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Abstract
DNA methylation is one of the most important components of epigenetics, which plays essential roles in maintaining genome stability and regulating gene expression. In recent years, DNA methylation measuring methods have been continuously optimized. Combined with next generation sequencing technologies, these approaches have enabled the detection of genome-wide cytosine methylation at single-base resolution. In this paper, we review the development of 5-methylcytosine and its oxidized derivatives measuring methods, and recent advancement of single-cell epigenome sequencing technologies, offering more referable information for the selection and optimization of DNA methylation sequencing technologies and related research.
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Kim HJ, Seo EH, Bae DH, Haam K, Jang HR, Park JL, Kim JH, Kim M, Kim SY, Jeong HY, Song KS, Kim YS. Methylation of the CDX2 promoter in Helicobacter pylori-infected gastric mucosa increases with age and its rapid demethylation in gastric tumors is associated with upregulated gene expression. Carcinogenesis 2021; 41:1341-1352. [PMID: 32706861 DOI: 10.1093/carcin/bgaa083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 12/19/2022] Open
Abstract
Pathological changes in the epigenetic landscape of chromatin are hallmarks of cancer. The caudal-type homeobox gene CDX2 is not expressed in normal gastric epithelia but rather in adult intestinal epithelia, and it is overexpressed in intestinal metaplasia (IM). However, it remains unclear how CDX2 transcription is suppressed in normal gastric epithelial cells and overexpressed in IM. Here, we demonstrate that methylation of the CDX2 promoter increases with age in Helicobacter pylori-positive, noncancerous gastric tissue, whereas the promoter is demethylated in paired gastric tumors in which CDX2 is upregulated. Moreover, we also found that the CDX2 promoter is demethylated in IM as well as gastric tumor. Immunohistochemistry revealed that CDX2 is present in foci of parts of the gastric mucosae but highly expressed in IM as well as in gastric tumors, suggesting that the elevated level of CDX2 in IM and gastric tumors may be attributable to promoter demethylation. Our data suggest that CDX2 repression may be associated with promoter methylation in noncancerous H. pylori-positive mucosa but its upregulation might be attributable to increased promoter activity mediated by chromatin remodeling during gastric carcinogenesis.
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Affiliation(s)
- Hee-Jin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Eun-Hye Seo
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Dong Hyuck Bae
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Keeok Haam
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hay-Ran Jang
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Mirang Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun-Yong Jeong
- Department of Internal Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyu-Sang Song
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Yong Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon, Republic of Korea
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3
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Luo X, Kang T, Zhu J, Wu P, Cai C. Sensitivity-Improved SERS Detection of Methyltransferase Assisted by Plasmonically Engineered Nanoholes Array and Hybridization Chain Reaction. ACS Sens 2020; 5:3639-3648. [PMID: 33147006 DOI: 10.1021/acssensors.0c02016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, we present a dual-amplification sensing strategy that is assisted by plasmonically enhanced Raman intensity at engineered nanoholes array, along with signal amplification by the hybridization chain reaction (HCR) for the ultrasensitive detection of M.SssI MTase activity and inhibitor screening. An engineered surface-enhanced Raman scattering (SERS) substrate, namely, a structured nanoholes array (NHA) with wavelength-matched surface plasmon resonance (SPR) at the wavelength of laser excitation (785 nm), was rationally designed through finite-difference time-domain (FDTD) simulations, precisely fabricated through master-assisted replication, and then used as a sensing platform. Uniform and intense SERS signals were achieved by turning on the plasmonic enhancement under the excitation of SPR. Probe DNA was designed to hybridize with target DNA (a BRCA1 gene fragment), and the formed dsDNA with the recognition site of M.SssI was assembled on the NHA. In the presence of M.SssI, the HCR process was triggered upon adding DNAs labeled with the Raman reporter Cy5, leading to an amplified SERS signal of Cy5. The intensity of Cy5 increases with increasing M.SssI activity, which establishes the basis of the assay for M.SssI. The developed assay displays an ultrasensitivity that has a broad linear range (0.002-200 U/mL) and a low detection limit (2 × 10-4 U/mL), which is superior to that of the reported SERS-based detection methods. Moreover, it can selectively detect M.SssI in human serum samples and evaluate the efficiency of M.SssI inhibitors.
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Affiliation(s)
- Xiaojun Luo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Tuli Kang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Jingtian Zhu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
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4
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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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5
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Wu Y, Lu Y, Xu C, Lin B. Positron emission tomography/computed tomography using 2-deoxy-2-fluoro-18-fluoro-D-glucose peri-tumoral halo uptake layer method outperforms magnetic resonance imaging and ultrasound methods in tumor size measurement of breast cancer. Oncol Lett 2020; 19:3881-3888. [PMID: 32391098 PMCID: PMC7206924 DOI: 10.3892/ol.2020.11492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 02/20/2020] [Indexed: 11/25/2022] Open
Abstract
As a non-invasive method, positron emission tomography (PET)/computed tomography (CT) using 2-deoxy-2-fluoro-18-fluoro-D-glucose (18F-FDG) is applied as a useful modality in the diagnosis of breast cancer. By evaluating glucose metabolism, this method can also be used in staging, restaging and post-therapeutic response evaluation. To evaluate the reliability of the 18F-FDG PET/CT-based peri-tumoral halo uptake layer (PHL) method for assessing tumor size, a total of 79 female patients with breast cancer who underwent 18F-FDG PET/CT, breast ultrasound and magnetic resonance imaging (MRI) evaluations were included in the present study. Upon examination by two independent nuclear medicine radiologists, tumor sizes were estimated by 18F-FDG PET/CT using margins defined as the inner line of the PHL. Pathological tumor sizes were evaluated on the direction of largest diameter indicated by previous imaging examination, which were also utilized as final standards. Statistical analysis of the results suggested that 18F-FDG PET/CT had a more linear correlation with pathology compared with breast ultrasound (r2=0.89 vs. 0.73) and MRI (r2=0.89 vs. 0.69) in terms of tumor size estimation, including a significantly lower bias in size difference relative to pathology. 18F-FDG PET/CT also exhibited improved performance compared with breast ultrasound and MRI in T stage assessment. These results indicated that the 18F-FDG PET/CT-based PHL method was superior to breast ultrasound and MRI, and that it provides sufficient reliability and high accuracy for measuring tumor size in patients with breast cancer.
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Affiliation(s)
- Yingzhe Wu
- Department of Radiology, Changxing People's Hospital, Huzhou, Zhejiang 313100, P.R. China
| | - Yuezhong Lu
- Department of Radiology, Changxing People's Hospital, Huzhou, Zhejiang 313100, P.R. China
| | - Chentao Xu
- Department of Radiology, Changxing People's Hospital, Huzhou, Zhejiang 313100, P.R. China
| | - Bin Lin
- Department of Pharmacy, Changxing People's Hospital, Huzhou, Zhejiang 313100, P.R. China
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Photoelectrochemical determination of the activity of M.SssI methyltransferase, and a method for inhibitor screening. Mikrochim Acta 2018; 185:498. [DOI: 10.1007/s00604-018-3033-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
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7
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Ediriweera MK, Tennekoon KH, Samarakoon SR. In vitro assays and techniques utilized in anticancer drug discovery. J Appl Toxicol 2018; 39:38-71. [DOI: 10.1002/jat.3658] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Meran Keshawa Ediriweera
- Institute of Biochemistry, Molecular Biology and Biotechnology; University of Colombo; Colombo 03 Sri Lanka
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology; University of Colombo; Colombo 03 Sri Lanka
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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9
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Ng IK, Ng C, Low JJ, Chiu L, Seah E, Ng CH, Chng WJ, Yan B, Ban KHK. Identifying large indels in targeted next generation sequencing assays for myeloid neoplasms: a cautionary tale of the ZRSR1 pseudogene. J Clin Pathol 2017; 70:1069-1073. [PMID: 28676493 DOI: 10.1136/jclinpath-2017-204440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/04/2022]
Abstract
Targeted next generation sequencing platforms have been increasingly utilised for identification of novel mutations in myeloid neoplasms, such as acute myeloid leukaemia (AML), and hold great promise for use in routine clinical diagnostics. In this study, we evaluated the utility of an open source variant caller in detecting large indels in a targeted sequencing of AML samples. While we found that this bioinformatics pipeline has the potential to accurately capture large indels (>20 bp) in patient samples, we highlighted the pitfall of a confounding ZRSR1 pseudogene that led to an erroneous ZRSR2 variant call. We further discuss possible clinical implications of the ZRSR1 pseudogene in myeloid neoplasms based on its molecular features. Knowledge of the confounding ZRSR1 pseudogene in ZRSR2 sequencing assays could be particularly important in AML diagnostics because the detection of ZRSR2 in AML patients is highly specific for an s-AML diagnosis.
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Affiliation(s)
- Isaac Ks Ng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christopher Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Jia Jin Low
- Department of Statistics, National University of Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Elaine Seah
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Chin Hin Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore
| | - Wee-Joo Chng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore.,Cancer Science Institute, National University of Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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10
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Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 92:668-678. [DOI: 10.1016/j.bios.2016.10.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 11/23/2022]
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11
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Ma L, Lei Z, Liu X, Liu D, Wang Z. Surface ligation-based resonance light scattering analysis of methylated genomic DNA on a microarray platform. Analyst 2016; 141:3084-9. [DOI: 10.1039/c6an00488a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A surface ligation-based RLS method is developed on a microarray platform for a sensitive and specific assay of methylated genomic DNA.
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Affiliation(s)
- Lan Ma
- Analysis and Testing Center
- Ningxia University
- Yinchuan
- P. R. China
- State Key Laboratory of Electroanalytical Chemistry
| | - Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Xia Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
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12
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Su F, Wang L, Sun Y, Liu C, Duan X, Li Z. Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction. Chem Commun (Camb) 2015; 51:3371-4. [PMID: 25621431 DOI: 10.1039/c4cc07688e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new ligase chain reaction-based colorimetric assay for detection of DNA methylation with ultrahigh sensitivity and selectivity. Using the proposed assay, as low as 0.01 fM methylated DNA can be detected by visualization of color changes of gold nanoparticles with the naked eye.
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Affiliation(s)
- Fengxia Su
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, P. R. China.
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13
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Pilozzi E, Maresca C, Duranti E, Giustiniani MC, Catalanotto C, Lucarelli M, Cogoni C, Ferri M, Ruco L, Zardo G. Left-sided early-onset vs late-onset colorectal carcinoma: histologic, clinical, and molecular differences. Am J Clin Pathol 2015; 143:374-84. [PMID: 25696795 DOI: 10.1309/ajcpnoc55iolxfud] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Carcinomas of the left colon represent a neoplasm of older patients (late onset), but epidemiologic evidence has been showing an increasing incidence in patients 50 years or younger (early onset). In this study, we investigate pathologic and molecular features of early- and late-onset carcinoma of the left colon. METHODS We selected 22 patients 50 years or younger and 21 patients 70 years or older with left-sided colorectal carcinoma (CRC). All samples were evaluated for pathologic features, microsatellite instability, and KRAS and BRAF mutations. Moreover, both groups were analyzed to identify CpG island methylator phenotype features and assessed with restriction landmark genome scanning (RLGS) to unveil differential DNA methylation patterns. RESULTS Early-onset patients had advanced pathologic stages compared with late-onset patients (P = .0482). All cases showed a microsatellite stable profile and BRAF wild-type sequence. Early-onset patients (43%) more frequently had mutations at KRAS codon 12 compared with late-onset patients (14%) (P =.0413). RLGS showed that patients younger than 50 years who had CRC had a significantly lower percentage of methylated loci than did patients 70 years or older (P = .04124), and differential methylation of several genomic loci was observed in the two groups. CONCLUSIONS Our results suggest that left-sided CRCs may present differential patterns of aberrant DNA methylation when they are separated by age.
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Affiliation(s)
- Emanuela Pilozzi
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Carmen Maresca
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Enrico Duranti
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | | | - Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Mario Ferri
- Department of Medical-Surgical Sciences and Translation Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Luigi Ruco
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
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Shen Q, Han L, Fan G, Abdel-Halim E, Jiang L, Zhu JJ. Highly sensitive photoelectrochemical assay for DNA methyltransferase activity and inhibitor screening by exciton energy transfer coupled with enzyme cleavage biosensing strategy. Biosens Bioelectron 2015; 64:449-55. [DOI: 10.1016/j.bios.2014.09.044] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/15/2014] [Accepted: 09/19/2014] [Indexed: 01/29/2023]
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15
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Chen J, Lutsik P, Akulenko R, Walter J, Helms V. AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing. J Bioinform Comput Biol 2015; 12:1442005. [PMID: 25553811 DOI: 10.1142/s0219720014420050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome bisulfite sequencing (WGBS) is an approach of growing importance. It is the only approach that provides a comprehensive picture of the genome-wide DNA methylation profile. However, obtaining a sufficient amount of genome and read coverage typically requires high sequencing costs. Bioinformatics tools can reduce this cost burden by improving the quality of sequencing data. We have developed a statistical method Ajusted Local Kernel Smoother (AKSmooth) that can accurately and efficiently reconstruct the single CpG methylation estimate across the entire methylome using low-coverage bisulfite sequencing (Bi-Seq) data. We demonstrate the AKSmooth performance on the low-coverage (~ 4 ×) DNA methylation profiles of three human colon cancer samples and matched controls. Under the best set of parameters, AKSmooth-curated data showed high concordance with the gold standard high-coverage sample (Pearson 0.90), outperforming the popular analogous method. In addition, AKSmooth showed computational efficiency with runtime benchmark over 4.5 times better than the reference tool. To summarize, AKSmooth is a simple and efficient tool that can provide an accurate human colon methylome estimation profile from low-coverage WGBS data. The proposed method is implemented in R and is available at https://github.com/Junfang/AKSmooth.
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Affiliation(s)
- Junfang Chen
- Center for Bioinformatics, Saarland University, Saarbrücken 66123, Germany , Department of Genetics, Saarland University, Saarbrücken 66123, Germany
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16
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Su F, Wang L, Sun Y, Liu C, Duan X, Li Z. Highly sensitive and multiplexed analysis of CpG methylation at single-base resolution with ligation-based exponential amplification. Chem Sci 2014; 6:1866-1872. [PMID: 28706642 PMCID: PMC5494546 DOI: 10.1039/c4sc03135k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 01/16/2023] Open
Abstract
DNA methylation is a primary epigenetic mechanism for transcriptional regulation during normal development and the occurrence of diseases, including cancers. DNA methylation has been increasingly utilized as a biomarker for cancer detection and differential diagnosis. Generally, one type of cancer is associated with several CpG methylation sites and detection of multiplexed CpG methylation can greatly improve the accuracy of cancer diagnosis. In this paper, we have developed a novel ligase chain reaction (LCR)-based method for multiplexed detection of CpG methylation in genomic DNA at single-base resolution. By rationally designing the two pairs of DNA probes for LCR, the bisulfite-treated methylated DNA target can be exponentially amplified by thermal cycling of the ligation reaction, in which one-base mismatch can be discriminated against, and thus high sensitivity and specificity for the detection of DNA methylation can be achieved. The LCR-based method can accurately determine as low as 10 aM methylated DNA fragment and 10 ng methylated genomic DNA. 0.1% methylated DNA can be detected in the presence of a large excess of unmethylated DNA. Moreover, by simply encoding one of the DNA probes in the LCR with a different length of poly(A) for detection of methylation at different CpG sites, the CpG methylation at different sites can produce LCR products with different lengths, and thus, can be simultaneously detected with one-tube LCR amplification and separation by capillary electrophoresis.
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Affiliation(s)
- Fengxia Su
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Limei Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Yueying Sun
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
| | - Xinrui Duan
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis , Ministry of Education , College of Chemistry and Environmental Science , Hebei University , Baoding 071002 , Hebei Province , P. R. China . ; ; Tel: +86 29 81530859.,Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China
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17
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AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping. Sci Rep 2014; 4:7300. [PMID: 25466435 PMCID: PMC4252907 DOI: 10.1038/srep07300] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/17/2014] [Indexed: 11/09/2022] Open
Abstract
We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding.
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Abstract
Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.
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Affiliation(s)
- Atul Grover
- a Biotechnology Division , Defence Institute of Bio Energy Research , Goraparao, P.O. Arjunpur , Haldwani , Uttarakhand , India and
| | - P C Sharma
- b University School of Biotechnology, Guru Gobind Singh Indraprastha University , Dwarka Sec. 16C , New Delhi , India
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Yan Z, Li Y, Zheng J, Zhou M. Electrogenerated chemiluminescence biosensing method for methyltransferase activity using tris(1, 10-phenanthroline) ruthenium-assembled graphene oxide. J Electroanal Chem (Lausanne) 2014. [DOI: 10.1016/j.jelechem.2014.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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20
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Distinguishing cytosine methylation using electrochemical, label-free detection of DNA hybridization and ds-targets. Biosens Bioelectron 2014; 64:74-80. [PMID: 25194799 DOI: 10.1016/j.bios.2014.08.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 08/14/2014] [Accepted: 08/21/2014] [Indexed: 11/22/2022]
Abstract
In this communication we report on two important effects related to the detection of DNAs. Firstly, we investigate the sensor response to target DNA when the target is in a double stranded (ds) form and compare the response to single stranded (ss) target DNA. The importance in evaluating such an effect lies in the fact that most biological DNA targets are found in ds form. Secondly, we use synthetic ds targets to investigate the effect of DNA methylation on the sensor response. DNA methylation is known to affect functional properties of DNA and is related to a number of diseases, including various cancers. In these studies, we utilize our previously developed sensor platform, which is based on the use of a glassy carbon electrode-confined conducting polymer that is covalently modified with DNA probe sequences. The signal detection methodology we use is measuring a change in the reaction kinetics of ferro-ferricyanide redox couple at the electrode upon hybridization by means of electrical impedance spectroscopy (EIS). Additionally, EIS is utilized to study the kinetics of the hybridization of the conducting polymer-bound probe with methylated vs. non-methylated ds-DNA. Preliminary results are proving valuable as a guide to the future design of sensors for gene methylation.
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He S, Pham MH, Pease M, Zada G, Giannotta SL, Wang K, Mack WJ. A review of epigenetic and gene expression alterations associated with intracranial meningiomas. Neurosurg Focus 2014; 35:E5. [PMID: 24289130 DOI: 10.3171/2013.10.focus13360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECT A more comprehensive understanding of the epigenetic abnormalities associated with meningioma tumorigenesis, growth, and invasion may provide useful targets for molecular classification and development of targeted therapies for meningiomas. METHODS The authors performed a review of the current literature to identify the epigenetic modifications associated with the formation and/or progression of meningiomas. RESULTS Several epigenomic alterations, mainly pertaining to DNA methylation, have been associated with meningiomas. Hypermethylation of TIMP3 inactivates its tumor suppression activity while CDKN2 (p14[ARF]) and TP73 gene hypermethylation and HIST1H1c upregulation interact with the p53 regulation of cell cycle control. Other factors such as HOX, IGF, WNK2, and TGF-β epigenetic modifications allow either upregulation or downregulation of critical pathways for meningioma development, progression, and recurrence. CONCLUSIONS Genome-wide methylation profiling demonstrated that global hypomethylation correlates with tumor grades and severity. Identification of additional epigenetic changes, such as histone modification and higher-order chromosomal structure, may allow for a more thorough understanding of tumorigenesis and enable future individualized treatment strategies for meningiomas.
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Couldrey C, Cave V. Assessing DNA methylation levels in animals: choosing the right tool for the job. Anim Genet 2014; 45 Suppl 1:15-24. [PMID: 24990588 DOI: 10.1111/age.12186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 12/16/2022]
Abstract
Selection of agricultural animals for improved performance based on genetics has seen significant progress made over the past few decades. Further improvements are likely by combining genetic selection with epigenetic selection or manipulation. However, before this can be undertaken, an understanding of epigenetic mechanisms is required, and this can be obtained only by precise and accurate analysis of epigenetic patterns. Even when one only considers a single epigenetic modification such as DNA methylation, the last 10 years have seen a wide array of technologies developed. For scientists whose primary training is in a field other than epigenetics, the choices can be confusing, and it can be challenging to determine which technology is best for the task at hand. There are many factors to take into consideration before beginning analysis of DNA methylation in animals. It is crucial that the most appropriate tools are selected to ensure that the best possible results are achieved. This review provides an overview of the most common methods of analysing DNA methylation in animals, when they are appropriate, what resolution of information they can provide and what their limitations are.
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Affiliation(s)
- Christine Couldrey
- Animal Productivity, AgResearch Ruakura Research Centre, 10 Bisley Road, Hamilton, 3214, New Zealand
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23
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Sensitive detection of DNA methyltransferase activity based on rolling circle amplification technology. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Wang GL, Luo HQ, Li NB. Gold nanorods-based FRET assay for ultrasensitive detection of DNA methylation and DNA methyltransferase activity. Analyst 2014; 139:4572-7. [DOI: 10.1039/c4an00206g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Kim KD, El Baidouri M, Jackson SA. Accessing epigenetic variation in the plant methylome. Brief Funct Genomics 2014; 13:318-27. [PMID: 24562692 DOI: 10.1093/bfgp/elu003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cytosine DNA methylation is the addition of a methyl group to the 5' position of a cytosine, which plays a crucial role in plant development and gene silencing. Genome-wide profiling of DNA methylation is now possible using various techniques and strategies. Using these technologies, we are beginning to elucidate the extent and impact of variation in DNA methylation between individuals and/or tissues. Here, we review the different techniques used to analyze the methylomes at the whole-genome level and their applications to better understand epigenetic variations in plants.
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Azad MAK, Morita K, Ohnishi JI, Kore-eda S. Isolation and characterization of a polyubiquitin gene and its promoter region from Mesembryanthemum crystallinum. Biosci Biotechnol Biochem 2013; 77:551-9. [PMID: 23470760 DOI: 10.1271/bbb.120807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcript levels of the polyubiquitin gene McUBI1 had been reported to be constant during Crassulacean acid metabolism (CAM) induction in the facultative CAM plant, Mesembryanthemum crystallinum. Here, we report the sequences of the full-length cDNA of McUBI1 and its promoter, and validation of the McUBI1 promoter as an internal control driving constitutive expression in transient assays using the dual-luciferase system to investigate the regulation of CAM-related gene expression. The McUBI1 promoter drove strong, constitutive expression during CAM induction. We compared the activities of this promoter with those of the cauliflower mosaic virus (CaMV) 35S promoter in detached C3- and CAM-performing M. crystallinum and tobacco leaves. We confirmed stable expression of the genes controlled by the McUBI1 promoter with far less variability than under the CaMV 35S promoter in M. crystallinum, whereas both promoters worked well in tobacco. We found the McUBI1 promoter more suitable than the CaMV 35S promoter as an internal control for transient expression assays in M. crystallinum.
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Affiliation(s)
- Muhammad Abul Kalam Azad
- Division of Life Sciences, Graduate School of Science and Engineering, Saitama University, Japan
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27
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Wang GL, Zhou LY, Luo HQ, Li NB. Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity. Anal Chim Acta 2013; 768:76-81. [DOI: 10.1016/j.aca.2013.01.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/07/2013] [Accepted: 01/12/2013] [Indexed: 02/05/2023]
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Wang Y, He X, Wang K, Su J, Chen Z, Yan G, Du Y. A label-free electrochemical assay for methyltransferase activity detection based on the controllable assembly of single wall carbon nanotubes. Biosens Bioelectron 2013; 41:238-43. [DOI: 10.1016/j.bios.2012.08.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/11/2012] [Accepted: 08/13/2012] [Indexed: 12/31/2022]
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Li Y, Luo X, Yan Z, Zheng J, Qi H. A label-free supersandwich electrogenerated chemiluminescence method for the detection of DNA methylation and assay of the methyltransferase activity. Chem Commun (Camb) 2013; 49:3869-71. [DOI: 10.1039/c3cc00203a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Electrogenerated chemiluminescence biosensing method for the detection of DNA methylation and assay of the methyltransferase activity. Biosens Bioelectron 2012; 38:407-10. [DOI: 10.1016/j.bios.2012.05.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 01/08/2023]
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31
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Olkhov-Mitsel E, Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med 2012; 1:237-60. [PMID: 23342273 PMCID: PMC3544446 DOI: 10.1002/cam4.22] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 12/13/2022] Open
Abstract
DNA methylation, consisting of the addition of a methyl group at the fifth-position of cytosine in a CpG dinucleotide, is one of the most well-studied epigenetic mechanisms in mammals with important functions in normal and disease biology. Disease-specific aberrant DNA methylation is a well-recognized hallmark of many complex diseases. Accordingly, various studies have focused on characterizing unique DNA methylation marks associated with distinct stages of disease development as they may serve as useful biomarkers for diagnosis, prognosis, prediction of response to therapy, or disease monitoring. Recently, novel CpG dinucleotide modifications with potential regulatory roles such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have been described. These potential epigenetic marks cannot be distinguished from 5-methylcytosine by many current strategies and may potentially compromise assessment and interpretation of methylation data. A large number of strategies have been described for the discovery and validation of DNA methylation-based biomarkers, each with its own advantages and limitations. These strategies can be classified into three main categories: restriction enzyme digestion, affinity-based analysis, and bisulfite modification. In general, candidate biomarkers are discovered using large-scale, genome-wide, methylation sequencing, and/or microarray-based profiling strategies. Following discovery, biomarker performance is validated in large independent cohorts using highly targeted locus-specific assays. There are still many challenges to the effective implementation of DNA methylation-based biomarkers. Emerging innovative methylation and hydroxymethylation detection strategies are focused on addressing these gaps in the field of epigenetics. The development of DNA methylation- and hydroxymethylation-based biomarkers is an exciting and rapidly evolving area of research that holds promise for potential applications in diverse clinical settings.
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Affiliation(s)
- Ekaterina Olkhov-Mitsel
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
| | - Bharati Bapat
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
- Department of Pathology, University Health Network, University of TorontoToronto, Ontario, Canada
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How Kit A, Nielsen HM, Tost J. DNA methylation based biomarkers: practical considerations and applications. Biochimie 2012; 94:2314-37. [PMID: 22847185 DOI: 10.1016/j.biochi.2012.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/16/2012] [Indexed: 02/06/2023]
Abstract
A biomarker is a molecular target analyzed in a qualitative or quantitative manner to detect and diagnose the presence of a disease, to predict the outcome and the response to a specific treatment allowing personalized tailoring of patient management. Biomarkers can belong to different types of biochemical molecules such as proteins, DNA, RNA or lipids, whereby protein biomarkers have been the most extensively studied and used, notably in blood-based protein quantification tests or immunohistochemistry. The rise of interest in epigenetic mechanisms has allowed the identification of a new type of biomarker, DNA methylation, which is of great potential for many applications. This stable and heritable covalent modification mostly affects cytosines in the context of a CpG dinucleotide in humans. It can be detected and quantified by a number of technologies including genome-wide screening methods as well as locus- or gene-specific high-resolution analysis in different types of samples such as frozen tissues and FFPE samples, but also in body fluids such as urine, plasma, and serum obtained through non-invasive procedures. In some cases, DNA methylation based biomarkers have proven to be more specific and sensitive than commonly used protein biomarkers, which could clearly justify their use in clinics. However, very few of them are at the moment used in clinics and even less commercial tests are currently available. The objective of this review is to discuss the advantages of DNA methylation as a biomarker, the practical considerations for their development, and their use in disease detection, prediction of outcome or treatment response, through multiple examples mainly focusing on cancer, but also to evoke their potential for complex diseases and prenatal diagnostics.
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Affiliation(s)
- Alexandre How Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, 75010 Paris, France
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Morita S, Takahashi RU, Yamashita R, Toyoda A, Horii T, Kimura M, Fujiyama A, Nakai K, Tajima S, Matoba R, Ochiya T, Hatada I. Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells. Int J Mol Sci 2012; 13:8259-8272. [PMID: 22942701 PMCID: PMC3430232 DOI: 10.3390/ijms13078259] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/19/2012] [Accepted: 06/27/2012] [Indexed: 11/16/2022] Open
Abstract
DNA methylation of promoters is linked to transcriptional silencing of protein-coding genes, and its alteration plays important roles in cancer formation. For example, hypermethylation of tumor suppressor genes has been seen in some cancers. Alteration of methylation in the promoters of microRNAs (miRNAs) has also been linked to transcriptional changes in cancers; however, no systematic studies of methylation and transcription of miRNAs have been reported. In the present study, to clarify the relation between DNA methylation and transcription of miRNAs, next-generation sequencing and microarrays were used to analyze the methylation and expression of miRNAs, protein-coding genes, other non-coding RNAs (ncRNAs), and pseudogenes in the human breast cancer cell lines MCF7 and the adriamycin (ADR) resistant cell line MCF7/ADR. DNA methylation in the proximal promoter of miRNAs is tightly linked to transcriptional silencing, as it is with protein-coding genes. In protein-coding genes, highly expressed genes have CpG-rich proximal promoters whereas weakly expressed genes do not. This is only rarely observed in other gene categories, including miRNAs. The present study highlights the epigenetic similarities and differences between miRNA and protein-coding genes.
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Affiliation(s)
- Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Ryou-u Takahashi
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; E-Mails: (R.T.); (T.O.)
| | - Riu Yamashita
- Department of Integrative Genomics, Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Aramaki, Aobaku, Sendai 980-8579, Japan; E-Mail:
| | - Atsushi Toyoda
- Center for Genetic Resource Information, National Institute of Genetics, Shizuoka 411-8540, Japan; E-Mails: (A.T.); (A.F.)
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
| | - Asao Fujiyama
- Center for Genetic Resource Information, National Institute of Genetics, Shizuoka 411-8540, Japan; E-Mails: (A.T.); (A.F.)
| | - Kenta Nakai
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; E-Mail:
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail:
| | - Ryo Matoba
- DNA Chip Research Inc., 1-1-43 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; E-Mails: (R.T.); (T.O.)
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan; E-Mails: (S.M.); (T.H.); (M.K.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-27-220-8057; Fax: +81-27-220-8110
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Park SJ, Jang HR, Kim M, Kim JH, Kwon OH, Park JL, Noh SM, Song KS, Kim SY, Kim YH, Kim YS. Epigenetic alteration of CCDC67 and its tumor suppressor function in gastric cancer. Carcinogenesis 2012; 33:1494-501. [PMID: 22610074 DOI: 10.1093/carcin/bgs178] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, the promoter of the gene coiled-coil domain-containing 67 (CCDC67) was found to be frequently methylated in gastric cancer cell lines and in primary gastric tumors, as examined by restriction landmark genomic scanning. In addition, CCDC67 expression was down-regulated in 72.7% of gastric cancer cell lines tested. In most cases, gene down-regulation was associated with CpG hypermethylation in the CCDC67 promoter. Treatment with 5-aza-2'-deoxycytidine and/or trichostatin A restored CCDC67 expression in down-regulated cell lines. Pyrosequencing analysis of 150 paired primary gastric cancer samples revealed that promoter CpG methylation was increased in 74% of tested tumors compared with paired adjacent normal tissues, and this hypermethylation correlated significantly with down-regulation of CCDC67. CCDC67 protein was localized to the cell membrane by immunocytochemistry. Stable transfection of a CCDC67 gene in one gastric cancer cell line inhibited adhesion-dependent and -independent colony formation, and CCDC67 expression suppressed tumorigenesis in nude mice. We suggest that CCDC67 is a putative tumor suppressor gene that is silenced in gastric cancers by promoter CpG methylation and that it may play an important role in cell signaling and migration related to tumorigenesis.
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Affiliation(s)
- Sung-Joon Park
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
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Abstract
The haploid human genome contains approximately 29 million CpGs that exist in a methylated, hydroxymethylated or unmethylated state, collectively referred to as the DNA methylome. The methylation status of cytosines in CpGs and occasionally in non-CpG cytosines influences protein–DNA interactions, gene expression, and chromatin structure and stability. The degree of DNA methylation at particular loci may be heritable transgenerationally and may be altered by environmental exposures and diet, potentially contributing to the development of human diseases. For the vast majority of normal and disease methylomes however, less than 1% of the CpGs have been assessed, revealing the formative stage of methylation mapping techniques. Thus, there is significant discovery potential in new genome-scale platforms applied to methylome mapping, particularly oligonucleotide arrays and the transformative technology of next-generation sequencing. Here, we outline the currently used methylation detection reagents and their application to microarray and sequencing platforms. A comparison of the emerging methods is presented, highlighting their degrees of technical complexity, methylome coverage and precision in resolving methylation. Because there are hundreds of unique methylomes to map within one individual and interindividual variation is likely to be significant, international coordination is essential to standardize methylome platforms and to create a full repository of methylome maps from tissues and unique cell types.
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Affiliation(s)
- Shaun D Fouse
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA 94158, USA.
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Jones A, Lechner M, Fourkala EO, Kristeleit R, Widschwendter M. Emerging promise of epigenetics and DNA methylation for the diagnosis and management of women's cancers. Epigenomics 2012; 2:9-38. [PMID: 22122746 DOI: 10.2217/epi.09.47] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Over the last two decades, survival rates from women's cancers (breast, ovarian, endometrial and cervical cancer) have all but modestly improved despite huge efforts from both research and clinical communities. In parallel with this, the field of epigenetics has grown from its infancy into a promising scientific discipline. In particular, DNA methylation analysis has been adopted by oncologists in an attempt to better understand and manage cancer. Now that the epigenetic technological base has caught up, the potential of methylation markers in cancer research is finally being realized. In this review, we present the current status of epigenetic research into women's cancers with a main focus on DNA methylation analysis. We provide an overview of technological development, current markers of risk prediction, early detection, diagnosis, prognosis and response to treatment, and highlight the progression of epigenetic therapies. Finally, we comment on the potential impact of epigenetic analyses on the future of women's health.
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Affiliation(s)
- Allison Jones
- Department of Gynecological Oncology, Institute for Women's Health, University College London, 149 Tottenham Court Road, London, UK
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Hypermethylation of CpG islands is more prevalent than hypomethylation across the entire genome in breast carcinogenesis. Clin Exp Med 2012; 13:1-9. [DOI: 10.1007/s10238-011-0173-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Accepted: 12/17/2011] [Indexed: 01/07/2023]
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Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay. Biosens Bioelectron 2012; 31:451-7. [DOI: 10.1016/j.bios.2011.11.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/23/2022]
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Harrison A, Parle-McDermott A. DNA methylation: a timeline of methods and applications. Front Genet 2011; 2:74. [PMID: 22303369 PMCID: PMC3268627 DOI: 10.3389/fgene.2011.00074] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/04/2011] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation is of paramount importance to biological health and disease. Recently, the quest to unravel the Human Epigenome commenced, calling for a modernization of previous DNA methylation profiling techniques. Here, we describe the major developments in the methodologies used over the past three decades to examine the elusive epigenome (or methylome). The earliest techniques were based on the separation of methylated and unmethylated cytosines via chromatography. The following years would see molecular techniques being employed to indirectly examine DNA methylation levels at both a genome-wide and locus-specific context, notably immunoprecipitation via anti-5'methylcytosine and selective digestion with methylation-sensitive restriction endonucleases. With the advent of sodium bisulfite treatment of DNA, a deamination reaction that converts cytosine to uracil only when unmethylated, the epigenetic modification can now be identified in the same manner as a DNA base-pair change. More recently, these three techniques have been applied to more technically advanced systems such as DNA microarrays and next-generation sequencing platforms, bringing us closer to unveiling a complete human epigenetic profile.
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Affiliation(s)
- Alan Harrison
- Nutritional Genomics Group, School of Biotechnology, Dublin City University Dublin, Ireland
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Chromosomal aberrations in solid tumors. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 95:55-94. [PMID: 21075329 DOI: 10.1016/b978-0-12-385071-3.00004-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Ever since the identification of the exact number of human chromosomes in 1956, several cancer-specific chromosomal abnormalities have been identified in different tumors. Among the various genetic changes, such as alterations in oncogenes, tumor suppressor genes, and microRNA genes, recurrent chromosome translocations have been identified as an important class of mutations in hematological malignancies, soft tissue sarcomas, and more recently in prostate cancer and lung cancer. Recurrent gene fusions are used for cancer classification and as diagnostic markers, and some have been successfully targeted for drug development. Recent advances in high-throughput sequencing technology and the ambitious undertaking of "The Cancer Genome Atlas" (TCGA) project will help drive the identification of the underlying genetic aberrations in most of the solid cancers. This chapter presents an overview on the current status of the knowledge on chromosome aberrations in solid cancers, cytogenetic and noncytogenetic methods for the characterization of changes at the DNA and RNA levels, technological advancements in high-throughput characterization of the cancer genome and transcriptome, and the current understanding of the molecular mechanism involved in the formation of gene fusions in solid cancer.
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González-Ramírez I, García-Cuellar C, Sánchez-Pérez Y, Granados-García M. DNA methylation in oral squamous cell carcinoma: molecular mechanisms and clinical implications. Oral Dis 2011; 17:771-8. [DOI: 10.1111/j.1601-0825.2011.01833.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Estécio MRH, Issa JPJ. Dissecting DNA hypermethylation in cancer. FEBS Lett 2011; 585:2078-86. [PMID: 21146531 PMCID: PMC3378045 DOI: 10.1016/j.febslet.2010.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 12/31/2022]
Abstract
There is compelling evidence to support the importance of DNA methylation alterations in cancer development. Both losses and gains of DNA methylation are observed, thought to contribute pathophysiologically by inactivating tumor suppressor genes, inducing chromosomal instability and ectopically activating gene expression. Lesser known are the causes of aberrant DNA methylation. Recent studies have pointed out that intrinsic gene susceptibility to DNA methylation, environmental factors and gene function all have an intertwined participation in this process. Overall, these data support a deterministic rather than a stochastic mechanism for de novo DNA methylation in cancer. In this review article, we discuss the technologies available to study DNA methylation and the endogenous and exogenous factors that influence the onset of de novo methylation in cancer.
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Affiliation(s)
- Marcos R H Estécio
- Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX 77030, United States.
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Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H, Held WA. Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics 2011; 12:231. [PMID: 21569359 PMCID: PMC3118215 DOI: 10.1186/1471-2164-12-231] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 05/11/2011] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Changes in DNA methylation in the mammalian genome during development are frequent events and play major roles regulating gene expression and other developmental processes. It is necessary to identify these events so that we may understand how these changes affect normal development and how aberrant changes may impact disease. RESULTS In this study Methylated DNA ImmunoPrecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island (CpGi) array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). Almost 5,000 adult T-DMRs and 10,000 DS-DMRs were identified. Surprisingly, almost all DS-DMRs were tissue specific (i.e. methylated in at least one tissue and unmethylated in one or more tissues). In addition our results indicate that many DS-DMRs are methylated at early development stages (E15 and NB) but are unmethylated in adult. There is a very strong bias for testis specific methylation in non-CpGi promoter regions (94%). Although the majority of T-DMRs and DS-DMRs tended to be in non-CpGi promoter regions, a relatively large number were also located in CpGi in promoter, intragenic and intergenic regions (>15% of the 15,979 CpGi on the array). CONCLUSIONS Our data suggests the vast majority of unique sequence DNA methylation has tissue specificity, that demethylation has a prominent role in tissue differentiation, and that DNA methylation has regulatory roles in alternative promoter selection and in non-promoter regions. Overall, our studies indicate changes in DNA methylation during development are a dynamic, widespread, and tissue-specific process involving both DNA methylation and demethylation.
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Affiliation(s)
- Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
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Liu S, Wu P, Li W, Zhang H, Cai C. An electrochemical approach for detection of DNA methylation and assay of the methyltransferase activity. Chem Commun (Camb) 2011; 47:2844-6. [DOI: 10.1039/c0cc05153e] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Restriction landmark genome scanning (RLGS) method is a high-resolution two-dimensional electrophoresis system for analyses of the whole genome DNA which is including methylation status. It has been used for cloning genes of model animals and human genomes, detection of imprinted genes, and genome-wide methylation research in cancer. The conventional RLGS detected both polymorphism and methylated NotI sites between samples. Here, we have developed improved RLGS method with isoschizomer restriction enzymes such as MspI and HpaII to specifically detect methylated sites, using differential sensitivity of the restriction enzymes to methylated sequences. Recently, by using the genome database information, the RLGS spot sites were efficiently identified by this improved method. Then, genome methylation sites of Arabidopsis were mapped, and a unique inheritance was detected in methylated gene in rice. Now, epigenetic research becomes easy with the improved RLGS and it also can be applied for animal genome. Therefore, RLGS method is useful to explore for novel epigenetic phenomenon.
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Affiliation(s)
- Hisato Okuizumi
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan.
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46
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Ong CAJ, Lao-Sirieix P, Fitzgerald RC. Biomarkers in Barrett’s esophagus and esophageal adenocarcinoma: Predictors of progression and prognosis. World J Gastroenterol 2010; 16:5669-81. [PMID: 21128316 PMCID: PMC2997982 DOI: 10.3748/wjg.v16.i45.5669] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Barrett’s esophagus is a well-known premalignant lesion of the lower esophagus that is characterized by intestinal metaplasia of the squamous epithelium. It is clinically important due to the increased risk (0.5% per annum) of progression to esophageal adenocarcinoma (EA), which has a poor outcome unless diagnosed early. The current clinical management of Barrett’s esophagus is hampered by the lack of accurate predictors of progression. In addition, when patients develop EA, the current staging modalities are limited in stratifying patients into different prognostic groups in order to guide the optimal therapy for an individual patient. Biomarkers have the potential to improve radically the clinical management of patients with Barrett’s esophagus and EA but have not yet entered mainstream clinical practice. This is in contrast to other cancers like breast and prostate for which biomarkers are utilized routinely to inform clinical decisions. This review aims to highlight the most promising predictive and prognostic biomarkers in Barrett’s esophagus and EA and to discuss what is required to move the field forward towards clinical application.
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Samuelsson JK, Alonso S, Yamamoto F, Perucho M. DNA fingerprinting techniques for the analysis of genetic and epigenetic alterations in colorectal cancer. Mutat Res 2010; 693:61-76. [PMID: 20851135 DOI: 10.1016/j.mrfmmm.2010.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/07/2010] [Accepted: 08/24/2010] [Indexed: 01/03/2023]
Abstract
Genetic somatic alterations are fundamental hallmarks of cancer. In addition to point and other small mutations targeting cancer genes, solid tumors often exhibit aneuploidy as well as multiple chromosomal rearrangements of large fragments of the genome. Whether somatic chromosomal alterations and aneuploidy are a driving force or a mere consequence of tumorigenesis remains controversial. Recently it became apparent that not only genetic but also epigenetic alterations play a major role in carcinogenesis. Epigenetic regulation mechanisms underlie the maintenance of cell identity crucial for development and differentiation. These epigenetic regulatory mechanisms have been found substantially altered during cancer development and progression. In this review, we discuss approaches designed to analyze genetic and epigenetic alterations in colorectal cancer, especially DNA fingerprinting approaches to detect changes in DNA copy number and methylation. DNA fingerprinting techniques, despite their modest throughput, played a pivotal role in significant discoveries in the molecular basis of colorectal cancer. The aim of this review is to revisit the fingerprinting technologies employed and the oncogenic processes that they unveiled.
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Affiliation(s)
- Johanna K Samuelsson
- Sanford-Burnham Medical Research Institute (SBMRI), 10901N. Torrey Pines Rd, La Jolla, CA 92037, United States
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Martinez-Arguelles DB, Papadopoulos V. Epigenetic regulation of the expression of genes involved in steroid hormone biosynthesis and action. Steroids 2010; 75:467-76. [PMID: 20156469 PMCID: PMC2860648 DOI: 10.1016/j.steroids.2010.02.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 01/16/2010] [Accepted: 02/08/2010] [Indexed: 11/26/2022]
Abstract
Steroid hormones participate in organ development, reproduction, body homeostasis, and stress responses. The steroid machinery is expressed in a development- and tissue-specific manner, with the expression of these factors being tightly regulated by an array of transcription factors (TFs). Epigenetics provides an additional layer of gene regulation through DNA methylation and histone tail modifications. Evidence of epigenetic regulation of key steroidogenic enzymes is increasing, though this does not seem to be a predominant regulatory pathway. Steroid hormones exert their action in target tissues through steroid nuclear receptors belonging to the NR3A and NR3C families. Nuclear receptor expression levels and post-translational modifications regulate their function and dictate their sensitivity to steroid ligands. Nuclear receptors and TFs are more likely to be epigenetically regulated than proteins involved in steroidogenesis and have secondary impact on the expression of these steroidogenic enzymes. Here we review evidence for epigenetic regulation of enzymes, transcription factors, and nuclear receptors related to steroid biogenesis and action.
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Affiliation(s)
- Daniel B. Martinez-Arguelles
- Department of Biochemistry & Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, United States
- The Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
| | - Vassilios Papadopoulos
- Department of Biochemistry & Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, United States
- The Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Departments of Medicine, Pharmacology & Therapeutics, and Biochemistry, McGill University, Montreal, Quebec, H3G 1A4, Canada
- Corresponding author at: The Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Avenue, Room C10-148, Montreal, Quebec H3G 1A4, Canada. Tel: 514-934-1934 ext. 44580. Fax: 514-934-8439.
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Fluorescent conjugated polymer-based FRET technique for detection of DNA methylation of cancer cells. Nat Protoc 2010; 5:1255-64. [PMID: 20595954 DOI: 10.1038/nprot.2010.79] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This protocol describes a homogeneous, convenient and sensitive DNA methylation detection method, using an optically amplifying cationic conjugated polymer (CCP, poly((1,4-phenylene)-2,7-[9,9-bis(6'-N,N,N-trimethyl ammonium)-hexyl fluorene] dibromide)). Genomic DNA from cancer cells is pretreated with a methylation-sensitive restriction endonuclease, followed by PCR amplification in the presence of fluorescein-labeled dNTP and Taq polymerase. The PCR only occurs for methylated DNA. DNA methylation of the gene sequence of interest is detected as a result of the fluorescence resonance energy transfer (FRET) between CCP and fluorescein that is incorporated into DNA. The methylated statuses of the p16, HPP1 and GALR2 promoters of five cancer cell lines (HT29, HepG2, A498, HL60 and M17) were assayed to provide an association study between the cancers and susceptibility genes, which shows great potential for early cancer diagnosis. This protocol simplifies previously available procedures by avoiding the need for primer labeling, isolation or purification steps, and sophisticated instruments. The assay takes about 20 h to obtain the methylated statuses of cancer cells.
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Kang S, Dong SM, Park NH. Frequent promoter hypermethylation of TGFBI in epithelial ovarian cancer. Gynecol Oncol 2010; 118:58-63. [PMID: 20421128 DOI: 10.1016/j.ygyno.2010.03.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Using pharmacologic unmasking and genome-wide differential methylation analysis, we identified a novel methylated gene in ovarian cancers. METHODS Two ovarian cancer cells (OVCAR-3, ES-2) that showed synergistic growth inhibition by 5-aza-dC and cisplatin were selected. After treatment with 5-aza-dC, differential expression profiles were compared using microarray that contained 38,500 genes. Reactivation of candidate genes and their promoter methylation were validated by real-time RT-PCR, MS-PCR and bisulfite sequencing. Methylation status was tested by MS-PCR in 56 patients with epithelial ovarian cancer and compared to the 38 normal ovarian tissues. RESULTS We identified 103 candidate genes that were reactivated by 5-aza-dC treatment. Among those, SFN and TGFBI were commonly reactivated in both cells. Since SFN is a well known methylated marker, we selected TGFBI for further validation. Bisulfite sequencing revealed complete promoter methylation in ES-2 and partial methylation in OVCAR-3. In addition, silencing of TGFBI at the transcription level was reversed by 5-aza-dC treatment. TGFBI methylation was observed in 23 out of 38 (60.5%) cases of ovarian cancer, in no normal ovarian tissues (0 of 38, P=0.001), and in 5 out of 18 (27.8%) borderline tumors (P=0.044). In our cohort, we did not observe any association between methylation of TGFBI and clinicopathologic variables or clinical outcomes. CONCLUSION Our results confirm that TGFBI is frequently methylated in ovarian cancer. Its methylation can be used as a novel epigenetic biomarker in discriminating ovarian cancer from non-cancer or borderline tumors.
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Affiliation(s)
- Sokbom Kang
- Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
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