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIMS To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling. METHODS DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K). RESULTS & CONCLUSION Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.
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Affiliation(s)
- Denise L Walker
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA
| | | | - Saurabh Baheti
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA
| | - Regenia L Smalley
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA
| | | | - Zhifu Sun
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.,Division of Experimental Pathology, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN, USA
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Bacalini MG, Boattini A, Gentilini D, Giampieri E, Pirazzini C, Giuliani C, Fontanesi E, Remondini D, Capri M, Del Rio A, Luiselli D, Vitale G, Mari D, Castellani G, Di Blasio AM, Salvioli S, Franceschi C, Garagnani P. A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging (Albany NY) 2015; 7:97-109. [PMID: 25701668 PMCID: PMC4359692 DOI: 10.18632/aging.100718] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Aging is characterized by a profound remodeling of the epigenetic architecture in terms of DNA methylation patterns. To date the most effective tool to study genome wide DNA methylation changes is Infinium HumanMethylation450 BeadChip (Infinium 450k). Despite the wealth of tools for Infinium 450k analysis, the identification of the most biologically relevant DNA methylation changes is still challenging. Here we propose an analytical pipeline to select differentially methylated regions (DMRs), tailored on microarray architecture, which is highly effective in highlighting biologically relevant results. The pipeline groups microarray probes on the basis of their localization respect to CpG islands and genic sequences and, depending on probes density, identifies DMRs through a single-probe or a region-centric approach that considers the concomitant variation of multiple adjacent CpG probes. We successfully applied this analytical pipeline on 3 independent Infinium 450k datasets that investigated age-associated changes in blood DNA methylation. We provide a consensus list of genes that systematically vary in DNA methylation levels from 0 to 100 years and that have a potentially relevant role in the aging process.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Personal Genomics S.r.l., Verona 37134, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Davide Gentilini
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Elisa Fontanesi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) National Research Council (CNR), Bologna 40126, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Daniela Mari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
| | - Anna Maria Di Blasio
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Milan 20095, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40138, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna 40126, Italy.,Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna 40138, Italy
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41
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The potential role of DNA methylation in the pathogenesis of abdominal aortic aneurysm. Atherosclerosis 2015; 241:121-9. [DOI: 10.1016/j.atherosclerosis.2015.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/20/2015] [Accepted: 05/03/2015] [Indexed: 12/18/2022]
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Sharp GC, Lawlor DA, Richmond RC, Fraser A, Simpkin A, Suderman M, Shihab HA, Lyttleton O, McArdle W, Ring SM, Gaunt TR, Davey Smith G, Relton CL. Maternal pre-pregnancy BMI and gestational weight gain, offspring DNA methylation and later offspring adiposity: findings from the Avon Longitudinal Study of Parents and Children. Int J Epidemiol 2015; 44:1288-304. [PMID: 25855720 PMCID: PMC4588865 DOI: 10.1093/ije/dyv042] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 01/08/2023] Open
Abstract
Background: Evidence suggests that in utero exposure to undernutrition and overnutrition might affect adiposity in later life. Epigenetic modification is suggested as a plausible mediating mechanism. Methods: We used multivariable linear regression and a negative control design to examine offspring epigenome-wide DNA methylation in relation to maternal and offspring adiposity in 1018 participants. Results: Compared with neonatal offspring of normal weight mothers, 28 and 1621 CpG sites were differentially methylated in offspring of obese and underweight mothers, respectively [false discovert rate (FDR)-corrected P-value < 0.05), with no overlap in the sites that maternal obesity and underweight relate to. A positive association, where higher methylation is associated with a body mass index (BMI) outside the normal range, was seen at 78.6% of the sites associated with obesity and 87.9% of the sites associated with underweight. Associations of maternal obesity with offspring methylation were stronger than associations of paternal obesity, supporting an intrauterine mechanism. There were no consistent associations of gestational weight gain with offspring DNA methylation. In general, sites that were hypermethylated in association with maternal obesity or hypomethylated in association with maternal underweight tended to be positively associated with offspring adiposity, and sites hypomethylated in association with maternal obesity or hypermethylated in association with maternal underweight tended to be inversely associated with offspring adiposity. Conclusions: Our data suggest that both maternal obesity and, to a larger degree, underweight affect the neonatal epigenome via an intrauterine mechanism, but weight gain during pregnancy has little effect. We found some evidence that associations of maternal underweight with lower offspring adiposity and maternal obesity with greater offspring adiposity may be mediated via increased DNA methylation.
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Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Abigail Fraser
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Andrew Simpkin
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Oliver Lyttleton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Wendy McArdle
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Susan M Ring
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK, School of Social and Community Medicine, University of Bristol, Bristol, UK and Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
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Ulahannan N, Greally JM. Genome-wide assays that identify and quantify modified cytosines in human disease studies. Epigenetics Chromatin 2015; 8:5. [PMID: 25788985 PMCID: PMC4363328 DOI: 10.1186/1756-8935-8-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/05/2015] [Indexed: 12/23/2022] Open
Abstract
The number of different assays that has been published to study DNA methylation is extensive, complemented by recently described assays that test modifications of cytosine other than the most abundant 5-methylcytosine (5mC) variant. In this review, we describe the considerations involved in choosing how to study 5mC throughout the genome, with an emphasis on the common application of testing for epigenetic dysregulation in human disease. While microarray studies of 5mC continue to be commonly used, these lack the additional qualitative information from sequencing-based approaches that is increasingly recognized to be valuable. When we test the representation of functional elements in the human genome by several current assay types, we find that no survey approach interrogates anything more than a small minority of the nonpromoter cis-regulatory sites where DNA methylation variability is now appreciated to influence gene expression and to be associated with human disease. However, whole-genome bisulphite sequencing (WGBS) adds a substantial representation of loci at which DNA methylation changes are unlikely to be occurring with transcriptional consequences. Our assessment is that the most effective approach to DNA methylation studies in human diseases is to use targeted bisulphite sequencing of the cis-regulatory loci in a cell type of interest, using a capture-based or comparable system, and that no single design of a survey approach will be suitable for all cell types.
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Affiliation(s)
- Netha Ulahannan
- Department of Genetics, Albert Einstein College of Medicine, Center for Epigenomics and Division of Computational Genetics, 1301 Morris Park Avenue, Bronx, NY 10461 USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Center for Epigenomics and Division of Computational Genetics, 1301 Morris Park Avenue, Bronx, NY 10461 USA
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Genome-wide analysis of methylation in bovine clones by methylated DNA immunoprecipitation (MeDIP). Methods Mol Biol 2015; 1222:267-80. [PMID: 25287353 DOI: 10.1007/978-1-4939-1594-1_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methylated DNA immunoprecipitation (MeDIP), when coupled to high-throughput sequencing or microarray hybridization, allows for the identification of methylated loci at a genome-wide scale. Genomic regions affected by incomplete reprogramming after nuclear transfer can potentially be delineated by comparing the MeDIP profiles of bovine clones and non-clones. This chapter presents a MeDIP protocol largely inspired from Mohn and colleagues (Mohn et al., Methods Mol Biol 507:55-64, 2009), with PCR primers specific for cattle, and when possible, overviews of experimental designs adapted to the comparison between clones and non-clones.
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45
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Corley MJ, Zhang W, Zheng X, Lum-Jones A, Maunakea AK. Semiconductor-based sequencing of genome-wide DNA methylation states. Epigenetics 2015; 10:153-66. [PMID: 25602802 PMCID: PMC4622511 DOI: 10.1080/15592294.2014.1003747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/15/2014] [Accepted: 12/22/2014] [Indexed: 12/17/2022] Open
Abstract
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we developed a MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is low cost, rapid, and scalable. We applied this protocol to demonstrate MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450 BeadChip array, and accurately identifies sites of differential DNA methylation. Furthermore, we applied an integrative approach to further investigate and confirm the role of DNA methylation in alternative splicing and to profile 5mC and 5hmC variants of DNA methylation in normal human brain tissue that is localized over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Wei Zhang
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Xin Zheng
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
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Jeschke J, Collignon E, Fuks F. DNA methylome profiling beyond promoters - taking an epigenetic snapshot of the breast tumor microenvironment. FEBS J 2014; 282:1801-14. [PMID: 25331982 DOI: 10.1111/febs.13125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/06/2014] [Accepted: 10/19/2014] [Indexed: 12/22/2022]
Abstract
Breast cancer, one of the most common and deadliest malignancies in developed countries, is a remarkably heterogeneous disease, which is clinically reflected by patients who display similar pathological features but respond differently to treatments. In the search for mediators of responsiveness, the tumor microenvironment (TME), in particular tumor-associated immune cells, has been pushed into the spotlight as it has become clear that the TME is an active component of breast cancer disease that affects clinical outcomes. Thus, the characterization of the TME in terms of cell identities and their frequencies has generated a great deal of interest. The common methods currently used for this purpose are either limited in accuracy or application, and DNA methylation has recently been proposed as an alternative approach. The aim of this review is to discuss DNA methylation profiling beyond promoters as a potential clinical tool for TME characterization and cell typing within tumors. With respect to this, we review the role of DNA methylation in breast cancer and cell-lineage specification, as well as inform about the composition and clinical relevance of the TME.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium
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47
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Epigenome-wide methylation in DNA from peripheral blood as a marker of risk for breast cancer. Breast Cancer Res Treat 2014; 148:665-73. [DOI: 10.1007/s10549-014-3209-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/11/2014] [Indexed: 02/07/2023]
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48
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Lockett GA, Patil VK, Soto-Ramírez N, Ziyab AH, Holloway JW, Karmaus W. Epigenomics and allergic disease. Epigenomics 2014; 5:685-99. [PMID: 24283882 DOI: 10.2217/epi.13.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Allergic disease development is affected by both genes and the environment, and epigenetic mechanisms are hypothesized to mediate these environmental effects. In this article, we discuss the link between the environment, DNA methylation and allergic disease, as well as questions of causality inherent to analyses of DNA methylation. From the practical side, we describe characteristics of allergic phenotypes and contrast different epidemiologic study designs used in epigenetic research. We examine methodological considerations, how best to conduct preprocessing and analysis of DNA methylation data sets, and the latest methods, technologies and discoveries in this rapidly advancing field. DNA methylation and other epigenetic marks are firmly entwined with allergic disease, a link that may hold the basis for future allergic disease diagnosis and treatment.
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Affiliation(s)
- Gabrielle A Lockett
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
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49
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Liyanage VRB, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR. DNA modifications: function and applications in normal and disease States. BIOLOGY 2014; 3:670-723. [PMID: 25340699 PMCID: PMC4280507 DOI: 10.3390/biology3040670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
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Affiliation(s)
- Vichithra R B Liyanage
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Nanditha Murugeshan
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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50
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Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep 2014; 4:6546. [PMID: 25306978 PMCID: PMC4194443 DOI: 10.1038/srep06546] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
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