1
|
Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
Collapse
Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Guan QH, Shi WJ, Zhou LS, Tao AL, Li L. Effect of epigallocatechin-3-gallate on the status of DNA methylation of E-cadherin promoter region on endometriosis mouse. J Obstet Gynaecol Res 2020; 46:2076-2083. [PMID: 32840012 DOI: 10.1111/jog.14358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/24/2020] [Accepted: 05/31/2020] [Indexed: 01/11/2023]
Abstract
AIM To evaluate whether epigallocatechin-3-gallate acts on endometriosis mouse, and changes the status of DNA methylation of E-cadherin promoter region. METHODS According to our previous research, the tracing nude mouse model of endometriosis was built up and randomly divided into three groups: control group (group A), epigallocatechin-3-gallate group (group B) and decitabine group (group C). Normal saline, epigallocatechin-3-gallate and decitabine were isometrically intraperitoneally injected into each group once in 2 days. In this period, the growth situations of lesions were monitored by living image system. After 16 days, the lesions were taken out and the distribution of E-cadherin and its methylated situation of promoter region were analyzed. RESULTS The region of interest of ectopic lesion increased from 4th to 16th day in group A (P < 0.01); in group B and C, the region of interest of ectopic lesion increased in the 0-8th day (P < 0.01), and decreased in the 8-16th day (P < 0.01). The positive expression rate of E-cadherin in group C was higher than group B, and group B was higher than group A (P < 0.01). The DNA methylation status of E-cadherin promoter region in group A was higher than group B, and group B was higher than group C (P < 0.01). CONCLUSION Epigallocatechin-3-gallate may inhibit the growth of endometrial lesion, affect the expression of E-cadherin on the cell membrane and reduce the status of DNA methylation of E-cadherin promoter region.
Collapse
Affiliation(s)
- Qi-Hui Guan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wen-Jing Shi
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Long-Shu Zhou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ai-Lin Tao
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
4
|
Lin KN, Grandhi TSP, Goklany S, Rege K. Chemotherapeutic Drug-Conjugated Microbeads Demonstrate Preferential Binding to Methylated Plasmid DNA. Biotechnol J 2018; 13:e1700701. [DOI: 10.1002/biot.201700701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Kevin N. Lin
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
| | - Taraka Sai Pavan Grandhi
- Biomedical Engineering, School of Biological and Health Systems Engineering, Arizona State University; Tempe AZ 85287 USA
| | - Sheba Goklany
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
| | - Kaushal Rege
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University; Tempe AZ 85287 USA
| |
Collapse
|
5
|
Sun FK, Gao S, Fan YC, Shi CH, Zhang ZH, Wang LY, Li F, Li XY, Ji XF, Zhao J, Wang K. High promoter methylation levels of glutathione-S-transferase M3 predict poor prognosis of acute-on-chronic hepatitis B liver failure. Hepatol Res 2017; 47:566-573. [PMID: 27442719 DOI: 10.1111/hepr.12777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 07/15/2016] [Accepted: 07/17/2016] [Indexed: 12/11/2022]
Abstract
AIM This study aimed to evaluate the prognostic value of glutathione-S-transferase M3 (GSTM3) gene promoter methylation in patients with acute-on-chronic hepatitis B liver failure (ACHBLF). METHODS A total of 119 patients with ACHBLF, 60 patients with chronic hepatitis B and 30 healthy controls were enrolled. We used a quantitative methylation detection technique, MethyLight, to examine the methylation levels of GSTM3 in peripheral blood mononuclear cells. RESULTS The GSTM3 methylation level was significantly higher in patients with ACHBLF than those in patients with chronic hepatitis B and healthy controls (both P < 0.05). In patients with ACHBLF, GSTM3 methylation level percentage of methylated reference (PMR) positively correlated with total bilirubin, international normalized ratio, and Model for End-stage Liver Disease (MELD) score, and negatively correlated with prothrombin activity and albumin (all P < 0.05). The PMR for GSTM3 of non-survivors was significantly increased compared to that of survivors (P < 0.05). Multivariate analysis indicated that GSTM3 methylation level was one of the independent prognostic factors for 3-month mortality of ACHBLF (P = 0.000). The area under the receiver-operator characteristic curve of PMR for GSTM3 in predicting 3-month mortality of ACHBLF was not statistically different from that of MELD score (0.798 vs. 0.716, P = 0.152). However, the area under the curve of PMR for GSTM3 was significantly higher than that of MELD score in predicting 1-month mortality (0.887 vs. 0.737, P = 0.020). CONCLUSION Promoter methylation levels of GSTM3 in peripheral blood mononuclear cells closely correlated with disease severity and could be used to predict prognosis of patients with ACHBLF.
Collapse
Affiliation(s)
- Feng-Kai Sun
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China.,Institute of Hepatology, Shandong University, Jinan, China
| | - Chang-He Shi
- Department of Hepatology, Qingdao Infectious Disease Hospital, Qingdao, China
| | - Zhao-Hua Zhang
- Department of Hepatology, Jinan Infectious Disease Hospital, Shandong University, Jinan, China
| | - Li-Yuan Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Feng Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xin-You Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiang-Fen Ji
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing Zhao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China.,Institute of Hepatology, Shandong University, Jinan, China
| |
Collapse
|
6
|
Yang B, Rodgers MT. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m(5)dCyd: Implications for the Stability of DNA i-Motif Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1394-1403. [PMID: 26002790 DOI: 10.1007/s13361-015-1144-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 06/04/2023]
Abstract
Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m(5)dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m(5)dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m(5)dCyd)H(+)(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | | |
Collapse
|
7
|
The epigenetics of prostate cancer diagnosis and prognosis: update on clinical applications. Curr Opin Urol 2015; 25:83-8. [PMID: 25405932 DOI: 10.1097/mou.0000000000000132] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW There is a major deficit in our ability to detect and predict the clinical behavior of prostate cancer (PCa). Epigenetic changes are associated with PCa development and progression. This review will focus on recent results in the clinical application of diagnostic and prognostic epigenetic markers. RECENT FINDINGS The development of high throughput technology has seen an enormous increase in the discovery of new markers that encompass epigenetic changes including those in DNA methylation and histone modifications. Application of these findings to urine and other biofluids, but also cancer and noncancerous prostate tissue, has resulted in new biomarkers. There has been a recent commercial development of a DNA methylation-based assay for identifying PCa risk from normal biopsy tissue. Other biomarkers are currently in the validation phase and encompass combinations of multiple genes. SUMMARY Epigenetic changes improve the specificity and sensitivity of PCa diagnosis and have the potential to help determine clinical prognosis. Additional studies will not only provide new and better biomarker candidates, but also have the potential to inform new therapeutic strategies given the reversibility of these processes.
Collapse
|
8
|
Carless MA. Investigation of genomic methylation status using methylation-specific and bisulfite sequencing polymerase chain reaction. Methods Mol Biol 2015; 1288:193-212. [PMID: 25827881 DOI: 10.1007/978-1-4939-2474-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Epigenetic modification plays a central role in the regulation of gene expression and therefore in the development of disease states. In particular, genomic methylation of cytosines within CpG dinucleotides is crucial to development, gene silencing, and chromosome inactivation. Importantly, aberrant methylation profiles of various genes are associated with cancer as well as autoimmune disease, psychiatric and neurodegenerative disorders, diabetes, and heart disease. Various methods are available for the detection and quantification of methylation in a given sample. Most of these methods rely upon bisulfite conversion of DNA, which converts unmethylated cytosines to uracil, while methylated cytosines remain as cytosines. Methylation-specific amplification of DNA can be used to detect methylation at one or more (typically up to about 4) CpG sites by using primers specific to either methylated or unmethylated DNA. Alternatively, amplification of both methylated and unmethylated DNA followed by sequencing can be used to detect methylation status at multiple CpG sites. The following chapter provides protocols for bisulfite conversion of DNA, methylation-specific PCR and bisulfite sequencing PCR.
Collapse
Affiliation(s)
- Melanie A Carless
- Texas Biomedical Research Institute, P.O. Box 760549, 7620 N. W. Loop 410 (at Military Drive), San Antonio, TX, 78245-0549, USA,
| |
Collapse
|
9
|
Wang Y, Ritzo B, Gu LQ. Silver(I) ions modulate the stability of DNA duplexes containing cytosine, methylcytosine and hydroxymethylcytosine at different salt concentrations. RSC Adv 2014; 5:2655-2658. [PMID: 31007904 DOI: 10.1039/c4ra14490b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Silver(I) ions can stabilize cytosine-cytosine, cytosine (C)-methylcytosine (5mC) and cytosine-hydroxymethylcytosine (5hmC) mismatched-base pairs. While cytosine modifications regulate DNA stability to regulate cellular functions, silver ions can modulate the stability of C-C, C-5mC and C-5hmC containing DNA duplexes in a salt concentration dependent manner.
Collapse
Affiliation(s)
- Yong Wang
- Department of Biological Engineering, University of Missouri, 134 research park, Columbia, MO 65211, USA. ; Tel: +1 573 8822086
| | - Brandon Ritzo
- Department of Biological Engineering, University of Missouri, 134 research park, Columbia, MO 65211, USA. ; Tel: +1 573 8822086
| | - Li-Qun Gu
- Department of Biological Engineering, University of Missouri, 134 research park, Columbia, MO 65211, USA. ; Tel: +1 573 8822086
| |
Collapse
|
10
|
Single molecule investigation of Ag+ interactions with single cytosine-, methylcytosine- and hydroxymethylcytosine-cytosine mismatches in a nanopore. Sci Rep 2014; 4:5883. [PMID: 25103463 PMCID: PMC4126007 DOI: 10.1038/srep05883] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 07/08/2014] [Indexed: 12/31/2022] Open
Abstract
Both cytosine-Ag-cytosine interactions and cytosine modifications in a DNA duplex have attracted great interest for research. Cytosine (C) modifications such as methylcytosine (mC) and hydroxymethylcytosine (hmC) are associated with tumorigenesis. However, a method for directly discriminating C, mC and hmC bases without labeling, modification and amplification is still missing. Additionally, the nature of coordination of Ag+ with cytosine-cytosine (C-C) mismatches is not clearly understood. Utilizing the alpha-hemolysin nanopore, we show that in the presence of Ag+, duplex stability is most increased for the cytosine-cytosine (C-C) pair, followed by the cytosine-methylcytosine (C-mC) pair, and the cytosine-hydroxymethylcytosine (C-hmC) pair, which has no observable Ag+ induced stabilization. Molecular dynamics simulations reveal that the hydrogen-bond-mediated paring of a C-C mismatch results in a binding site for Ag+. Cytosine modifications (such as mC and hmC) disrupted the hydrogen bond, resulting in disruption of the Ag+ binding site. Our experimental method provides a novel platform to study the metal ion-DNA interactions and could also serve as a direct detection method for nucleobase modifications.
Collapse
|
11
|
Wang LJ, Zhang HW, Zhou JY, Liu Y, Yang Y, Chen XL, Zhu CH, Zheng RD, Ling WH, Zhu HL. Betaine attenuates hepatic steatosis by reducing methylation of the MTTP promoter and elevating genomic methylation in mice fed a high-fat diet. J Nutr Biochem 2013; 25:329-36. [PMID: 24456734 DOI: 10.1016/j.jnutbio.2013.11.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/08/2013] [Accepted: 11/16/2013] [Indexed: 01/04/2023]
Abstract
Aberrant DNA methylation contributes to the abnormality of hepatic gene expression, one of the main factors in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Betaine is a methyl donor and has been considered to be a lipotropic agent. However, whether betaine supplementation improves NAFLD via its effect on the DNA methylation of specific genes and the genome has not been explored. Male C57BL/6 mice were fed either a control diet or high-fat diet (HFD) supplemented with 0%, 1% and 2% betaine in water (wt/vol) for 12 weeks. Betaine supplementation ameliorated HFD-induced hepatic steatosis in a dose-dependent manner. HFD up-regulated FAS and ACOX messenger RNA (mRNA) expression and down-regulated PPARα, ApoB and MTTP mRNA expression; however, these alterations were reversed by betaine supplementation, except ApoB. MTTP mRNA expression was negatively correlated with the DNA methylation of its CpG sites at -184, -156, -63 and -60. Methylation of these CpG sites was lower in both the 1% and 2% betaine-supplemented groups than in the HFD group (averages; 25.55% and 14.33% vs. 30.13%). In addition, both 1% and 2% betaine supplementation significantly restored the methylation capacity [S-adenosylmethionine (SAM) concentration and SAM/S-adenosylhomocysteine ratios] and genomic methylation level, which had been decreased by HFD (0.37% and 0.47% vs. 0.25%). These results suggest that the regulation of aberrant DNA methylation by betaine might be a possible mechanism of the improvements in NAFLD upon betaine supplementation.
Collapse
Affiliation(s)
- Li-jun Wang
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Hong-wei Zhang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, University of Sun Yat-Sen, 510120 Guangzhou, People's Republic of China
| | - Jing-ya Zhou
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Yan Liu
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Yang Yang
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Xiao-ling Chen
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Cui-hong Zhu
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Rui-dan Zheng
- Research and Therapy Center for Liver Disease, the Affiliated Dongnan Hospital of Xiamen University, 363000 Zhangzhou, People's Republic of China
| | - Wen-hua Ling
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China
| | - Hui-lian Zhu
- Faculty of Nutrition, School of Public Health, Sun Yat-Sen University, 510080 Guangzhou, People's Republic of China.
| |
Collapse
|
12
|
Ooki A, Yamashita K, Yamaguchi K, Mondal A, Nishimiya H, Watanabe M. DNA damage-inducible gene, reprimo functions as a tumor suppressor and is suppressed by promoter methylation in gastric cancer. Mol Cancer Res 2013; 11:1362-74. [PMID: 23982217 DOI: 10.1158/1541-7786.mcr-13-0091] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In several types of human cancer, the gene expression of Reprimo, a highly glycosylated protein, is frequently silenced via methylation of its promoter. The aim of this study was to characterize the epigenetic inactivation of Reprimo and its biologic function and clinical relevance in gastric cancer. The correlation between Reprimo methylation and clinical relevance was assessed in 83 primary human gastric cancer tissues. The effects of Reprimo expression were also examined using in vitro and in vivo assays. Reprimo methylation was cancer specific and frequently observed. In two gastric cancer cell lines without Reprimo methylation, we observed faint or weak Reprimo expression under normal conditions and high expression under DNA-damaging conditions. In four gastric cancer cell lines with Reprimo methylation, however, Reprimo expression remained faint even under DNA-damaging conditions, with expression being restored in combination with agents that induce demethylation. Enforced Reprimo expression robustly inhibited cell proliferation and anchorage-independent colony formation and enhanced DNA damage-induced apoptosis. Inverse effects were observed via siRNA-mediated knockdown of endogenous Reprimo. Reprimo expression inhibited tumorigenesis in vivo. Reprimo methylation was also associated with a poor response in patients with gastric cancer treated with chemotherapy (P¼ 0.028), and a poor prognosis in patients with advanced gastric cancer (P¼ 0.03). In conclusion, Reprimo expression is normally induced in response to DNA damage, acting as a novel tumor suppressor in gastric cancer. However, Reprimo methylation abrogates its expression and effects. The clinical assessment of Reprimo promoter methylation may serve not only as a predictive marker for chemotherapy, but also as a marker for tumor aggressiveness.
Collapse
Affiliation(s)
- Akira Ooki
- Department of Surgery, Kitasato University School of Medicine, Kitasato 1-15-1, Sagamihara 228-8555, Kanagawa, Japan.
| | | | | | | | | | | |
Collapse
|
13
|
Wu Y, Zhang B, Guo LH. Label-Free and Selective Photoelectrochemical Detection of Chemical DNA Methylation Damage Using DNA Repair Enzymes. Anal Chem 2013; 85:6908-14. [DOI: 10.1021/ac401346x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yiping Wu
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bintian Zhang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liang-Hong Guo
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
14
|
Larkin J, Carson S, Stoloff DH, Wanunu M. Nanopore-Based Analysis of Chemically Modified DNA and Nucleic Acid Drug Targets. Isr J Chem 2013. [DOI: 10.1002/ijch.201300006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
15
|
Akinfieva O, Nabiev I, Sukhanova A. New directions in quantum dot-based cytometry detection of cancer serum markers and tumor cells. Crit Rev Oncol Hematol 2013; 86:1-14. [DOI: 10.1016/j.critrevonc.2012.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/18/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022] Open
|
16
|
Gan JK, Zhang DX, He DL, Zhang XQ, Chen ZY, Luo QB. Promoter methylation negatively correlated with mRNA expression but not tissue differential expression after heat stress. GENETICS AND MOLECULAR RESEARCH 2013; 12:809-19. [PMID: 23546965 DOI: 10.4238/2013.march.15.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA methylation plays a central role in gene expression. In this study, we detected the promoter methylation pattern of the chicken heat shock protein 70 (HSP70) gene and its association with messenger RNA (mRNA) expression before and after heat shock. The results showed that mRNA expression increased in response to heat stress and peaked at 3 h before dropping. Hypomethylation of the HSP70 promoter occurred in all of the groups studied, but the difference between groups within tissue type was not significant. The DNA methylation level of the control and the 6-h treatment groups was slightly higher than that of the 3-h treatment group in brain tissue and leg muscle. Correlation analysis between mRNA expression and DNA methylation of HSP70 showed that DNA methylation was negatively associated with mRNA expression in leg muscle (P = 0.0124), indicating that DNA methylation may be negatively associated with the expression of HSP70, although the difference was not significant. We concluded that the expression of HSP70 is heat inducible and tissue dependent and that heat induction may correlate with DNA methylation pattern in the HSP70 promoter, whereas tissue dependence is unrelated to DNA methylation pattern.
Collapse
Affiliation(s)
- J K Gan
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | | | | | | | | | | |
Collapse
|
17
|
Truong M, Yang B, Jarrard DF. Toward the detection of prostate cancer in urine: a critical analysis. J Urol 2012; 189:422-9. [PMID: 23017522 DOI: 10.1016/j.juro.2012.04.143] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2012] [Indexed: 01/04/2023]
Abstract
PURPOSE Prostate specific antigen and digital rectal examination have low specificity for detecting prostate cancer and they poorly predict the presence of aggressive disease. Urine is readily available and noninvasive, and it represents a promising source of biomarkers for the early detection and prediction of prostate cancer prognosis. We identified promising biomarkers for urine based prostate cancer, examined trends and outlined potential pitfalls. MATERIALS AND METHODS We performed PubMed® and Web of Science® database searches of the peer reviewed literature on urine based testing for prostate cancer. Original studies of this subject as well as a small number of reviews were analyzed, including the strengths and weaknesses. We provide a comprehensive review of urine based testing for prostate cancer that covers the technical aspects, including the methodology of urine collection, as well as recent developments in biomarkers spanning the fields of genomics, epigenetics, transcriptomics, proteomics and metabolomics. RESULTS The process of urine collection is subject to variability, which may result in conflicting clinical results. Detecting prostate cancer in urine is technically feasible, as demonstrated by numerous proof of principle studies, but few markers have been validated in multiple large sample sets. Biomarker development using urine has been accelerating in recent years with numerous studies identifying DNA, RNA, protein and metabolite based biomarkers in urine. Advanced clinical studies have identified PCA3 and TMPRSS2:ERG fusion transcripts as promising RNA markers for cancer detection and possibly prognosis. DNA methylation analysis of multiple genes improves specificity and represents a promising platform for developing clinical grade assays. CONCLUSIONS Urine based testing is noninvasive and represents a rich source of novel biomarkers for prostate cancer. Although urine shows promise for detecting cancer, the ability to identify aggressive subsets of prostate cancer needs further development.
Collapse
Affiliation(s)
- Matthew Truong
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | | | | |
Collapse
|
18
|
Gao T, Nie Y, Guo J. Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile. Mol Biol Rep 2012; 39:6591-8. [PMID: 22327645 DOI: 10.1007/s11033-012-1489-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 01/24/2012] [Indexed: 12/31/2022]
Abstract
In order to identify epigenetic markers of β-thalassemia, a genome-wide profiling method named differential methylation hybridization was used to search these differentially methylated genes. Unsupervised hierarchical clustering and molecular annotation system were used to analyze the data, and methylation-specific PCR and real-time PCR were used to confirm the differentially methylated genes. This system was validated by detecting 13 cases, 10 of which were homo-zygous β-thalassaemia. Totally 113 genes were identified as methlyation-enriched genes (ratio ≥ 2.0, P < 0.05) and 96 genes were identified as hypomethylated genes in both groups (ratio ≤ 0.5, P < 0.05). The promoter of the gene of La ribonucleoprotein domain family (LARP2) was significantly hypermethylated in β-thalassemia, and the expression of LARP2 was significantly lower in β-thalassemia. Hypermethylation of the LARP2 promoter was correlated with its lower expression in β-thalassemia and our chip-based DNA methylation detection system can provide earlier diagnosis of β-thalassemia using this epigenetic marker.
Collapse
Affiliation(s)
- Tian Gao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital, Chongqiang Medical University, Chongqing, China
| | | | | |
Collapse
|
19
|
Grønbæk K, Müller-Tidow C, Perini G, Lehmann S, Bach Treppendahl M, Mills K, Plass C, Schlegelberger B. A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies. Haematologica 2012; 97:1380-8. [PMID: 22491733 DOI: 10.3324/haematol.2011.058305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Research over the past decade has confirmed that epigenetic alterations act in concert with genetic lesions to deregulate gene expression in acute myeloid leukemia and myelodysplastic syndromes. Epigenetic alterations may serve as markers of disease, and may potentially be used for classification, prognostication and to monitor minimal residual disease. In addition, we now have the capability to pharmaceutically target epigenetic modifications, and there is an urgent need for early validation of the efficacy of the drugs. Also, an improved understanding of the functionality of epigenetic modifications may further pave the road towards individualized therapy. The recent advances in biotechnology and bioinformatics provide a plethora of novel tools for characterizing the epigenome in clinical samples, but at this point the practical, clinical utility of these methodologies needs further exploration. Here, we provide the pros and cons of the currently most feasible methods used for characterizing the methylome in clinical samples, and give a brief introduction to novel approaches to sequencing that may revolutionize our abilities to characterize the genomes and epigenomes in acute myeloid leukemia and myelodysplastic syndrome patients.
Collapse
Affiliation(s)
- Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
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]
|
21
|
High-resolution quantitative methylation analysis of microRNA genes using Pyrosequencing™. Methods Mol Biol 2012; 878:229-40. [PMID: 22674137 DOI: 10.1007/978-1-61779-854-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNA (miRNA) genes have been shown to perform a crucial role in breast cancer metastasis. The epigenetic inactivation of such microRNA genes, as a result of aberrant DNA methylation, is frequently found in human tumours including those of the breast, and this is an area of considerable research activity.Pyrosequencing™ is a new quantitative method for the assessment of DNA methylation, with single CpG site resolution. Pyrosequencing™ can easily be performed in a 96-well-plate format with a cost-effective medium-sized throughput.This chapter provides a general outline of DNA methylation analysis, a detailed protocol of the Pyrosequencing™ procedure, and guidelines for the design of new assays. The strengths and limitations of this approach are discussed throughout the chapter.
Collapse
|
22
|
Steinmann K, Richter AM, Dammann RH. Epigenetic silencing of erythropoietin in human cancers. Genes Cancer 2011; 2:65-73. [PMID: 21779481 DOI: 10.1177/1947601911405043] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/15/2011] [Accepted: 02/27/2011] [Indexed: 12/24/2022] Open
Abstract
The glycoprotein hormone erythropoietin (EPO) is a key regulator in the production of red blood cells. EPO is produced mainly in the embryonic liver and kidney of adults. Other organs are also known to express varying amounts of EPO. In our study, we have analyzed the epigenetic regulation of EPO in human cancer cell lines by DNA methylation assays, chromatin immunoprecipitation, RT-PCR, and promoter analysis under different growth conditions. Moreover, the growth-related effects of ectopic EPO expression were analyzed in a head and neck cancer cell line. We found frequent DNA hypermethylation of the CpG island promoter and enhancer of EPO in different cancer cell lines. Aberrant methylation of EPO promoter was observed in primary lung, head and neck, breast, and liver cancers. Hypermethylation of EPO was associated with a decreased expression of EPO in cancer cells. Treatment of cancer cell lines with 5-aza-2'-deoxycytidine (Aza), an inhibitor of DNA methylation, reactivated EPO expression under hypoxia. In contrast, in the liver cancer cell line HepB3, the EPO promoter was unmethylated, and a high EPO expression was observed independently of Aza treatment. Moreover, in vitro hypermethylation of the EPO promoter and enhancer reduced expression of a reporter gene under normoxia and hypoxia. Induction of EPO under hypoxia was accompanied by increased histone H3 acetylation and reduced histone H3 lysine 9 trimethylation. In a head and neck cancer cell line, which exhibited low EPO levels, ectopic expression of EPO significantly enhanced proliferation under normoxia and hypoxia. In summary, we show that hypermethylation of regulatory sequences of EPO is frequently observed in tumors and that this aberrant methylation induces epigenetic silencing of EPO in cancer cells.
Collapse
Affiliation(s)
- Katrin Steinmann
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | | | | |
Collapse
|
23
|
Zheng Y, Chen L, Li J, Yu B, Su L, Chen X, Yu Y, Yan M, Liu B, Zhu Z. Hypermethylated DNA as potential biomarkers for gastric cancer diagnosis. Clin Biochem 2011; 44:1405-11. [PMID: 21945024 DOI: 10.1016/j.clinbiochem.2011.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/31/2011] [Accepted: 09/04/2011] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To demonstrate the diagnostic significance of methylation, an important molecular event in gastric carcinogenesis. DESIGN AND METHODS We used methylation microarray to determine candidate genes, and performed MSP to evaluate the methylation status of them in tissues and sera. The effect of demethylation on mRNA expression was investigated by rt-PCR after gastric cancer cell lines were treated with 5-Aza-dC for 96 h. RESULTS In tissues and sera of gastric cancer patients, a higher prevalence of methylation was observed for BX141696, WT1, CYP26B1, and KCNA4, compared to healthy people (p<0.05, respectively). Detection of the methylation prevalence of KCNA4 and CYP26B1 together in serum demonstrated the good sensitivity (91.3%) and specificity (92.1%). After 5-Aza-dC treatment in gastric cancer cell lines, the mRNA expression level of these genes was restored. CONCLUSIONS This study underscores the potential application of measurement of serum DNA methylation of these genes, as promising tool for gastric cancer detection.
Collapse
Affiliation(s)
- Yanan Zheng
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Nasu K, Kawano Y, Tsukamoto Y, Takano M, Takai N, Li H, Furukawa Y, Abe W, Moriyama M, Narahara H. Aberrant DNA methylation status of endometriosis: epigenetics as the pathogenesis, biomarker and therapeutic target. J Obstet Gynaecol Res 2011; 37:683-95. [PMID: 21651673 DOI: 10.1111/j.1447-0756.2011.01663.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Endometriosis, a common, benign, estrogen-dependent disease affecting 3-10% of women of reproductive age, is characterized by the ectopic growth of endometrial tissue that is found primarily in the peritoneum, ovaries and rectovaginal septum. Recently, endometriosis has been alternatively described as an immune disease, a genetic disease and a disease caused by exposure to environmental factors, in addition to its usual description as a hormonal disease. In addition, accumulating evidence suggests that various epigenetic aberrations play definite roles in the pathogenesis of endometriosis. Epigenetic alterations reported to date in endometriosis include the genomic DNA methylation of progesterone receptor-B, E-cadherin, homeobox A10, estrogen receptor-β, steroidogenic factor-1 and aromatase. Aberrant expression of DNA methyltransferases, which attach a methyl group to the 5-carbon position of cytosine bases in the CpG island of the promoter region and silence the corresponding gene expression, has also been demonstrated in endometriosis. This review summarizes the recent studies on the aberrant DNA methylation status and aberrant expression of DNA methyltransferases, which regulate DNA methylation, in endometriosis. We also discuss the recent information on the diagnostic and therapeutic implications of epigenetic alterations occurring in endometriosis.
Collapse
Affiliation(s)
- Kaei Nasu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Oita University, Oita, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Yang SY, Yang XL, Yao LF, Wang HB, Sun CK. Effect of CpG methylation on DNA binding protein: molecular dynamics simulations of the homeodomain PITX2 bound to the methylated DNA. J Mol Graph Model 2011; 29:920-7. [PMID: 21498098 DOI: 10.1016/j.jmgm.2011.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
A large number of studies have argued that aberrant CpG methylation is associated with some human cancers. One possible mechanism of the cancer caused by CpG methylation is the gene repression, which is a binding-inhibition of the sequence-specific transcription factors bound to specific DNA-binding sites. Exploring the effects of CpG methylation on the structure and the thermodynamic property of DNA-binding transcription factors will help to gain an insight into how CpG methylation affects the repression of gene transcription in cancer. We have performed molecular dynamics (MD) simulations and free energy calculations of the protein bound to the native or the methylated DNA, in which the solution structure of the K50-class homeodomain PITX2 bound to DNA was used as a template. The simulation results indicate that the methylated CpG located at the DNA major groove can enhance the protein-DNA interactions, and the residue side-chains near the methylated CpG pair appear to have an unusually high affinity with DNA. The structural analysis and calculated energy values demonstrate that the binding-induced structural changes were further encouraged as the CpG methylation upon the complexation. Moreover, the CpG methylation may reduce the unfavorable effect of the conformational entropy and increase the electrostatic contribution to the binding free energy of DNA-PITX2. The changes in specific binding sites and the excessive affinity between DNA and protein caused by the CpG methylation could affect the gene transcriptional activity.
Collapse
Affiliation(s)
- Si-Ya Yang
- School of Chemistry and Chemical Engineering, Qujing Normal University, Sanjiang Road, Qinig District, Qujing City 655011, Yunnan Province, PR China.
| | | | | | | | | |
Collapse
|
26
|
Ziech D, Franco R, Pappa A, Panayiotidis MI. Reactive oxygen species (ROS)--induced genetic and epigenetic alterations in human carcinogenesis. Mutat Res 2011; 711:167-73. [PMID: 21419141 DOI: 10.1016/j.mrfmmm.2011.02.015] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/26/2011] [Accepted: 02/28/2011] [Indexed: 12/12/2022]
Abstract
Cancer is a multistage and complex process characterized by molecular alterations that underlie all three phases of its development: (i) initiation, (ii) promotion and (iii) progression. Some of these molecular events include alterations in gene expression that are regulated by both genetic and epigenetic mechanisms. On the other hand, "oxidative stress" implies a cellular state where ROS production exceeds the cell's ability to metabolize them resulting in excessive accumulation of ROS that overwhelms cellular defenses. Such state has been shown to regulate both genetic and epigenetic cascades underlying altered gene expression in human disease including cancer. Throughout this manuscript, we review the current state of knowledge on the role of ROS-induced oxidative stress in altering the genetic and epigenetic involvement during human carcinogenesis.
Collapse
Affiliation(s)
- Dominique Ziech
- Department of Student Success Services, University of Nevada, Reno, NV 89557, USA
| | | | | | | |
Collapse
|
27
|
Park YJ, Claus R, Weichenhan D, Plass C. Genome-wide epigenetic modifications in cancer. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:25-49. [PMID: 21141723 PMCID: PMC3066002 DOI: 10.1007/978-3-7643-8989-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Epigenetic alterations in cancer include changes in DNA methylation and associated histone modifications that influence the chromatin states and impact gene expression patterns. Due to recent technological advantages, the scientific community is now obtaining a better picture of the genome-wide epigenetic changes that occur in a cancer genome. These epigenetic alterations are associated with chromosomal instability and changes in transcriptional control which influence the overall gene expression differences seen in many human malignancies. In this review, we will briefly summarize our current knowledge of the epigenetic patterns and mechanisms of gene regulation in healthy tissues and relate this to what is known for cancer genomes. Our focus will be on DNA methylation. We will review the current standing of technologies that have been developed over recent years. This field is experiencing a revolution in the strategies used to measure epigenetic alterations, which includes the incorporation of next generation sequencing tools. We also will review strategies that utilize epigenetic information for translational purposes, with a special emphasis on the potential use of DNA methylation marks for early disease detection and prognosis. The review will close with an outlook on challenges that this field is facing.
Collapse
Affiliation(s)
- Yoon Jung Park
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
28
|
Wallace EVB, Stoddart D, Heron AJ, Mikhailova E, Maglia G, Donohoe TJ, Bayley H. Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun (Camb) 2010; 46:8195-7. [PMID: 20927439 PMCID: PMC3147113 DOI: 10.1039/c0cc02864a] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two DNA bases, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (hmC), marks of epigenetic modification, are recognized in immobilized DNA strands and distinguished from G, A, T and C by nanopore current recording. Therefore, if further aspects of nanopore sequencing can be addressed, the approach will provide a means to locate epigenetic modifications in unamplified genomic DNA.
Collapse
Affiliation(s)
- Emma V. B. Wallace
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - Andrew J. Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - Ellina Mikhailova
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - Timothy J. Donohoe
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, OX1 3TA, Oxford, UK
| |
Collapse
|
29
|
Cowin PA, Anglesio M, Etemadmoghadam D, Bowtell DDL. Profiling the cancer genome. Annu Rev Genomics Hum Genet 2010; 11:133-59. [PMID: 20590430 DOI: 10.1146/annurev-genom-082509-141536] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer profiling studies have had a profound impact on our understanding of the biology of cancers in a number of ways, including providing insights into the biological heterogeneity of specific cancer types, identification of novel oncogenes and tumor suppressors, and defining pathways that interact to drive the growth of individual cancers. Several large-scale genomic studies are underway that aim to catalog all biologically significant mutational events in each cancer type, and these findings will allow researchers to understand how mutational networks function within individual tumors. The identification of molecular predictive and prognostic tools to facilitate treatment decisions is an important step for individualized patient therapy and, ultimately, in improving patient outcomes. Whereas there are still significant challenges to implementing genomic testing and targeted therapy into routine clinical practice, rapid technological advancements provide hope for overcoming these obstacles.
Collapse
Affiliation(s)
- Prue A Cowin
- Peter MacCallum Cancer Center, East Melbourne, Australia 3002.
| | | | | | | |
Collapse
|
30
|
|
31
|
Huang THM, Esteller M. Chromatin remodeling in mammary gland differentiation and breast tumorigenesis. Cold Spring Harb Perspect Biol 2010; 2:a004515. [PMID: 20610549 DOI: 10.1101/cshperspect.a004515] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA methylation and histone modifications have essential roles in remodeling chromatin structure of genes necessary for multi-lineage differentiation of mammary stem/progenitor cells. The role of this well-defined epigenetic programming is to heritably maintain transcriptional plasticity of these loci over multiple cell divisions in the differentiated progeny. Epigenetic events can be deregulated in progenitor cells chronically exposed to xenoestrogen or inflammatory microenvironment. In addition, epigenetically mediated silencing of genes associated with tumor suppression can take place, resulting in clonal proliferation of undifferentiated or semidifferentiated cells. Alternatively, microRNAs that negatively regulate the expression of their protein-coding targets may become epigenetically repressed, leading to oncogenic expression of these genes. Here we further discuss interactions between DNA methylation and histone modifications that have significant contributions to the differentiation of mammary stem/progenitor cells and to tumor initiation and progression.
Collapse
Affiliation(s)
- Tim H-M Huang
- Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43220, USA.
| | | |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Ziech D, Franco R, Pappa A, Malamou-Mitsi V, Georgakila S, Georgakilas AG, Panayiotidis MI. The role of epigenetics in environmental and occupational carcinogenesis. Chem Biol Interact 2010; 188:340-9. [PMID: 20599843 DOI: 10.1016/j.cbi.2010.06.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/20/2010] [Indexed: 02/07/2023]
Abstract
Over the last few years there has been an increasing effort in identifying environmental and occupational carcinogenic agents and linking them to the incidence of a variety of human cancers. The carcinogenic process itself is multistage and rather complex involving several different mechanisms by which various carcinogenic agents exert their effect. Amongst them are epigenetic mechanisms often involving silencing of tumor suppressor genes and/or activation of proto-oncogenes, respectively. These alterations in gene expression are considered critical during carcinogenesis and have been observed in many environmental- and occupational-induced human cancers. Some of the underlying mechanisms proposed to account for such differential gene expression include alterations in DNA methylation and/or histone modifications. Throughout this article, we aim to provide a current account of our understanding on how the epigenetic pathway is involved in contributing to an altered gene expression profile during human carcinogenesis that ultimately will allow us for better cancer diagnostics and therapeutic strategies.
Collapse
Affiliation(s)
- Dominique Ziech
- Nevada Center for Ethics and Health Policy, University of Nevada, Reno, 89557, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Wagner MK, Li F, Li J, Li XF, Le XC. Use of quantum dots in the development of assays for cancer biomarkers. Anal Bioanal Chem 2010; 397:3213-24. [DOI: 10.1007/s00216-010-3847-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 05/11/2010] [Accepted: 05/13/2010] [Indexed: 02/02/2023]
|
35
|
Potential utility of HOP homeobox gene promoter methylation as a marker of tumor aggressiveness in gastric cancer. Oncogene 2010; 29:3263-75. [PMID: 20228841 DOI: 10.1038/onc.2010.76] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HOP homeobox (HOPX) is an unusual homeobox gene encoding three spliced transcript variants, among which the only HOPX-beta promoter harbors CpG islands. The characteristics of its promoter methylation was analyzed using bisulfite sequencing and quantitative-methylation-specific polymerase chain reaction (Q-MSP), and the effects of HOPX expression were also examined. HOPX-beta expression was silenced in all gastric cancer cell lines tested; its expression could be restored by treatment with demethylating agent. On Q-MSP, HOPX-beta hypermethylation (cut-off value of 3.55) was found in 84% (67 out of 80) of primary tumor tissues and 10% (8 out of 80) of the corresponding normal tissues and could discriminate normal from tumor tissues (P<0.0001). The prognosis of the advanced cases with HOPX-beta hypermethylation was as poor as those with stage IV disease when cut-off value was set at 11.28. This finding was validated in an independent cohort of 90 advanced gastric cancers. The HOPX-beta hypermethylation was also an independent prognostic factor (P=0.029) on multivariate analysis. Exogenous HOPX expression significantly inhibited cell proliferation, colony formation and invasion as well as enhanced apoptosis. Taken together, HOPX-beta promoter methylation is a frequent and cancer-specific event in gastric cancer. Quantitative assessment of HOPX-beta methylation has great clinical potential as a marker of tumor aggressiveness.
Collapse
|
36
|
Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
Collapse
Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
| |
Collapse
|
37
|
Seliger B, Handke D, Schabel E, Bukur J, Lichtenfels R, Dammann R. Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma. J Transl Med 2009; 7:90. [PMID: 19857250 PMCID: PMC2775027 DOI: 10.1186/1479-5876-7-90] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/26/2009] [Indexed: 12/12/2022] Open
Abstract
Background The ubiquitin carboxyl-terminal hydrolase 1 (UCHL1) gene involved in the regulation of cellular ubiquitin levels plays an important role in different cellular processes including cell growth and differentiation. Aberrant expression of UCHL1 has been found in a number of human solid tumors including renal cell carcinoma (RCC). In RCC, UCHL1 overexpression is associated with tumor progression and an altered von Hippel Lindau gene expression. Methods To determine the underlying mechanisms for the heterogeneous UCHL1 expression pattern in RCC the UCHL1 promoter DNA methylation status was determined in 17 RCC cell lines as well as in 32 RCC lesions and corresponding tumor adjacent kidney epithelium using combined bisulfite restriction analysis as well as bisulfite DNA sequencing. Results UCHL1 expression was found in all 32 tumor adjacent kidney epithelium samples. However, the lack of or reduced UCHL1 mRNA and/or protein expression was detected in 13/32 RCC biopsies and 7/17 RCC cell lines and due to either a total or partial methylation of the UCHL1 promoter DNA. Upon 2'-deoxy-5-azacytidine treatment an induction of UCHL1 mRNA and protein expression was found in 9/17 RCC cell lines, which was linked to the demethylation degree of the UCHL1 promoter DNA. Conclusion Promoter hypermethylation represents a mechanism for the silencing of the UCHL1 gene expression in RCC and supports the concept of an epigenetic control for the expression of UCHL1 during disease progression.
Collapse
Affiliation(s)
- Barbara Seliger
- Martin Luther University Halle-Wittenberg, Institute of Medical Immunology, Halle, Germany.
| | | | | | | | | | | |
Collapse
|
38
|
Hoque MO. DNA methylation changes in prostate cancer: current developments and future clinical implementation. Expert Rev Mol Diagn 2009; 9:243-57. [PMID: 19379083 DOI: 10.1586/erm.09.10] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Promoter hypermethylation is associated with the loss of expression of tumor-suppressor genes in cancer. Currently, several genome-wide technologies are available and have been utilized to examine the extent of DNA methylation in discovery-based studies involving several physiological and disease states. Although early in the process, aberrant DNA methylation is gaining strength in the fields of cancer risk assessment, diagnosis and therapy monitoring in different cancer types. There is a need to improve existing methods for early diagnosis of prostate cancer and to identify men at risk for developing aggressive disease. Because of the ubiquity of DNA methylation changes and the ability to detect methylated DNA in several body fluids (e.g., blood and urine), this specifically altered DNA may serve, on one hand, as a possible new screening marker for prostate cancer and, on the other hand, as a tool for therapy monitoring in patients having had neoplastic disease of the prostate. Since many prostate cancer patients present with advanced disease and some present with nonspecific elevation of prostate-specific antigen without prostate cancer, early detection with high specificity and sensitivity is considered to be one of the most important approaches to reduce mortality and unwanted tension of the men with high prostate-specific antigen. Therefore, an effective screening test would have substantial clinical benefits. Furthermore, methylation markers of risk of progression of disease in patients having prostate cancer permits immediate commencement of specific treatment regimens and probably longer survival and better quality of life. This review illustrates the current benefits and limitations of potentially useful prostate cancer methylation markers that have considerable existing data and touches upon other future markers as well as the field of methylation in prostate cancer.
Collapse
Affiliation(s)
- Mohammad Obaidul Hoque
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II, 5M.07, Baltimore, MD 21231, USA.
| |
Collapse
|
39
|
Malentacchi F, Forni G, Vinci S, Orlando C. Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol. Nucleic Acids Res 2009; 37:e86. [PMID: 19454604 PMCID: PMC2709587 DOI: 10.1093/nar/gkp383] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is a key regulator of gene transcription. Alterations in DNA methylation patterns are common in most cancers, occur early in carcinogenesis and can be detected in body fluids. Reliable and sensitive quantitative assays are required to improve the diagnostic role of methylation in the management of cancer patients. Here we present an optimized procedure, based on differential-high resolution melting analysis (D-HRMA), for the rapid and accurate quantification of methylated DNA. Two sets of primers are used in a single tube for the simultaneous amplification of the methylated (M) and unmethylated (Um) DNA sequences in D-HRMA. After HRM, differential fluorescence was calculated at the specific melting temperature after automatic subtraction of UM-DNA fluorescence. Quantification was calculated by interpolation on an external standard curve generated by serial dilutions of M-DNA. To optimize the protocol, nine primer sets were accurately selected on the basis of the number of CpG on promoters of hTERT and Bcl2 genes. The use of optimized D-HRMA allowed us to detect up to 0.025% M-DNA. D-HRMA results of DNA from 85 bladder cancers were comparable to those obtained with real time quantitative methylation specific PCR. In addition, D-HRMA appears suitable for rapid and efficient measurements in 'in vitro' experiments on methylation patterns after treatment with demethylating drugs.
Collapse
Affiliation(s)
- Francesca Malentacchi
- Clinical Biochemistry Unit, Department of Clinical Physiopathology, University of Florence, Viale Pieraccini 6, 50139, Florence, Italy
| | | | | | | |
Collapse
|
40
|
Liu Z, Wu J, Xie Z, Liu S, Fan-Havard P, Huang THM, Plass C, Marcucci G, Chan KK. Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry. Anal Biochem 2009; 391:106-13. [PMID: 19442645 DOI: 10.1016/j.ab.2009.05.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/04/2009] [Accepted: 05/07/2009] [Indexed: 12/31/2022]
Abstract
Promoter hypermethylation-associated tumor suppressor gene (TSG) silencing has been explored as a therapeutic target for hypomethylating agents. Promoter methylation change may serve as a pharmacodynamic endpoint for evaluation of the efficacy of these agents and predict the patient's clinical response. Here a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay has been developed for quantitative regional DNA methylation analysis using the molar ratio of 5-methyl-2'-deoxycytidine (5mdC) to 2'-deoxycytidine (2dC) in the enzymatic hydrolysate of fully methylated bisulfite-converted polymerase chain reaction (PCR) amplicons as the methylation indicator. The assay can differentiate 5% of promoter methylation level with an intraday precision ranging from 3 to 16% using two TSGs: HIN-1 and RASSF1A. This method was applied to characterize decitabine-induced promoter DNA methylation changes of these two TSGs in a breast cancer MCF-7 cell line. Promoter methylation of these TSGs was found to decrease in a dose-dependent manner. Correspondingly, the expression of these TSGs was enhanced. The sensitivity and reproducibility of the method make it a valuable tool for specific gene methylation analysis that could aid characterization of hypomethylating activity on specific genes by hypomethylating agents in a clinical setting.
Collapse
Affiliation(s)
- Zhongfa Liu
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Investigation of genomic methylation status using methylation-specific and bisulfite sequencing polymerase chain reaction. Methods Mol Biol 2009; 523:217-34. [PMID: 19381936 DOI: 10.1007/978-1-59745-190-1_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Epigenetic modification plays a central role in the regulation of gene expression and therefore in the development of disease states. In particular, genomic methylation of cytosines within CpG dinucleotides is crucial to development, gene silencing and chromosome inactivation. Importantly, aberrant methylation profiles of various genes are associated with cancer and potentially autoimmune disease, brain-related disease, diabetes and heart disease. Various methods are available for the detection and quantification of methylation in a given sample. Most of these methods rely upon bisulfite conversion of DNA, which converts unmethylated cytosines to uracil, while methylated cytosines remain as cytosines. Methylation-specific amplification of DNA can be used to detect methylation at one or more (typically up to about 4) CpG sites by using primers specific to either methylated or unmethylated DNA. Alternatively, amplification of both methylated and unmethylated DNA followed by sequencing can be used to detect methylation status at multiple CpG sites. The following chapter provides protocols for bisulfite conversion of DNA, methylation-specific PCR and bisulfite sequencing PCR.
Collapse
|
42
|
Pavlova TV, Kashuba VI, Muravenko OV, Yenamandra SP, Ivanova TA, Zabarovska VI, Rakhmanaliev ER, Petrenko LA, Pronina IV, Loginov VI, Yurkevich OY, Kisselev LL, Zelenin AV, Zabarovsky ER. Use of NotI microarrays in analysis of epigenetic and structural changes in epithelial tumor genomes by the example of human chromosome 3. Mol Biol 2009. [DOI: 10.1134/s0026893309020137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
43
|
TSC-22 contributes to hematopoietic precursor cell proliferation and repopulation and is epigenetically silenced in large granular lymphocyte leukemia. Blood 2009; 113:5558-67. [PMID: 19329776 DOI: 10.1182/blood-2009-02-205732] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant methylation of tumor suppressor genes can lead to their silencing in many cancers. TSC-22 is a gene silenced in several solid tumors, but its function and the mechanism(s) responsible for its silencing are largely unknown. Here we demonstrate that the TSC-22 promoter is methylated in primary mouse T or natural killer (NK) large granular lymphocyte (LGL) leukemia and this is associated with down-regulation or silencing of TSC-22 expression. The TSC-22 deregulation was reversed in vivo by a 5-aza-2'-deoxycytidine therapy of T or NK LGL leukemia, which significantly increased survival of the mice bearing this disease. Ectopic expression of TSC-22 in mouse leukemia or lymphoma cell lines resulted in delayed in vivo tumor formation. Targeted disruption of TSC-22 in wild-type mice enhanced proliferation and in vivo repopulation efficiency of hematopoietic precursor cells (HPCs). Collectively, our data suggest that TSC-22 normally contributes to the regulation of HPC function and is a putative tumor suppressor gene that is hypermethylated and silenced in T or NK LGL leukemia.
Collapse
|
44
|
Vinci S, Giannarini G, Selli C, Kuncova J, Villari D, Valent F, Orlando C. Quantitative methylation analysis of BCL2, hTERT, and DAPK promoters in urine sediment for the detection of non-muscle-invasive urothelial carcinoma of the bladder: a prospective, two-center validation study. Urol Oncol 2009; 29:150-6. [PMID: 19272801 DOI: 10.1016/j.urolonc.2009.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2008] [Revised: 01/08/2009] [Accepted: 01/12/2009] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Urinary hypermethylation of BCL2, hTERT, and DAPK promoters has been previously demonstrated as an accurate biomarker for the detection of urothelial carcinoma of the bladder (UCB) in patients undergoing radical cystectomy. In the present study, we investigated with a validation intent the frequency and levels of methylation of the same 3 genes in tumor tissue and urine sediment of patients undergoing transurethral resection (TUR) for non-muscle-invasive (NMI) UCB. MATERIALS AND METHODS A total of 108 consecutive patients with NMI UCB and 105 controls with no genitourinary malignancies were enrolled in this prospective study conducted in 2 tertiary referral academic urological departments with an advanced molecular laboratory. The frequency and levels of methylated BCL2, hTERT, and DAPK promoters were evaluated with quantitative methylation-specific real-time polymerase chain reaction in DNA extracted from tumor tissue and paired normal bladder mucosa retrieved at the time of TUR in patients, and from urine in patients and controls. RESULTS In tumor tissue, at least 1 gene was hypermethylated in 91% patients (BCL2 in 62%, hTERT in 53%, DAPK in 48%). Methylation of hTERT was significantly correlated with tumor grade (P = 0.026). In urine sediment sensitivity and specificity were 76% and 98%, respectively, using BCL2 and hTERT. The number of methylated genes was highly correlated with tumor grade (P = 0.005). Methylated BCL2 and hTERT in urine sediment were highly correlated with those of the corresponding bladder tumor qualitatively (P < 0.001), and only BCL2 also quantitatively (P = 0.005). Methylation levels of BCL2 and hTERT were variably associated with tumor grade and stage, but were significantly correlated with patient age (P = 0.004 and P = 0.027, respectively). CONCLUSIONS These findings suggest that quantitative methylation analysis of BCL2 and hTERT, but not DAPK, in urine sediment may be a useful tool in the diagnosis of NMI UCB, deserving future applicability studies.
Collapse
Affiliation(s)
- Serena Vinci
- Clinical Biochemistry Unit, Department of Clinical Physiopathology, University of Florence, Florence, Italy
| | | | | | | | | | | | | |
Collapse
|
45
|
Brena RM, Plass C. Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol Biol 2009; 507:257-69. [PMID: 18987820 DOI: 10.1007/978-1-59745-522-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA methylation is the best-studied epigenetic modification, and in mammals it describes the conversion of cytosine to 5-methylcytosine in the context of CpG dinucleotides. In recent years, it has become evident that epigenetic mechanisms are severely disrupted in human neoplasia, and evidence suggests that alterations of DNA methylation patterns may be an integral mechanism in the etiology of other diseases such as bipolar disorder and schizophrenia. The main effect of altered DNA methylation is the disruption of normal patterns of gene expression through genomic instability and hypermethylation of CpG islands, which together could lead to uncontrolled cell proliferation. DNA methylation can be reversed through pharmacological intervention via the systemic administration of DNA methylation inhibitors. Thus, the ability to accurately quantify DNA methylation levels in genomic sequences is a prerequisite to assess not only treatment efficacy, but also the effect of the DNA methylation inhibitors on bystander tissues. Several methods are currently available for the analysis of DNA methylation. Nonetheless, accurate and reproducible quantification of DNA methylation remains challenging. Here, we describe Bio-COBRA, a modified protocol for combined bisulfite restriction analysis (COBRA) that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. Bio-COBRA provides a platform for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. Its sensitivity and reproducibility also make it an excellent tool for the analysis of DNA methylation in clinical samples.
Collapse
Affiliation(s)
- Romulo Martin Brena
- Division of Human Cancer Genetics, The Ohio State University, Columbus, OH, USA
| | | |
Collapse
|
46
|
Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment. Semin Cancer Biol 2009; 19:165-71. [PMID: 19429480 DOI: 10.1016/j.semcancer.2009.02.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 02/11/2009] [Indexed: 12/24/2022]
Abstract
Epigenetic alterations of the genome such as DNA promoter methylation and chromatin remodeling play an important role in tumorigenesis. Recent findings indicate epigenetic modifications as key factors in breast carcinogenesis. These modifications are quite appealing as targets for preventative care and therapeutics because of their potential for reversal. Future medical care for breast cancer patients will likely depend upon a better understanding of the roles epigenetic modifications play in carcinogenesis. Here, we discuss the importance of epigenetics in breast cancer detection, prognosis, and therapy with an emphasis on mechanisms and epigenetic contributions to field cancerization effects.
Collapse
|
47
|
Jiang SW, Li J, Podratz K, Dowdy S. Application of DNA methylation biomarkers for endometrial cancer management. Expert Rev Mol Diagn 2009; 8:607-16. [PMID: 18785809 DOI: 10.1586/14737159.8.5.607] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It has become clear that aberrant gene expression, via alterations in promoter methylation or histone acetylation, is a contributing factor for carcinogenesis, perhaps as important as genetic mutation. This is particularly evident in endometrial cancer, in which multiple genes are silenced through hypermethylation. In this review, we discuss the field of epigenetics and relevant techniques to characterize methylation and acetylation alterations. The CpG island methylator phenotype, epimutations and the effects of aging on methylation are also discussed. In endometrial cancer there is evidence that hypermethylation of relevant genes can be reversed using epigenetic inhibitors, resulting in re-expression of silenced genes. Preliminary data also suggest that a panel of methylation biomarkers could be useful for diagnosis and even screening in selected populations at high risk. This disease is particularly well suited for such a strategy given that the endometrium is readily accessible for testing and endometrial cancer precursors are well defined.
Collapse
Affiliation(s)
- Shi-Wen Jiang
- Department of Biomedical Science, Mercer University School of Medicine at Savannah, 4700, Waters Avenue, Savannah, GA 31404, USA.
| | | | | | | |
Collapse
|
48
|
Marlowe J, Teo SS, Chibout SD, Pognan F, Moggs J. Mapping the epigenome--impact for toxicology. EXS 2009; 99:259-88. [PMID: 19157065 DOI: 10.1007/978-3-7643-8336-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in technological approaches for mapping and characterizing the epigenome are generating a wealth of new opportunities for exploring the relationship between epigenetic modifications, human disease and the therapeutic potential of pharmaceutical drugs. While the best examples for xenobiotic-induced epigenetic perturbations come from the field of non-genotoxic carcinogenesis, there is growing evidence for the relevance of epigenetic mechanisms associated with a wide range of disease areas and drug targets. The application of epigenomic profiling technologies to drug safety sciences has great potential for providing novel insights into the molecular basis of long-lasting cellular perturbations including increased susceptibility to disease and/or toxicity, memory of prior immune stimulation and/or drug exposure, and transgenerational effects.
Collapse
Affiliation(s)
- Jennifer Marlowe
- Novartis Pharma AG, Investigative Toxicology, Preclinical Safety, Basel, Switzerland.
| | | | | | | | | |
Collapse
|
49
|
Abstract
It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.
Collapse
|
50
|
Jackson S, Patel I, LeClerc J, Cebula T, Mammel M, Kotewicz M, Mukherjee A, Mahata S, Rodriguez Flores J, Mahata M, O’Connor D, Srinivasan J. Principles of Functional Genomic Analysis. Genomics 2008. [DOI: 10.3109/9781420067064-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|