1
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Chen T, Mahdadi S, Vidal M, Desbène-Finck S. Non-nucleoside inhibitors of DNMT1 and DNMT3 for targeted cancer therapy. Pharmacol Res 2024; 207:107328. [PMID: 39079576 DOI: 10.1016/j.phrs.2024.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
DNA methylation can deactivate tumor suppressor genes thus causing cancers. Two DNA methylation inhibitors have been approved by the Food and Drug Administration (FDA) and have entered clinical use. However, these inhibitors are nucleoside analogues that can be incorporated into DNA or RNA and induce significant side effects. DNMT1 and DNMT3 are key enzymes involved in DNA methylation. In the acute myeloid leukemia model, a non-nucleoside DNMT1-specific inhibitor has shown lower toxicity and improved pharmacokinetics compared to traditional nucleoside drugs. DNMT3 is also implicated in certain specific cancers. Thus, developing non-nucleoside inhibitors for DNMT1 or DNMT3 can help in understanding their roles in carcinogenesis and provide targeted treatment options in certain cancers. Although no non-nucleoside inhibitors have yet entered clinical trials, in this review, we focus on DNMT1 or DNMT3 selective inhibitors. For DNMT1 selective inhibitors, we have compiled information on the repurposed drugs, derivative compounds and selective inhibitors identified through virtual screening. Additionally, we have outlined potential targets for DNMT1, including protein-protein complex, RNA mimics and aptamers. Compared to DNMT1, research on DNMT3-specific inhibitors has been less extensive. In this context, our exploration has identified a limited number of molecular inhibitors, and we have proposed specific long non-coding RNAs (lncRNAs) as potential contributors to the selective inhibition of DNMT3. This collective effort aims to offer valuable insights into the development of non-nucleoside inhibitors that selectively target DNMT1 or DNMT3.
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Affiliation(s)
- Ting Chen
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Syrine Mahdadi
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France
| | - Michel Vidal
- UMR 8038 CNRS, U1268 INSERM, UFR de pharmacie, Université Paris cité, 75270, France; Toxicology, Cochin Hospital, HUPC, APHP, Paris 75014, France
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2
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Miao N, Zeng Z, Lee T, Guo Q, Zheng W, Cai W, Chen W, Wang J, Sun T. Integrative epigenome profiling of 47XXY provides insights into whole genomic DNA hypermethylation and active chromatin accessibility. Front Mol Biosci 2023; 10:1128739. [PMID: 37051325 PMCID: PMC10083376 DOI: 10.3389/fmolb.2023.1128739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Klinefelter syndrome (KS, 47XXY) is a disorder characterized by sex chromosomal aneuploidy, which may lead to changes in epigenetic regulations of gene expression. To define epigenetic architectures in 47XXY, we annotated DNA methylation in euploid males (46XY) and females (46XX), and 47XXY individuals using whole genome bisulfite sequencing (WGBS) and integrated chromatin accessbilty, and detected abnormal hypermethylation in 47XXY. Furthermore, we detected altered chromatin accessibility in 47XXY, in particular in chromosome X, using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) in cultured amniotic cells. Our results construct the whole genome-wide DNA methylation map in 47XXY, and provide new insights into the early epigenomic dysregulation resulting from an extra chromosome X in 47XXY.
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Affiliation(s)
- Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Zhiwei Zeng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, New York, NY, United States
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Wenwei Zheng
- Quanzhou Women and Children’s Hospital, Quanzhou, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wanhua Chen
- Department of Clinical Laboratory, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
- *Correspondence: Tao Sun,
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3
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Sapozhnikov DM, Szyf M. Enzyme-free targeted DNA demethylation using CRISPR-dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Nat Protoc 2022; 17:2840-2881. [PMID: 36207463 DOI: 10.1038/s41596-022-00741-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
DNA methylation involves the enzymatic addition of a methyl group primarily to cytosine residues in DNA. This protocol describes how to produce complete and minimally confounded DNA demethylation of specific sites in the genome of cultured cells by clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and without the involvement of an epigenetic-modifying enzyme, the purpose of which is the evaluation of the functional (i.e., gene expression or phenotypic) consequences of DNA demethylation of specific sites that have been previously implicated in particular pathological or physiological contexts. This protocol maximizes the ability of the easily reprogrammable CRISPR-dCas9 system to assess the impact of DNA methylation from a causal rather than correlational perspective: alternative protocols for CRISPR-dCas9-based site-specific DNA methylation or demethylation rely on the recruitment of epigenetic enzymes that exhibit additional nonspecific activities at both the targeted site and throughout the genome, confounding conclusions of causality of DNA methylation. Inhibition or loss of DNA methylation is accomplished by three consecutive lentiviral transductions. The first two lentiviruses establish stable expression of dCas9 and a guide RNA, which will physically obstruct either maintenance or de novo DNA methyltransferase activity at the guide RNA target site. A third lentivirus introduces Cre recombinase to delete the dCas9 transgene, which leads to loss of dCas9 from the target site, allowing transcription factors and/or the transcription machinery to interact with the demethylated target site. This protocol requires 3-8 months to complete owing to prolonged cell passaging times, but there is little hands-on time, and no specific skills beyond basic molecular biology techniques are necessary.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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4
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Kolkman R, Michel-Souzy S, Wasserberg D, Segerink LI, Huskens J. Density Control over MBD2 Receptor-Coated Surfaces Provides Superselective Binding of Hypermethylated DNA. ACS APPLIED MATERIALS & INTERFACES 2022; 14:40579-40589. [PMID: 36052432 PMCID: PMC9478954 DOI: 10.1021/acsami.2c09641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Using the biomarker hypermethylated DNA (hmDNA) for cancer detection requires a pretreatment to isolate or concentrate hmDNA from nonmethylated DNA. Affinity chromatography using a methyl binding domain-2 (MBD2) protein can be used, but the relatively low enrichment selectivity of MBD2 limits its clinical applicability. Here, we developed a superselective, multivalent, MBD2-coated platform to improve the selectivity of hmDNA enrichment. The multivalent platform employs control over the MBD2 surface receptor density, which is shown to strongly affect the binding of DNA with varying degrees of methylation, improving both the selectivity and the affinity of DNAs with higher numbers of methylation sites. Histidine-10-tagged MBD2 was immobilized on gold surfaces with receptor density control by tuning the amount of nickel nitrilotriacetic acid (NiNTA)-functionalized thiols in a thiol-based self-assembled monolayer. The required MBD2 surface receptor densities for DNA surface binding decreases for DNA with higher degrees of methylation. Both higher degrees of superselectivity and surface coverages were observed upon DNA binding at increasing methylation levels. Adopting the findings of this study into hmDNA enrichment of clinical samples has the potential to become more selective and sensitive than current MBD2-based methods and, therefore, to improve cancer diagnostics.
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Affiliation(s)
- Ruben
W. Kolkman
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Sandra Michel-Souzy
- Biomolecular
Nanotechnology Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Dorothee Wasserberg
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Loes I. Segerink
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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5
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Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022; 12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g., methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.
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Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:1-19. [DOI: 10.1007/978-3-031-11454-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Vasishta S, Umakanth S, Adiga P, Joshi MB. Extrinsic and intrinsic factors influencing metabolic memory in type 2 diabetes. Vascul Pharmacol 2021; 142:106933. [PMID: 34763098 DOI: 10.1016/j.vph.2021.106933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/18/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022]
Abstract
Direct and indirect influence of pathological conditions in Type 2 Diabetes (T2D) on vasculature manifests in micro and/or macro vascular complications that act as a major source of morbidity and mortality. Although preventive therapies exist to control hyperglycemia, diabetic subjects are always at risk to accrue vascular complications. One of the hypotheses explained is 'glycemic' or 'metabolic' memory, a process of permanent epigenetic change in different cell types whereby diabetes associated vascular complications continue despite glycemic control by antidiabetic drugs. Epigenetic mechanisms including DNA methylation possess a strong influence on the association between environment and gene expression, thus indicating its importance in the pathogenesis of a complex disease such as T2D. The vascular system is more prone to environmental influences and present high flexibility in response to physiological and pathological challenges. DNA methylation based epigenetic changes during metabolic memory are influenced by sustained hyperglycemia, inflammatory mediators, gut microbiome composition, lifestyle modifications and gene-nutrient interactions. Hence, understanding underlying mechanisms in manifesting vascular complications regulated by DNA methylation is of high clinical importance. The review provides an insight into various extrinsic and intrinsic factors influencing the regulation of DNA methyltransferases contributing to the pathogenesis of vascular complications during T2D.
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Affiliation(s)
- Sampara Vasishta
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shashikiran Umakanth
- Department of Medicine, Dr. T.M.A. Pai Hospital, Manipal Academy of Higher Education, Udupi 576101, Karnataka, India
| | - Prashanth Adiga
- Department of Reproductive Medicine and Surgery (MARC), Kasturba Hospital, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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8
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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9
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Application of 5-Methylcytosine DNA Glycosylase to the Quantitative Analysis of DNA Methylation. Int J Mol Sci 2021; 22:ijms22031072. [PMID: 33499041 PMCID: PMC7865733 DOI: 10.3390/ijms22031072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 02/03/2023] Open
Abstract
In higher eukaryotes DNA methylation is a prominent epigenetic mark important for chromatin structure and gene expression. Thus, profiling DNA methylation is important for predicting gene expressions associated with specific traits or diseases. DNA methylation is achieved by DNA methyltransferases and can be actively removed by specific enzymes in a replication-independent manner. DEMETER (DME) is a bifunctional 5-methylcytosine (5mC) DNA glycosylase responsible for active DNA demethylation that excises 5mC from DNA and cleaves a sugar-phosphate bond generating a single strand break (SSB). In this study, DME was used to analyze DNA methylation levels at specific epialleles accompanied with gain or loss of DNA methylation. DME treatment on genomic DNA generates SSBs in a nonsequence-specific fashion proportional to 5mC density, and thus DNA methylation levels can be easily measured when combined with the quantitative PCR (qPCR) method. The DME-qPCR analysis was applied to measure DNA methylation levels at the FWA gene in late-flowering Arabidopsis mutants and the CNR gene during fruit ripening in tomato. Differentially methylated epialleles were successfully distinguished corresponding to their expression levels and phenotypes. DME-qPCR is proven a simple yet effective method for quantitative DNA methylation analysis, providing advantages over current techniques based on methylation-sensitive restriction digestion.
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10
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Abstract
A complete understanding of the dynamics and function of cytosine modifications in mammalian biology is lacking. Central to achieving this understanding is the availability of techniques that permit sensitive and specific genome-wide mapping of DNA modifications in mammalian DNA. The last decade has seen the development of a vast arsenal of novel profiling approaches enabling epigeneticists to tackle research questions that were previously out of reach. Here, we review the techniques currently available for profiling DNA modifications in mammals, discuss their strengths and weaknesses, and speculate on the future direction of DNA modification profiling technologies.
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Affiliation(s)
- Antonio Lentini
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Colm E Nestor
- Department of Biomedical and Clinical Sciences (BKV), Crown Princess Victoria Children's Hospital, Linköping University, Linköping, Sweden.
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11
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Galardi F, De Luca F, Romagnoli D, Biagioni C, Moretti E, Biganzoli L, Di Leo A, Migliaccio I, Malorni L, Benelli M. Cell-Free DNA-Methylation-Based Methods and Applications in Oncology. Biomolecules 2020; 10:E1677. [PMID: 33334040 PMCID: PMC7765488 DOI: 10.3390/biom10121677] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy based on cell-free DNA (cfDNA) enables non-invasive dynamic assessment of disease status in patients with cancer, both in the early and advanced settings. The analysis of DNA-methylation (DNAm) from cfDNA samples holds great promise due to the intrinsic characteristics of DNAm being more prevalent, pervasive, and cell- and tumor-type specific than genomics, for which established cfDNA assays already exist. Herein, we report on recent advances on experimental strategies for the analysis of DNAm in cfDNA samples. We describe the main steps of DNAm-based analysis workflows, including pre-analytics of cfDNA samples, DNA treatment, assays for DNAm evaluation, and methods for data analysis. We report on protocols, biomolecular techniques, and computational strategies enabling DNAm evaluation in the context of cfDNA analysis, along with practical considerations on input sample requirements and costs. We provide an overview on existing studies exploiting cell-free DNAm biomarkers for the detection and monitoring of cancer in early and advanced settings, for the evaluation of drug resistance, and for the identification of the cell-of-origin of tumors. Finally, we report on DNAm-based tests approved for clinical use and summarize their performance in the context of liquid biopsy.
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Affiliation(s)
- Francesca Galardi
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Francesca De Luca
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Dario Romagnoli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Erica Moretti
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Laura Biganzoli
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Angelo Di Leo
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Ilenia Migliaccio
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
| | - Luca Malorni
- «Sandro Pitigliani» Translational Research Unit, Hospital of Prato, 59100 Prato, Italy; (F.G.); (F.D.L.); (I.M.); (L.M.)
- «Sandro Pitigliani» Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy; (E.M.); (L.B.); (A.D.L.)
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy; (D.R.); (C.B.)
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12
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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13
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Lecamwasam A, Ekinci EI, Saffery R, Dwyer KM. Potential for Novel Biomarkers in Diabetes-Associated Chronic Kidney Disease: Epigenome, Metabolome, and Gut Microbiome. Biomedicines 2020; 8:E341. [PMID: 32927866 PMCID: PMC7555227 DOI: 10.3390/biomedicines8090341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022] Open
Abstract
Diabetes-associated chronic kidney disease is a pandemic issue. Despite the global increase in the number of individuals with this chronic condition together with increasing morbidity and mortality, there are currently only limited therapeutic options to slow disease progression. One of the reasons for this is that the current-day "gold standard" biomarkers lack adequate sensitivity and specificity to detect early diabetic chronic kidney disease (CKD). This review focuses on the rapidly evolving areas of epigenetics, metabolomics, and the gut microbiome as potential sources of novel biomarkers in diabetes-associated CKD and discusses their relevance to clinical practice. However, it also highlights the problems associated with many studies within these three areas-namely, the lack of adequately powered longitudinal studies, and the lack of reproducibility of results which impede biomarker development and clinical validation in this complex and susceptible population.
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Affiliation(s)
- Ashani Lecamwasam
- Epigenetics Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Endocrinology, Austin Health, Ivanhoe, VIC 3079, Australia;
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds, VIC 3220, Australia;
| | - Elif I. Ekinci
- Department of Endocrinology, Austin Health, Ivanhoe, VIC 3079, Australia;
- Department of Medicine, University of Melbourne, Parkville, VIC 3010, Australia
| | - Richard Saffery
- Epigenetics Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Karen M. Dwyer
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds, VIC 3220, Australia;
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14
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Pajares MJ, Palanca-Ballester C, Urtasun R, Alemany-Cosme E, Lahoz A, Sandoval J. Methods for analysis of specific DNA methylation status. Methods 2020; 187:3-12. [PMID: 32640317 DOI: 10.1016/j.ymeth.2020.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/16/2020] [Accepted: 06/28/2020] [Indexed: 01/08/2023] Open
Abstract
Methylation of CpG dinucleotides plays a crucial role in the regulation of gene expression and therefore in the development of different pathologies. Aberrant methylation has been associated to the majority of the diseases, including cancer, neurodegenerative, cardiovascular and autoimmune disorders. Analysis of DNA methylation patterns is crucial to understand the underlying molecular mechanism of these diseases. Moreover, DNA methylation patterns could be used as biomarker for clinical management, such as diagnosis, prognosis and treatment response. Nowadays, a variety of high throughput methods for DNA methylation have been developed to analyze the methylation status of a high number of CpGs at once or even the whole genome. However, identification of specific methylation patterns at specific loci is essential for validation and also as a tool for diagnosis. In this review, we describe the most commonly used approaches to evaluate specific DNA methylation. There are three main groups of techniques that allow the identification of specific regions that are differentially methylated: bisulfite conversion-based methods, restriction enzyme-based approaches, and affinity enrichment-based assays. In the first group, specific restriction enzymes recognize and cleave unmethylated DNA, leaving methylated sequences intact. Bisulfite conversion methods are the most popular approach to distinguish methylated and unmethylated DNA. Unmethylated cytosines are deaminated to uracil by sodium bisulfite treatment, while the methyl cytosines remain unconverted. In the last group, proteins with methylation binding domains or antibodies against methyl cytosines are used to recognize methylated DNA. In this review, we provide the theoretical basis and the framework of each technique as well as the analysis of their strength and the weaknesses.
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Affiliation(s)
- María J Pajares
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain; IDISNA Navarra's Health Research Institute, 31008 Pamplona, Spain
| | - Cora Palanca-Ballester
- Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain
| | - Raquel Urtasun
- Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
| | - Ester Alemany-Cosme
- Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain
| | - Agustin Lahoz
- Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain.
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain; Epigenomics Core Facility, Health Research Institute la Fe, 46026 Valencia, Spain.
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15
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Li L, Lim SF, Puretzky A, Riehn R, Hallen HD. DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy. Biophys J 2019; 114:2498-2506. [PMID: 29874601 DOI: 10.1016/j.bpj.2018.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/22/2018] [Accepted: 04/10/2018] [Indexed: 01/04/2023] Open
Abstract
We show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm-1 and changes in the Raman peaks in the 1200-1700 cm-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm-1 and spectral intensity inversion at 1324 (C5=C6) and 1473 cm-1 (C4=N3) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C5=C6) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ∼1470 cm-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ∼1000 cm-1 peak and distribution of the signal in the 1200-1700 cm-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. The Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ∼259 nm excitation wavelength.
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Affiliation(s)
- Ling Li
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Shuang Fang Lim
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Alexander Puretzky
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Hans D Hallen
- Department of Physics, North Carolina State University, Raleigh, North Carolina.
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16
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Singh RK, Diaz PE, Binette F, Nasonkin IO. Immunohistochemical Detection of 5-Methylcytosine and 5-Hydroxymethylcytosine in Developing and Postmitotic Mouse Retina. J Vis Exp 2018. [PMID: 30222161 PMCID: PMC6235063 DOI: 10.3791/58274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The epigenetics of retinal development is a well-studied research field, which promises to bring a new level of understanding about the mechanisms of a variety of human retinal degenerative diseases and pinpoint new treatment approaches. The nuclear architecture of mouse retina is organized in two different patterns: conventional and inverted. Conventional pattern is universal where heterochromatin is localized to the periphery of the nucleus, while active euchromatin resides in the nuclear interior. In contrast, inverted nuclear pattern is unique to the adult rod photoreceptor cell nuclei where heterochromatin localizes to the nuclear center, and euchromatin resides in the nuclear periphery. DNA methylation is predominantly observed in chromocenters. DNA methylation is a dynamic covalent modification on the cytosine residues (5-methylcytosine, 5mC) of CpG dinucleotides that are enriched in the promoter regions of many genes. Three DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) participate in methylation of DNA during development. Detecting 5mC with immunohistochemical techniques is very challenging, contributing to variability in results, as all DNA bases including 5mC modified bases are hidden within the double-stranded DNA helix. However, detailed delineation of 5mC distribution during development is very informative. Here, we describe a reproducible technique for robust immunohistochemical detection of 5mC and another epigenetic DNA marker 5-hydroxymethylcytosine (5hmC), which colocalizes with the "open", transcriptionally active chromatin in developing and postmitotic mouse retina.
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17
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Martin LJ, Chang Q. DNA Damage Response and Repair, DNA Methylation, and Cell Death in Human Neurons and Experimental Animal Neurons Are Different. J Neuropathol Exp Neurol 2018; 77:636-655. [PMID: 29788379 PMCID: PMC6005106 DOI: 10.1093/jnen/nly040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurological disorders affecting individuals in infancy to old age elude interventions for meaningful protection against neurodegeneration, and preclinical work has not translated to humans. We studied human neuron responses to injury and death stimuli compared to those of animal neurons in culture under similar settings of insult (excitotoxicity, oxidative stress, and DNA damage). Human neurons were differentiated from a cortical neuron cell line and the embryonic stem cell-derived H9 line. Mouse neurons were differentiated from forebrain neural stem cells and embryonic cerebral cortex; pig neurons were derived from forebrain neural stem cells. Mitochondrial morphology was different in human and mouse neurons. Human and mouse neurons challenged with DNA-damaging agent camptothecin showed different chromatin condensation, cell death, and DNA damage sensor activation. DNA damage accumulation and repair kinetics differed among human, mouse, and pig neurons. Promoter CpG island methylation microarrays showed significant differential DNA methylation in human and mouse neurons after injury. Therefore, DNA damage response, DNA repair, DNA methylation, and autonomous cell death mechanisms in human neurons and experimental animal neurons are different.
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Affiliation(s)
- Lee J Martin
- Department of Pathology, Division of Neuropathology
- Pathobiology Graduate Training Program
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qing Chang
- Department of Pathology, Division of Neuropathology
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18
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Identification and expression of alternatively spliced novel isoforms of cancer associated MYD88 lacking death domain in mouse. Mol Biol Rep 2018; 45:699-711. [DOI: 10.1007/s11033-018-4209-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022]
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19
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Dinka H, Le MT. Analysis of Pig Vomeronasal Receptor Type 1 (V1R) Promoter Region Reveals a Common Promoter Motif but Poor CpG Islands. Anim Biotechnol 2017; 29:293-300. [PMID: 29120694 DOI: 10.1080/10495398.2017.1383915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Promoters are, generally, located immediately upstream of a transcription start site (TSS) and have a variety of regulatory motifs, such as transcription factors (TFs) and CpG islands (CGIs), that participate in the regulation of gene expression. Here analysis of the promoter region for pig vomeronasal receptor type 1 (V1R) was described. In the analysis, TSSs for pig V1R genes was first identified and five motifs (MV1, MV2, MV3, MV4, and MV5) were found that are shared by at least 50% of the pig V1R promoter input sequences from both strands. Among the five motifs, MV2 was identified as a common promoter motif shared by all (100%) pig V1R promoters. For further analysis, to better characterize and get deeper biological insight associated with MV2, TOMTOM web application was used. MV2 was compared to the known motif databases (such as JASPAR) to see if they are similar to a known regulatory motif (transcription factor). Hence, it was revealed that MV2 serves as the binding site mainly for the BetaBetaAlpha-zinc finger (BTB-ZF) transcription factor gene family to regulate expression of pig V1R genes. Moreover, it was shown that pig V1R promoters are CpG poor, suggesting that their gene expression regulation pattern is in tissue specific manner.
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Affiliation(s)
- Hunduma Dinka
- a Department of Applied Biology, School of Applied Natural Sciences , Adama Science and Technology University , Adama , Ethiopia.,b Department of Animal Biotechnology , Konkuk University , Seoul , South Korea
| | - Minh Thong Le
- b Department of Animal Biotechnology , Konkuk University , Seoul , South Korea
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20
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Angarica VE, Del Sol A. Bioinformatics Tools for Genome-Wide Epigenetic Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:489-512. [PMID: 28523562 DOI: 10.1007/978-3-319-53889-1_25] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetics play a central role in the regulation of many important cellular processes, and dysregulations at the epigenetic level could be the source of serious pathologies, such as neurological disorders affecting brain development, neurodegeneration, and intellectual disability. Despite significant technological advances for epigenetic profiling, there is still a need for a systematic understanding of how epigenetics shapes cellular circuitry, and disease pathogenesis. The development of accurate computational approaches for analyzing complex epigenetic profiles is essential for disentangling the mechanisms underlying cellular development, and the intricate interaction networks determining and sensing chromatin modifications and DNA methylation to control gene expression. In this chapter, we review the recent advances in the field of "computational epigenetics," including computational methods for processing different types of epigenetic data, prediction of chromatin states, and study of protein dynamics. We also discuss how "computational epigenetics" has complemented the fast growth in the generation of epigenetic data for uncovering the main differences and similarities at the epigenetic level between individuals and the mechanisms underlying disease onset and progression.
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Affiliation(s)
- Vladimir Espinosa Angarica
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg.
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg
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21
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Singh RK, Mallela RK, Hayes A, Dunham NR, Hedden ME, Enke RA, Fariss RN, Sternberg H, West MD, Nasonkin IO. Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina. Exp Eye Res 2017; 159:132-146. [PMID: 27865785 DOI: 10.1016/j.exer.2016.11.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 10/21/2016] [Accepted: 11/14/2016] [Indexed: 11/18/2022]
Abstract
Characterizing the role of epigenetic regulation in the mammalian retina is critical for understanding fundamental mechanisms of retinal development and disease. DNA methylation, an epigenetic modifier of genomic DNA, plays an important role in modulating networks of tissue and cell-specific gene expression. However, the impact of DNA methylation on retinal development and homeostasis of retinal neurons remains unclear. Here, we have created a tissue-specific DNA methyltransferase (Dnmt) triple mutant mouse in an effort to characterize the impact of DNA methylation on retinal development and homeostasis. An Rx-Cre transgene was used to drive targeted mutation of all three murine Dnmt genes in the mouse retina encoding major DNA methylation enzymes DNMT1, DNMT3A and DNMT3B. The triple mutant mice represent a hypomorph model since Dnmt1 catalytic activity was still present and excision of Dnmt3a and Dnmt3b had only about 90% efficiency. Mutation of all three Dnmts resulted in global genomic hypomethylation and dramatic reorganization of the photoreceptor and synaptic layers within retina. Transcriptome and proteomic analyses demonstrated enrichment of dysregulated phototransduction and synaptic genes. The 5 mC signal in triple mutant retina was confined to the central heterochromatin but reduced in the peripheral heterochromatin region of photoreceptor nuclei. In addition, we found a reduction of the 5 mC signal in ganglion cell nuclei. Collectively, this data suggests cooperation of all three Dnmts in the formation and homeostasis of photoreceptors and other retinal neurons within the mammalian retina, and highlight the relevance of epigenetic regulation to sensory retinal disorders and vision loss.
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Affiliation(s)
- Ratnesh K Singh
- Department of Ophthalmology, University of Pittsburgh Medical School, USA.
| | - Ramya K Mallela
- Department of Ophthalmology, University of Pittsburgh Medical School, USA
| | - Abigail Hayes
- Department of Ophthalmology, West Virginia University, USA
| | | | | | - Raymond A Enke
- Department of Biology, James Madison University, USA; Center for Genome and Metagenome Studies, James Madison University, USA
| | - Robert N Fariss
- Biological Imaging Core, National Eye Institute, Bethesda, MD 20892, USA
| | - Hal Sternberg
- BioTime, 1010 Atlantic Avenue, Alameda, CA 94501, USA
| | | | - Igor O Nasonkin
- Department of Ophthalmology, University of Pittsburgh Medical School, USA.
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22
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Liu Y, Song C, Ladas I, Fitarelli-Kiehl M, Makrigiorgos GM. Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease. Nucleic Acids Res 2017; 45:e39. [PMID: 27903892 PMCID: PMC5389605 DOI: 10.1093/nar/gkw1166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes.
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Affiliation(s)
- Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariana Fitarelli-Kiehl
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA,To whom correspondence should be addressed. Tel: +1 617 525 7122; Fax: +1 617 582 6037;
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23
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Kong EY, Cheng SH, Yu KN. Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation. Int J Mol Sci 2016; 17:ijms17122108. [PMID: 27983682 PMCID: PMC5187908 DOI: 10.3390/ijms17122108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into “targeted” effects and “non-targeted” effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology. This review briefly describes both “targeted” and “non-targeted” effects, describes the findings in radiation biology using zebrafish as a model and highlights the potential of zebrafish to assess the epigenetic effects of IR, including DNA methylation, histone modifications and miRNA expression. Other in vivo models are included to compare observations made with zebrafish, or to illustrate the feasibility of in vivo models when the use of zebrafish was unavailable. Finally, tools to study epigenetic modifications in zebrafish, including changes in genome-wide DNA methylation, histone modifications and miRNA expression, are also described in this review.
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Affiliation(s)
- Eva Yi Kong
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
| | - Shuk Han Cheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
| | - Kwan Ngok Yu
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
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24
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von Watzdorf J, Marx A. 6-Substituted 2-Aminopurine-2'-deoxyribonucleoside 5'-Triphosphates that Trace Cytosine Methylation. Chembiochem 2016; 17:1532-40. [PMID: 27253512 PMCID: PMC5095873 DOI: 10.1002/cbic.201600245] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 12/26/2022]
Abstract
Gene expression is extensively regulated by the occurrence and distribution of the epigenetic marker 2′‐deoxy 5‐methylcytosine (5mC) in genomic DNA. Because of its effects on tumorigenesis there is an important link to human health. In addition, detection of 5mC can serve as an outstanding biomarker for diagnostics as well as for disease therapy. Our previous studies have already shown that, by processing O6‐alkylated 2′‐deoxyguanosine triphosphate (dGTP) analogues, DNA polymerases are able to sense the presence of a single 5mC unit in a template. Here we present the synthesis and evaluation of an extended toolbox of 6‐substituted 2‐aminopurine‐2′‐deoxyribonucleoside 5′‐triphosphates modified at position 6 with various functionalities. We found that sensing of 5‐methylation by this class of nucleotides is more general, not being restricted to O6‐alkyl modification of dGTP but also applying to other functionalities.
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Affiliation(s)
- Janina von Watzdorf
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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25
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Ansari J, Shackelford RE, El-Osta H. Epigenetics in non-small cell lung cancer: from basics to therapeutics. Transl Lung Cancer Res 2016; 5:155-71. [PMID: 27186511 DOI: 10.21037/tlcr.2016.02.02] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer remains the number one cause of cancer-related deaths worldwide with 221,200 estimated new cases and 158,040 estimated deaths in 2015. Approximately 80% of cases are non-small cell lung cancer (NSCLC). The diagnosis is usually made at an advanced stage where the prognosis is poor and therapeutic options are limited. The evolution of lung cancer is a multistep process involving genetic, epigenetic, and environmental factor interactions that result in the dysregulation of key oncogenes and tumor suppressor genes, culminating in activation of cancer-related signaling pathways. The past decade has witnessed the discovery of multiple molecular aberrations that drive lung cancer growth, among which are epidermal growth factor receptor (EGFR) mutations and translocations involving the anaplastic lymphoma kinase (ALK) gene. This has translated into therapeutic agent developments that target these molecular alterations. The absence of targetable mutations in 50% of NSCLC cases and targeted therapy resistance development underscores the importance for developing alternative therapeutic strategies for treating lung cancer. Among these strategies, pharmacologic modulation of the epigenome has been used to treat lung cancer. Epigenetics approaches may circumvent the problem of tumor heterogeneity by affecting the expression of multiple tumor suppression genes (TSGs), halting tumor growth and survival. Moreover, it may be effective for tumors that are not driven by currently recognized druggable mutations. This review summarizes the molecular pathology of lung cancer epigenetic aberrations and discusses current efforts to target the epigenome with different pharmacological approaches. Our main focus will be on hypomethylating agents, histone deacetylase (HDAC) inhibitors, microRNA modulations, and the role of novel epigenetic biomarkers. Last, we will address the challenges that face this old-new strategy in treating lung cancer.
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Affiliation(s)
- Junaid Ansari
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Rodney E Shackelford
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Hazem El-Osta
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
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26
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von Watzdorf J, Leitner K, Marx A. Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine. Angew Chem Int Ed Engl 2016; 55:3229-32. [PMID: 26835661 PMCID: PMC4949677 DOI: 10.1002/anie.201511520] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/31/2022]
Abstract
5‐Methyl‐2′‐deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. Therefore, the detection of 5mC can serve as an important biomarker for diagnostics. Here we describe that modified dGTP analogues as well as modified primers are able to sense the presence or absence of a single methylation of C, even though this modification does not interfere directly with Watson–Crick nucleobase pairing. By screening several modified nucleotide scaffolds, O6‐modified 2′‐deoxyguanosine analogues were identified as discriminating between C and 5mC. These modified nucleotides might find application in site‐specific 5mC detection, for example, through real‐time PCR approaches.
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Affiliation(s)
- Janina von Watzdorf
- Fachbereich Chemie, Graduiertenschule Chemische, Biologie Konstanz, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Deutschland
| | - Kim Leitner
- Fachbereich Chemie, Graduiertenschule Chemische, Biologie Konstanz, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische, Biologie Konstanz, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Deutschland.
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27
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von Watzdorf J, Leitner K, Marx A. Modifizierte Nukleotide für die Diskriminierung zwischen Cytosin und dem epigenetischen Marker 5-Methylcytosin. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Janina von Watzdorf
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Kim Leitner
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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28
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Xu C, Wu J, Liu W, Hong T, Wang T, Zhang X, Fu B, Wu F, Wu Z, Zhou X. Detecting 5-methylcytosine using an enzyme-free DNA strand exchange reaction without pretreatment under physiological conditions. Chem Commun (Camb) 2016; 52:6833-6. [DOI: 10.1039/c6cc03138b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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Choi M, Lee J, Le MT, Nguyen DT, Park S, Soundrarajan N, Schachtschneider KM, Kim J, Park JK, Kim JH, Park C. Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA Res 2015; 22:343-55. [PMID: 26358297 PMCID: PMC4596400 DOI: 10.1093/dnares/dsv017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/31/2015] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays a major role in the epigenetic regulation of gene expression. Although a few DNA methylation profiling studies of porcine genome which is one of the important biomedical models for human diseases have been reported, the available data are still limited. We tried to study methylation patterns of diverse pig tissues as a study of the International Swine Methylome Consortium to generate the swine reference methylome map to extensively evaluate the methylation profile of the pig genome at a single base resolution. We generated and analysed the DNA methylome profiles of five different tissues and a cell line originated from pig. On average, 39.85 and 62.1% of cytosine and guanine dinucleotides (CpGs) of CpG islands and 2 kb upstream of transcription start sites were covered, respectively. We detected a low rate (an average of 1.67%) of non-CpG methylation in the six samples except for the neocortex (2.3%). The observed global CpG methylation patterns of pigs indicated high similarity to other mammals including humans. The percentage of CpG methylation associated with gene features was similar among the tissues but not for a 3D4/2 cell line. Our results provide essential information for future studies of the porcine epigenome.
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Affiliation(s)
- Minkyeung Choi
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Jongin Lee
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Min Thong Le
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Dinh Truong Nguyen
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Suhyun Park
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | | | - Kyle M Schachtschneider
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Jin-Ki Park
- Animal Biotechnology Division, National Institute of Animal Science, Suwon, Korea
| | - Jin-Hoi Kim
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Chankyu Park
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
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Ji L, Neumann DA, Schmitz RJ. Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes. MOLECULAR PLANT 2015; 8:860-70. [PMID: 25638564 PMCID: PMC5121661 DOI: 10.1016/j.molp.2015.01.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 05/19/2023]
Abstract
DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically heritable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base resolution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methylation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be targeted for reactivation leading to phenotypic variation.
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Affiliation(s)
- Lexiang Ji
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Drexel A Neumann
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Jung M, Kadam S, Xiong W, Rauch TA, Jin SG, Pfeifer GP. MIRA-seq for DNA methylation analysis of CpG islands. Epigenomics 2015; 7:695-706. [PMID: 25881900 PMCID: PMC4607651 DOI: 10.2217/epi.15.33] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Aim: To develop a reliable method for whole genome analysis of DNA methylation. Materials & methods: Genome-scale analysis of DNA methylation includes affinity-based approaches such as enrichment using methyl-CpG-binding proteins. One of these methods, the methylated-CpG island recovery assay (MIRA), is based on the high affinity of the MBD2b-MBD3L1 complex for CpG-methylated DNA. Here we provide a detailed description of MIRA and combine it with next generation sequencing platforms (MIRA-seq). Results: We assessed the performance of MIRA-seq and compared the data with whole genome bisulfite sequencing. Conclusion: MIRA-seq is a reliable, genome-scale DNA methylation analysis platform for scoring DNA methylation differences at CpG-rich genomic regions. The method is not limited by primer or probe design and is cost effective.
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Affiliation(s)
- Marc Jung
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Swati Kadam
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Wenying Xiong
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Tibor A Rauch
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Seung-Gi Jin
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.,Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.,Van Andel Research Institute, Grand Rapids, MI 49503, USA
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Shire A, Lomberk G, Lai JP, Zou H, Tsuchiya N, Aderca I, Moser CD, Gulaid KH, Oseini A, Hu C, Warsame O, Jenkins RB, Roberts LR. Restoration of epigenetically silenced SULF1 expression by 5-aza-2-deoxycytidine sensitizes hepatocellular carcinoma cells to chemotherapy-induced apoptosis. ACTA ACUST UNITED AC 2015; 3:1-18. [PMID: 26236329 PMCID: PMC4520440 DOI: 10.1159/000375461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is the second most frequent cause of cancer death worldwide. Sulfatase 1 (SULF1) functions as a tumor suppressor in HCC cell lines in vitro but also has an oncogenic effect in some HCCs in vivo. Aim The purpose of this study was to examine the mechanisms regulating SULF1 and its function in HCC. Methods First, SULF1 mRNA and protein expression were examined. Second, we examined SULF1 gene copy numbers in HCC cells. Third, we assessed whether DNA methylation or methylation and/or acetylation of histone marks on the promoter regulate SULF1 expression. Finally, we examined the effect of 5-aza-2′-deoxycytidine (5-Aza-dC) on sulfatase activity and drug-induced apoptosis. Results SULF1 mRNA was downregulated in nine of eleven HCC cell lines, but only in six of ten primary tumors. SULF1 mRNA correlated with protein expression. Gene copy number assessment by fluorescence in situ hybridization showed intact SULF1 alleles in low-SULF1-expressing cell lines. CpG island methylation in the SULF1 promoter and two downstream CpG islands did not show an inverse correlation between DNA methylation and SULF1 expression. However, chromatin immunoprecipitation showed that the SULF1 promoter acquires a silenced chromatin state in low-SULF1-expressing cells through an increase in di/trimethyl-K9H3 and trimethyl-K27H3 and a concomitant loss of activating acetyl K9, K14H3 marks. 5-Aza-dC restored SULF1 mRNA expression in SULF1-negative cell lines, with an associated increase in sulfatase activity and sensitization of HCC cells to cisplatin-induced apoptosis. Conclusion SULF1 gene silencing in HCC occurs through histone modifications on the SULF1 promoter. Restoration of SULF1 mRNA expression by 5-Aza-dC sensitized HCC cells to drug-induced apoptosis.
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Affiliation(s)
- Abdirashid Shire
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Gwen Lomberk
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Jin-Ping Lai
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Hongzhi Zou
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Norihiko Tsuchiya
- Department of Urology, Akita University School of Medicine, Akita 010-8543 Japan
| | - Ileana Aderca
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Catherine D Moser
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Kadra H Gulaid
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Abdul Oseini
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Chunling Hu
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Omar Warsame
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
| | - Robert B Jenkins
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology College of Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic and Mayo Clinic Cancer Center, Rochester, MN, 55905 USA
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Schübeler D. ESCI award lecture: regulation, function and biomarker potential of DNA methylation. Eur J Clin Invest 2015; 45:288-93. [PMID: 25608229 DOI: 10.1111/eci.12403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/15/2015] [Indexed: 12/19/2022]
Abstract
Methylation of DNA and modifications of histones have emerged as intricately involved in gene regulation as they cross-talk and respond in multiple ways to the activity of transcription factors. Measuring these epigenome components has become a powerful tool to identify regulatory principles and biomarkers that predict cellular state during development or disease. Here, I will focus on DNA methylation as a reversible epigenetic modification of DNA that has been studied in great detail at the level of the genome. Recent advances in sequencing have identified unexpected dynamics of this modification, which are tightly linked to gene regulation. Understanding how DNA methylation patterns are read and how they contribute to regulation will be critical to interpret and utilize genomic maps of DNA methylation. As these patterns are dynamic during cellular differentiation and perturbed in disease, they present an opportunity to use DNA methylation as a biomarker.
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Affiliation(s)
- Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Faculty of Science, Basel, Switzerland
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34
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Oh G, Wang SC, Pal M, Chen ZF, Khare T, Tochigi M, Ng C, Yang YA, Kwan A, Kaminsky ZA, Mill J, Gunasinghe C, Tackett JL, Gottesman II, Willemsen G, de Geus EJ, Vink JM, Slagboom PE, Wray NR, Heath AC, Montgomery GW, Turecki G, Martin NG, Boomsma DI, McGuffin P, Kustra R, Petronis A. DNA modification study of major depressive disorder: beyond locus-by-locus comparisons. Biol Psychiatry 2015; 77:246-255. [PMID: 25108803 PMCID: PMC4277915 DOI: 10.1016/j.biopsych.2014.06.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 06/06/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) exhibits numerous clinical and molecular features that are consistent with putative epigenetic misregulation. Despite growing interest in epigenetic studies of psychiatric diseases, the methodologies guiding such studies have not been well defined. METHODS We performed DNA modification analysis in white blood cells from monozygotic twins discordant for MDD, in brain prefrontal cortex, and germline (sperm) samples from affected individuals and control subjects (total N = 304) using 8.1K CpG island microarrays and fine mapping. In addition to the traditional locus-by-locus comparisons, we explored the potential of new analytical approaches in epigenomic studies. RESULTS In the microarray experiment, we detected a number of nominally significant DNA modification differences in MDD and validated selected targets using bisulfite pyrosequencing. Some MDD epigenetic changes, however, overlapped across brain, blood, and sperm more often than expected by chance. We also demonstrated that stratification for disease severity and age may increase the statistical power of epimutation detection. Finally, a series of new analytical approaches, such as DNA modification networks and machine-learning algorithms using binary and quantitative depression phenotypes, provided additional insights on the epigenetic contributions to MDD. CONCLUSIONS Mapping epigenetic differences in MDD (and other psychiatric diseases) is a complex task. However, combining traditional and innovative analytical strategies may lead to identification of disease-specific etiopathogenic epimutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Art Petronis
- Institute of Systems Biology and Bioinformatics, National Central University, Chungli, Taiwan.
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Abstract
The introduction of novel technologies that can be applied to the investigation of the molecular underpinnings of human cancer has allowed for new insights into the mechanisms associated with tumor development and progression. They have also advanced the diagnosis, prognosis and treatment of cancer. These technologies include microarray and other analysis methods for the generation of large-scale gene expression data on both mRNA and miRNA, next-generation DNA sequencing technologies utilizing a number of platforms to perform whole genome, whole exome, or targeted DNA sequencing to determine somatic mutational differences and gene rearrangements, and a variety of proteomic analysis platforms including liquid chromatography/mass spectrometry (LC/MS) analysis to survey alterations in protein profiles in tumors. One other important advancement has been our current ability to survey the methylome of human tumors in a comprehensive fashion through the use of sequence-based and array-based methylation analysis (Bock et al., Nat Biotechnol 28:1106-1114, 2010; Harris et al., Nat Biotechnol 28:1097-1105, 2010). The focus of this chapter is to present and discuss the evidence for key genes involved in prostate tumor development, progression, or resistance to therapy that are regulated by methylation-induced silencing.
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Affiliation(s)
- Tawnya C McKee
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, Diagnostic Biomarkers and Technology Branch, National Cancer Institute, Bethesda, MD, 20892-7430, USA
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36
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Abstract
Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
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37
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Kubik G, Summerer D. Achieving single-nucleotide resolution of 5-methylcytosine detection with TALEs. Chembiochem 2014; 16:228-31. [PMID: 25522353 DOI: 10.1002/cbic.201402408] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Indexed: 12/30/2022]
Abstract
We report engineered transcription-activator-like effectors (TALEs) as the first DNA-binding molecules that detect 5-methylcytosine (mC) at single-nucleotide resolution with fully programmable sequence selectivity. This is achieved by a design strategy such that a single cytosine (C) in a DNA sequence is selectively interrogated for its mC-modification level by targeting with a discriminatory TALE repeat; other Cs are ignored by targeting with universal-binding TALE repeats.
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Affiliation(s)
- Grzegorz Kubik
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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Kungulovski G, Kycia I, Tamas R, Jurkowska RZ, Kudithipudi S, Henry C, Reinhardt R, Labhart P, Jeltsch A. Application of histone modification-specific interaction domains as an alternative to antibodies. Genome Res 2014; 24:1842-53. [PMID: 25301795 PMCID: PMC4216925 DOI: 10.1101/gr.170985.113] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we successfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies.
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Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Ina Kycia
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Raluca Tamas
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | | | | | | | | | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany;
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Abstract
The skin is composed of a variety of cell types expressing specific molecules and possessing different properties that facilitate the complex interactions and intercellular communication essential for maintaining the structural integrity of the skin. Importantly, a single mutation in one of these molecules can disrupt the entire organization and function of these essential networks, leading to cell separation, blistering, and other striking phenotypes observed in inherited skin diseases. Over the past several decades, the genetic basis of many monogenic skin diseases has been elucidated using classical genetic techniques. Importantly, the findings from these studies has shed light onto the many classes of molecules and essential genetic as well as molecular interactions that lend the skin its rigid, yet flexible properties. With the advent of the human genome project, next-generation sequencing techniques, as well as several other recently developed methods, tremendous progress has been made in dissecting the genetic architecture of complex, non-Mendelian skin diseases.
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Affiliation(s)
- Gina M DeStefano
- Department of Genetics and Development, Columbia University, New York, New York 10032
| | - Angela M Christiano
- Department of Genetics and Development, Columbia University, New York, New York 10032 Department of Dermatology, Columbia University, New York, New York 10032
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Methylation-associated gene silencing of RARB in areca carcinogens induced mouse oral squamous cell carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:378358. [PMID: 25197641 PMCID: PMC4150525 DOI: 10.1155/2014/378358] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/08/2014] [Accepted: 06/10/2014] [Indexed: 12/17/2022]
Abstract
Regarding oral squamous cell carcinoma (OSCC) development, chewing areca is known to be a strong risk factor in many Asian cultures. Therefore, we established an OSCC induced mouse model by 4-nitroquinoline-1-oxide (4-NQO), or arecoline, or both treatments, respectively. These are the main two components of the areca nut that could increase the occurrence of OSCC. We examined the effects with the noncommercial MCGI (mouse CpG islands) microarray for genome-wide screening the DNA methylation aberrant in induced OSCC mice. The microarray results showed 34 hypermethylated genes in 4-NQO plus arecoline induced OSCC mice tongue tissues. The examinations also used methylation-specific polymerase chain reaction (MS-PCR) and bisulfite sequencing to realize the methylation pattern in collected mouse tongue tissues and human OSCC cell lines of different grades, respectively. These results showed that retinoic acid receptor β (RARB) was indicated in hypermethylation at the promoter region and the loss of expression during cancer development. According to the results of real-time PCR, it was shown that de novo DNA methyltransferases were involved in gene epigenetic alternations of OSCC. Collectively, our results showed that RARB hypermethylation was involved in the areca-associated oral carcinogenesis.
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Aschenbrenner J, Drum M, Topal H, Wieland M, Marx A. Direct sensing of 5-methylcytosine by polymerase chain reaction. Angew Chem Int Ed Engl 2014; 53:8154-8. [PMID: 24923910 PMCID: PMC4499253 DOI: 10.1002/anie.201403745] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/22/2022]
Abstract
The epigenetic control of genes by the methylation of cytosine resulting in 5-methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3'-mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation-specific PCR approach directly from untreated human genomic DNA.
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Affiliation(s)
- Joos Aschenbrenner
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Matthias Drum
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Hüsnü Topal
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Markus Wieland
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of KonstanzUniversitätsstrasse 10, 78457 Konstanz (Germany)
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Aschenbrenner J, Drum M, Topal H, Wieland M, Marx A. Detektion von 5-Methylcytosin in unbehandelter genomischer DNA durch Polymerasekettenreaktion. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Shojaei Saadi HA, O'Doherty AM, Gagné D, Fournier É, Grant JR, Sirard MA, Robert C. An integrated platform for bovine DNA methylome analysis suitable for small samples. BMC Genomics 2014; 15:451. [PMID: 24912542 PMCID: PMC4092217 DOI: 10.1186/1471-2164-15-451] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/28/2014] [Indexed: 01/16/2023] Open
Abstract
Background Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10 ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability. Results The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions (shore, shelf and open-sea) and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts. Conclusions This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-451) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Institut des nutraceutiques et des aliments fonctionnels, Faculté des sciences de l'agriculture et de l'alimentation, Pavillon des services, Université Laval, Québec G1V 0A6, Canada.
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44
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Kubik G, Schmidt MJ, Penner JE, Summerer D. Programmierbare und hochaufgelöste In-vitro-Detektion von genomischem 5-Methylcytosin durch TALEs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Kubik G, Schmidt MJ, Penner JE, Summerer D. Programmable and highly resolved in vitro detection of 5-methylcytosine by TALEs. Angew Chem Int Ed Engl 2014; 53:6002-6. [PMID: 24801054 DOI: 10.1002/anie.201400436] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/25/2014] [Indexed: 01/20/2023]
Abstract
Gene expression is extensively regulated by specific patterns of genomic 5-methylcytosine (mC), but the ability to directly detect this modification at user-defined genomic loci is limited. One reason is the lack of molecules that discriminate between mC and cytosine (C) and at the same time provide inherent, programmable sequence-selectivity. Programmable transcription-activator-like effectors (TALEs) have been observed to exhibit mC-sensitivity in vivo, but to only a limited extent in vitro. We report an mC-detection assay based on TALE control of DNA replication that displays unexpectedly strong mC-discrimination ability in vitro. The status and level of mC modification at single positions in oligonucleotides can be determined unambiguously by this assay, independently of the overall target sequence. Moreover, discrimination is reliably observed for positions bound by N-terminal and central regions of TALEs. This indicates the wide scope and robustness of the approach for highly resolved mC detection and enabled the detection of a single mC in a large, eukaryotic genome.
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Affiliation(s)
- Grzegorz Kubik
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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Abollo-Jiménez F, Campos-Sánchez E, Toboso-Navasa A, Vicente-Dueñas C, González-Herrero I, Alonso-Escudero E, González M, Segura V, Blanco O, Martínez-Climent JA, Sánchez-García I, Cobaleda C. Lineage-specific function of Engrailed-2 in the progression of chronic myelogenous leukemia to T-cell blast crisis. Cell Cycle 2014; 13:1717-26. [PMID: 24675889 DOI: 10.4161/cc.28629] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In hematopoietic malignancies, oncogenic alterations interfere with cellular differentiation and lead to tumoral development. Identification of the proteins regulating differentiation is essential to understand how they are altered in malignancies. Chronic myelogenous leukemia (CML) is a biphasic disease initiated by an alteration taking place in hematopoietic stem cells. CML progresses to a blast crisis (BC) due to a secondary differentiation block in any of the hematopoietic lineages. However, the molecular mechanisms of CML evolution to T-cell BC remain unclear. Here, we have profiled the changes in DNA methylation patterns in human samples from BC-CML, in order to identify genes whose expression is epigenetically silenced during progression to T-cell lineage-specific BC. We have found that the CpG-island of the ENGRAILED-2 (EN2) gene becomes methylated in this progression. Afterwards, we demonstrate that En2 is expressed during T-cell development in mice and humans. Finally, we further show that genetic deletion of En2 in a CML transgenic mouse model induces a T-cell lineage BC that recapitulates human disease. These results identify En2 as a new regulator of T-cell differentiation whose disruption induces a malignant T-cell fate in CML progression, and validate the strategy used to identify new developmental regulators of hematopoiesis.
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Affiliation(s)
- Fernando Abollo-Jiménez
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer; CSIC/ Universidad de Salamanca; Campus M. de Unamuno; Institute of Biomedical Research of Salamanca (IBSAL); Salamanca, Spain
| | - Elena Campos-Sánchez
- Centro de Biología Molecular Severo Ochoa; CSIC/Universidad Autónoma de Madrid; Campus de Cantoblanco; Madrid, Spain
| | - Amparo Toboso-Navasa
- Centro de Biología Molecular Severo Ochoa; CSIC/Universidad Autónoma de Madrid; Campus de Cantoblanco; Madrid, Spain; Current affiliation: Immunity and Cancer Laboratory; London Research Institute; Cancer Research UK; London, UK
| | - Carolina Vicente-Dueñas
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer; CSIC/ Universidad de Salamanca; Campus M. de Unamuno; Institute of Biomedical Research of Salamanca (IBSAL); Salamanca, Spain
| | - Inés González-Herrero
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer; CSIC/ Universidad de Salamanca; Campus M. de Unamuno; Institute of Biomedical Research of Salamanca (IBSAL); Salamanca, Spain
| | - Esther Alonso-Escudero
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer; CSIC/ Universidad de Salamanca; Campus M. de Unamuno; Institute of Biomedical Research of Salamanca (IBSAL); Salamanca, Spain
| | - Marcos González
- Department of Hematology, University Hospital of Salamanca; Institute of Biomedical Research of Salamanca; Salamanca, Spain
| | - Víctor Segura
- Bioinformatics Unit; Center for Applied Medical Research; University of Navarra; Pamplona, Spain
| | - Oscar Blanco
- Departamento de Anatomía Patológica; Universidad de Salamanca; Salamanca, Spain
| | | | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer; CSIC/ Universidad de Salamanca; Campus M. de Unamuno; Institute of Biomedical Research of Salamanca (IBSAL); Salamanca, Spain
| | - César Cobaleda
- Centro de Biología Molecular Severo Ochoa; CSIC/Universidad Autónoma de Madrid; Campus de Cantoblanco; Madrid, Spain
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Jiménez-Chillarón JC, Díaz R, Ramón-Krauel M. Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00004-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
Epigenetics has undergone an explosion in the past decade. DNA methylation, consisting of the addition of a methyl group at the fifth position of cytosine (5-methylcytosine, 5-mC) in a CpG dinucleotide, is a well-recognized epigenetic mark with important functions in cellular development and pathogenesis. Numerous studies have focused on the characterization of DNA methylation marks associated with disease development as they may serve as useful biomarkers for diagnosis, prognosis, and prediction of response to therapy. Recently, novel cytosine modifications with potential regulatory roles such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC) have been discovered. Study of the functions of 5-mC and its oxidation derivatives promotes the understanding of the mechanism underlying association of epigenetic modifications with disease biology. In this respect, much has been accomplished in the development of methods for the discovery, detection, and location analysis of 5-mC and its oxidation derivatives. In this review, we focus on the recent advances for the global detection and location study of 5-mC and its oxidation derivatives 5-hmC, 5-foC, and 5-caC.
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Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med 2013; 5:169ra10. [PMID: 23345608 DOI: 10.1126/scitranslmed.3005211] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cancers almost ubiquitously harbor epigenetic alterations. Although such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. We carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation "cityscape" plots to visualize these complex data. We show that somatic DNA methylation alterations, despite showing marked interindividual heterogeneity among men with lethal metastatic prostate cancer, were maintained across all metastases within the same individual. The overall extent of maintenance in DNA methylation changes was comparable to that of genetic copy number alterations. Regions that were frequently hypermethylated across individuals were markedly enriched for cancer- and development/differentiation-related genes. Additionally, regions exhibiting high consistency of hypermethylation across metastases within individuals, even if variably hypermethylated across individuals, showed enrichment for cancer-related genes. Whereas some regions showed intraindividual metastatic tumor heterogeneity in promoter methylation, such methylation alterations were generally not correlated with gene expression. This was despite a general tendency for promoter methylation patterns to be strongly correlated with gene expression, particularly at regions that were variably methylated across individuals. These findings suggest that DNA methylation alterations have the potential for producing selectable driver events in carcinogenesis and disease progression and highlight the possibility of targeting such epigenome alterations for development of longitudinal markers and therapeutic strategies.
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Affiliation(s)
- Martin J Aryee
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
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50
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Fukushige S, Horii A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. TOHOKU J EXP MED 2013; 229:173-85. [PMID: 23419314 DOI: 10.1620/tjem.229.173] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Initiation and progression of human cancer not only depends on genetic alterations but also on epigenetic changes such as DNA methylation and histone modifications. Aberrant DNA hypermethylation in the promoter regions of genes is the most well-defined epigenetic change in tumors and is associated with inappropriate gene silencing. This feature can be utilized to search for tumor-specific DNA methylation biomarkers and to examine candidate DNA biomarkers for clinical use. DNA methylation biomarker is defined as a molecular target that undergoes DNA methylation changes in carcinogenesis. Such a biomarker is useful for early detection of cancer, predicting and/or monitoring the therapeutic response, and detection of recurrent cancer. In this review, we describe the mechanism that establishes and maintains DNA methylation patterns as well as the mechanism of aberrant gene silencing in cancer, and then we introduce methods to isolate the DNA methylation biomarkers. We also summarize the current status of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including tissue factor pathway inhibitor 2 (TFPI2), septin 9 (SEPT9), glutathione S-transferase pi 1 (GSTP1), and O(6)-methylguanine-DNA methyltransferase (MGMT), and assess the clinical potential of these biomarkers for risk assessment, early diagnosis, prognosis, treatment, and the prevention of cancer. Finally we describe the possible involvement of 5-hydroxymethylcytosine in cancer; this is a recently discovered 5-methylcytosine oxidation derivative and might have a diagnostic potential in certain cancers. Abnormal DNA methylations are leading candidates for the development of specific markers for cancer diagnosis and therapy.
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Affiliation(s)
- Shinichi Fukushige
- Department of Molecular Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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