1
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Botezatu IV, Kondratova VN, Stroganova AM, Dranko SL, Lichtenstein AV. Aberrant methylation scanning by quantitative DNA melting analysis with hybridization probes as exemplified by liquid biopsy of SEPT9 and HIST1H4F in colorectal cancer. Clin Chim Acta 2023; 551:117591. [PMID: 37832390 DOI: 10.1016/j.cca.2023.117591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/05/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
OBJECTIVE The generally accepted method of quantifying hypermethylated DNA by qPCR using methylation-specific primers has the risk of underestimating DNA methylation and requires data normalization. This makes the analysis complicated and less reliable. METHODS The end-point PCR method, called qDMA-HP (for quantitative DNA Melting Analysis with hybridization probes), which excludes the normalization procedure, is multiplexed and quantitative, has been proposed. qDMA-HP is characterized by the following features: (i) asymmetric PCR with methylation-independent primers; (ii) fluorescent dual-labeled, self-quenched probes (commonly known as TaqMan probes) covering several interrogated CpGs; (iii) post-PCR melting analysis of amplicon/probe hybrids; (iv) quantitation of unmethylated and methylated DNA alleles by measuring the areas under the corresponding melt peaks. RESULTS qDMA-HP was tested in liquid biopsy of colorectal cancer by evaluating SEPT9 and HIST1H4F methylations simultaneously in the single-tube reaction. Differences in the methylation levels in healthy donors versus cancer patients were statistically significant (p < 0.0001), AUCROC values were 0.795-0.921 for various marker combinations. CONCLUSIONS This proof-of-concept study shows that qDMA-HP is a simple, normalization-independent, quantitative, multiplex and "closed tube" method easily adapted to clinical settings. It is demonstrated, for the first time, that HIST1H4F is a perspective marker for liquid biopsy of colorectal cancer.
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Affiliation(s)
- Irina V Botezatu
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Valentina N Kondratova
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Anna M Stroganova
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Svetlana L Dranko
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia
| | - Anatoly V Lichtenstein
- N.N. Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115478, Russia.
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2
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Hosokawa M, Seiki R, Iwakawa S, Ogawara KI. Combination of azacytidine and curcumin is a potential alternative in decitabine-resistant colorectal cancer cells with attenuated deoxycytidine kinase. Biochem Biophys Res Commun 2021; 578:157-162. [PMID: 34571370 DOI: 10.1016/j.bbrc.2021.09.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Decitabine (DAC), a DNA methyltransferase (DNMT) inhibitor is a novel anti-cancer drug regulating epigenetic mechanisms. Similar to conventional anti-cancer drugs, drug resistance to DAC also has been reported, resulting in tumor recurrence. Our previous study using colorectal cancer HCT116 cells found the decrease in deoxycytidine kinase (dCK) (activation enzyme of DAC) and the increase in cytidine deaminase (inactivation enzyme of DAC) in acquired DAC-resistant HCT116 (HCT116/DAC) cells. The aim of our study was to clarify the involvement of dCK and CDA in DAC resistance. In order to tackle DAC resistance, it was also examined whether other DNMT inhibitors such as azacytidine (AC) and polyphenols are effective in DAC-resistant cancer cells. When dCK siRNA was transfected into HCT116 cells, IC50 value of DAC increased by about 74-fold and reached that of HCT116/DAC cells with attenuated dCK. dCK siRNA to HCT116 cells also abolished DNA demethylation effects of DAC. In contrast, CDA siRNA to HCT116 cells did not influence the efficacy of DAC. In addition, CDA siRNA to HCT116/DAC cells with increased CDA did not restore the compromised effects of DAC. These results suggested that attenuated dCK but not increased CDA mainly contributed to DAC resistance. Regarding dCK in HCT116/DAC cells, a point mutation with amino acid substitution was observed while the product size and expression of mRNA coding region did not change, suggesting that dCK protein was decreased by post-transcriptional regulation. AC and polyphenols showed no cross-resistance in HCT116/DAC cells. AC but not polyphenols exerted DNA demethylation effect. Among polyphenols, curcumin (Cur) showed the most synergistic cytotoxicity in combination with AC while DNA demethylation effect of AC was partly maintained. Taken together, combination of AC and Cur would be a promising alternative to tackle DAC resistance mainly due to attenuated dCK.
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Affiliation(s)
- Mika Hosokawa
- Department of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita, Higashinada, Kobe, 658-8558, Japan.
| | - Risako Seiki
- Department of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita, Higashinada, Kobe, 658-8558, Japan
| | - Seigo Iwakawa
- Department of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita, Higashinada, Kobe, 658-8558, Japan
| | - Ken-Ichi Ogawara
- Department of Pharmaceutics, Kobe Pharmaceutical University, 4-19-1 Motoyamakita, Higashinada, Kobe, 658-8558, Japan
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3
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The Zebrafish Model to Understand Epigenetics in Renal Diseases. Int J Mol Sci 2021; 22:ijms22179152. [PMID: 34502062 PMCID: PMC8431166 DOI: 10.3390/ijms22179152] [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: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modifications are able to alter gene expression and include DNA methylation, different histone variants, and post-transcriptional modifications (PTMs), such as acetylation or phosphorylation, and through short/long RNAs, respectively. In this review, we focus on current knowledge concerning epigenetic modifications in gene regulation. We describe different forms of epigenetic modifications and explain how epigenetic changes can be detected. The relevance of epigenetics in renal diseases is highlighted with multiple examples and the use of the zebrafish model to study glomerular diseases in general and epigenetics in renal diseases in particular is discussed. We end with an outlook on how to use epigenetic modifications as a therapeutic target for different diseases. Here, the zebrafish model can be employed as a high-throughput screening tool not only to discover epigenetic alterations contributing to disease, but also to test novel substances that change epigenetic signatures in vivo. Therefore, the zebrafish model harbors the opportunity to find novel pathogenic pathways allowing a pre-selection of potential targets and compounds to be tested for renal diseases.
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4
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Magadán S, Mikelez-Alonso I, Borrego F, González-Fernández Á. Nanoparticles and trained immunity: Glimpse into the future. Adv Drug Deliv Rev 2021; 175:113821. [PMID: 34087325 DOI: 10.1016/j.addr.2021.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022]
Abstract
Emerging evidences show that innate immune cells can display changes in their functional programs after infection or vaccination, which lead to immunomodulation (increased or reduced responsiveness) upon secondary activation to the same stimuli or even to a different one. Innate cells acquire features of immunological memory, nowadays using the new term of "trained immunity" or "innate immune memory", which is different from the specific memory immune response elicited by B and T lymphocytes. The review focused on the concept of trained immunity, mostly on myeloid cells. Special attention is dedicated to the pathogen recognition along the evolution (bacteria, plants, invertebrate and vertebrate animals), and to techniques used to study epigenetic reprogramming and metabolic rewiring. Nanomaterials can be recognized by immune cells offering a very promising way to learn about trained immunity. Nanomaterials could be modified in order to immunomodulate the responses ad hoc. Many therapeutic possibilities are opened, and they should be explored.
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5
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Tiedemann RL, Eden HE, Huang Z, Robertson KD, Rothbart SB. Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays. Methods Mol Biol 2021; 2272:97-140. [PMID: 34009611 DOI: 10.1007/978-1-0716-1294-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.
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Affiliation(s)
| | - Hope E Eden
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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6
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SLAM-MS: Mutation scanning of stem-loop amplicons with TaqMan probes by quantitative DNA melting analysis. Sci Rep 2020; 10:5476. [PMID: 32214156 PMCID: PMC7096437 DOI: 10.1038/s41598-020-62173-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022] Open
Abstract
DNA Melting Analysis (DMA) with a TaqMan probe covering the mutation “hot spot” is a simple, sensitive, and “closed tube” method of mutation detection. However, DMA requires asymmetric PCR to produce single-stranded amplicons capable of interacting with TaqMan probes. This makes quantitative analysis impossible owing to low amplification efficiency. Moreover, bi-strand mutation detection necessitates two independent PCRs. The SLAM-MS (Stem-Loop AMplicon Mutation Scanning) assay, in which symmetric PCR is performed using primers with 5'-universal primer sequence (UPS), has been developed to detect KRAS mutations. Some of the resulting amplicons, sense and antisense, adopt single-stranded stem-loop conformation and become unable to renature, but able to hybridize with TaqMan probes. Hybrids of stem-loops and complementary TaqMan probes are suitable for melting analysis and simultaneous bi-strand mutation scanning. In addition, the areas under the melting peaks are determined by the PeakFit software, a non-linear iterative curve fitting program, to evaluate the wild-type/mutant allele ratio. Thus, the SLAM-MS assay permits quantification of both the number of copies of the target sequence and the percentage of mutant alleles. For mutant enrichment, the SLAM-MS assay uses TaqMan probes as PCR blocking agents allowing an ~10 times higher mutation detection sensitivity than High Resolution Melting (HRM) assay.
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7
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Liu Y, Guo S, Yin C, Guo X, Liu M, Yuan Z, Zhao Z, Jia Y, Xing J. Optimized PCR-Based Enrichment Improves Coverage Uniformity and Mutation Detection in Mitochondrial DNA Next-Generation Sequencing. J Mol Diagn 2020; 22:503-512. [PMID: 32036083 DOI: 10.1016/j.jmoldx.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing-based methods have been commonly used for detecting mutations of mitochondrial genome (mtDNA). PCR amplification is a highly effective method of mtDNA enrichment before sequencing. However, it has been observed that highly variable sequencing depth within PCR amplicons severely reduces the coverage uniformity and accuracy of mutation calling. Therefore, it is necessary to develop an optimized PCR-based strategy for mtDNA sequencing. Herein, the effect of DNA quality on the efficiency of PCR amplification was analyzed and the effects of different primer-design methods, including the number of primer pairs, overlap length of amplicons, and modification of primers, on coverage uniformity and mutation calling in mtDNA sequencing were assessed. Results showed that DNA quality significantly affected the efficiency of PCR amplification. Importantly, over- and under-representation of coverage depth at overlap regions of amplicons were observed when amplicons were not modified and overlap was shorter than two sequencing fragment sizes (800 bp). Then, under-representation was overcome by increasing the overlap length of the amplicons, and over-representation was effectively reduced by 5'-block modification of primers and sticky-end ligation of amplicons. Moreover, findings indicated that these two optimized PCR-based sequencing strategies effectively improved mutation calling in primer-binding regions. Optimized PCR-based mtDNA enrichment and sequencing approaches have been established, which laid a foundation for accurate mutation detection of mtDNA in diseases.
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Affiliation(s)
- Yang Liu
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Chun Yin
- Department of Cardiovascular Medicine, the 902nd Hospital of PLA Joint Service Support Force, Bengbu, People's Republic of China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Manling Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zhidong Yuan
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zheng Zhao
- Third Department of Medical Oncology, Shanxi Provincial Cancer Hospital, Xi'an, People's Republic of China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China.
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China.
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8
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
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9
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Šestáková Š, Šálek C, Remešová H. DNA Methylation Validation Methods: a Coherent Review with Practical Comparison. Biol Proced Online 2019; 21:19. [PMID: 31582911 PMCID: PMC6771119 DOI: 10.1186/s12575-019-0107-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/09/2019] [Indexed: 12/25/2022] Open
Abstract
Here, we present a practical overview of four commonly used validation methods for DNA methylation assessment: methylation specific restriction endonucleases (MSRE) analysis, pyrosequencing, methylation specific high-resolution DNA melting (MS-HRM) and quantitative methylation specific polymerase chain reaction (qMSP). Using these methods, we measured DNA methylation levels of three loci in human genome among which one was highly methylated, one intermediately methylated and one unmethylated. We compared the methods in terms of primer design demands, methods' feasibility, accuracy, time and money consumption, and usability for clinical diagnostics. Pyrosequencing and MS-HRM proved to be the most convenient methods. Using pyrosequencing, it is possible to analyze every CpG in a chosen region. The price of the instrument may represent the main limitation of this methodology. MS-HRM is a simple PCR-based method. The measurement was quick, cheap and very accurate. MSRE analysis is based on a methylation specific digestion of DNA. It does not require a bisulfite conversion of DNA as the other methods. MSRE analysis was very easy to perform, however, it was not suitable for intermediately methylated regions and it was also quite expensive. qMSP is a qPCR-based method that uses primers designed specifically for methylated and unmethylated alleles of a chosen region. This was the least accurate method and also the primer design and optimization of PCR conditions were highly demanding.
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Affiliation(s)
- Šárka Šestáková
- 1Institute of Clinical and Experimental Hematology, First Faculty of Medicine, Charles University and Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,2Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Cyril Šálek
- 1Institute of Clinical and Experimental Hematology, First Faculty of Medicine, Charles University and Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,2Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Remešová
- 2Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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10
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Ren J, Cui JP, Luo M, Liu H, Hao P, Wang X, Zhang GH. The prevalence and persistence of aberrant promoter DNA methylation in benzene-exposed Chinese workers. PLoS One 2019; 14:e0220500. [PMID: 31381583 PMCID: PMC6681966 DOI: 10.1371/journal.pone.0220500] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
Aberrant DNA methylation patterns are common in cancers and environmental pollutant exposed subjects. Up to date, few studies have examined the aberrant DNA methylation patterns in benzene exposed workers. We recruited 141 benzene-exposed workers, including 83 benzene-exposed workers from a shoe factory in Wenzhou and 58 workers from a painting workshop in Wuhu, 35 workers in Wuhu were followed from 2009 to 2013, and 48 indoor workers as controls from Wenzhou. We used high-resolution melting (HRM) to quantitate human samples of DNA methylation in long interspersed nuclear element-1 (LINE-1), (6)-methylguanine-DNA methyltransferase (MGMT), and DNA mismatch repair gene human mutator L homologue 1 (hMLH1). AML-5 cells were treated with benzoquinone (BQ) and hydroquinone (HQ), and the promoter methylation of MGMT and hMLH1 was detected using the bisulfite sequencing PCR method. The degree of LINE-1 methylation in benzene-exposed workers was significantly lower than that of the controls (p<0.001), and the degree of MGMT (p<0.001) and hMLH1 (p = 0.01) methylation was significantly higher than that of the controls. The in vitro study validated the aberrant hypermethylation of hMLH1 after treatment with BQ. Among the cohort workers who were followed from 2009 to 2013, the LINE1 methylation elevated in 2013 than 2009 (p = 0.004), and premotor methylation in hMLH1 reduced in 2013 than 2009 (p = 0.045) with the reduction of the benzene exposure. This study provides evidence that benzene exposure can induce LINE-1 hypomethylation and DNA repair gene hypermethylation.
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Affiliation(s)
- Jingchao Ren
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Jun-peng Cui
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Mengkai Luo
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Huan Liu
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Pengfei Hao
- Xinxiang Center for Disease Control and Prevention, Xinxiang, China
| | - Xiao Wang
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
- * E-mail: (GZ); (XW)
| | - Guang-hui Zhang
- Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, Medicine, School of Public Health, Xinxiang Medical University, Xinxiang, China
- * E-mail: (GZ); (XW)
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11
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Zhang Y, Cui Y, An R, Liang X, Li Q, Wang H, Wang H, Fan Y, Dong P, Li J, Cheng K, Wang W, Wang S, Wang G, Xue C, Komiyama M. Topologically Constrained Formation of Stable Z-DNA from Normal Sequence under Physiological Conditions. J Am Chem Soc 2019; 141:7758-7764. [PMID: 30844265 DOI: 10.1021/jacs.8b13855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Z-DNA, a left-handed duplex, has been shown to form in vivo and regulate expression of the corresponding gene. However, its biological roles have not been satisfactorily understood, mainly because Z-DNA is easily converted to the thermodynamically favorable B-DNA. Here we present a new idea to form stable Z-DNA under normal physiological conditions and achieve detailed analysis on its fundamental features. Simply by mixing two complementary minicircles of single-stranded DNA with no chemical modification, the hybridization spontaneously induces topological constraint which twines one-half of the double-stranded DNA into stable Z-DNA. The formation of Z-conformation with high stability has been proved by using circular dichroism spectroscopy, Z-DNA-specific antibody binding assay, nuclease digestion, etc. Even at a concentration of MgCl2 as low as 0.5 mM, Z-DNA was successfully obtained, avoiding the use of high salt conditions, limited sequences, ancillary additives, or chemical modifications, criteria which have hampered Z-DNA research. The resultant Z-DNA has the potential to be used as a canonical standard sample in Z-DNA research. By using this approach, further developments of Z-DNA science and its applications become highly promising.
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Affiliation(s)
- Yaping Zhang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yixiao Cui
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Qi Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Haiting Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Hao Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yiqiao Fan
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ping Dong
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Jing Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Kai Cheng
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Weinan Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Sai Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Changhu Xue
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
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12
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Association of BER and NER pathway polymorphism haplotypes and micronucleus frequencies with global DNA methylation in benzene-exposed workers of China: Effects of DNA repair genes polymorphisms on genetic damage. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 839:13-20. [PMID: 30744808 DOI: 10.1016/j.mrgentox.2019.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/19/2018] [Accepted: 01/16/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The base excision repair (BER) pathway and nucleotide excision repair (NER) pathway play important roles in the repair of benzene-induced genetic damage, and the effects of polymorphisms in these pathways on genetic damage and global DNA methylation are of great interest. METHODS Ten single nucleotide polymorphisms (SNPs) in the BER (XRCC1: rs25489, rs25487; APE1: rs1130409) and NER pathways (XPA: rs1800975; XPC: rs2228000, rs2228002; XPD: rs13181, rs1799793; XPG: rs17655; ERCC1: rs3212986) were analyzed by a Kompetitive allele-specific PCR (KASP) assay to find associations with cytokinesis-block micronucleus (MN) frequency and global DNA methylation in 294 shoe factory workers and 102 control participants. RESULTS Workers who possessed the following genotypes were associated with high MN frequency: rs25487 AA (FR (95% CI): 1.50 (1.16,1.9), p = 0.002, reference GG); rs1130409 GG (FR (95% CI): 1.28 (1.05,1.55), p = 0.010, reference TT); rs17655 GC (FR (95% CI): 1.18 (1.02,1.38), p = 0.038, reference GG); and rs3212986 TT (FR (95% CI): 1.55 (1.31,1.83), p < 0.001, reference GG). Workers with four and three mutant alleles showed 3.72-fold (OR (95% CI): 3.72 (1.34, 10.03), p = 0.009) and 2.48-fold (OR (95% CI): 2.48 (1.27, 4.88), p = 0.008) increased risk of genetic damage compared with workers with no or one mutant allele, and a dose-response relationship was found by the trend test (p = 0.006). The rs1130409 variant allele (GG+GT) was associated with low global DNA methylation (β=-0.20, 95% CI: -0.42, 0.03, p = 0.045). CONCLUSION In benzene-exposed workers, BER and NER pathway polymorphism haplotypes are associated with different levels of chromosome damage and had little effect on global DNA methylation.
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Agrimonti C, Sanangelantoni AM, Marmiroli N. Simultaneous enumeration of Campylobacter jejuni and Salmonella enterica genome equivalents by melting curve analysis following duplex real time PCR in the presence of SYBR Green. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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miR-494-3p is a novel tumor driver of lung carcinogenesis. Oncotarget 2018; 8:7231-7247. [PMID: 27980227 PMCID: PMC5352317 DOI: 10.18632/oncotarget.13933] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/07/2016] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of tumor-related death worldwide and more efforts are needed to elucidate lung carcinogenesis. Here we investigated the expression of 641 miRNAs in lung tumorigenesis in a K-Ras(+/LSLG12Vgeo);RERTn(ert/ert) mouse model and 113 human tumors. The conserved miRNA cluster on chromosome 12qF1 was significantly and progressively upregulated during murine lung carcinogenesis. In particular, miR-494-3p expression was correlated with lung cancer progression in mice and with worse survival in lung cancer patients. Mechanistically, ectopic expression of miR-494-3p in A549 lung cancer cells boosted the tumor-initiating population, enhanced cancer cell motility, and increased the expression of stem cell-related genes. Importantly, miR-494-3p improved the ability of A549 cells to grow and metastasize in vivo, modulating NOTCH1 and PTEN/PI3K/AKT signaling.Overall, these data identify miR-494-3p as a key factor in lung cancer onset and progression and possible therapeutic target.
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Kajta M, Wnuk A, Rzemieniec J, Litwa E, Lason W, Zelek-Molik A, Nalepa I, Rogóż Z, Grochowalski A, Wojtowicz AK. Depressive-like effect of prenatal exposure to DDT involves global DNA hypomethylation and impairment of GPER1/ESR1 protein levels but not ESR2 and AHR/ARNT signaling. J Steroid Biochem Mol Biol 2017; 171:94-109. [PMID: 28263910 DOI: 10.1016/j.jsbmb.2017.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 01/01/2023]
Abstract
Several lines of evidence suggest that exposures to Endocrine Disrupting Chemicals (EDCs) such as pesticides increase the risks of neuropsychiatric disorders. Despite extended residual persistence of dichlorodiphenyltrichloroethane (DDT) in the environment, the mechanisms of perinatal actions of DDT that could account for adult-onset of depression are largely unknown. This study demonstrated the isomer-specific induction of depressive-like behavior and impairment of Htr1a/serotonin signaling in one-month-old mice that were prenatally exposed to DDT. The effects were reversed by the antidepressant citalopram as evidenced in the forced swimming (FST) and tail suspension (TST) tests in the male and female mice. Prenatally administered DDT accumulated in mouse brain as determined with gas chromatography and tandem mass spectrometry, led to global DNA hypomethylation, and altered the levels of methylated DNA in specific genes. The induction of depressive-like behavior and impairment of Htr1a/serotonin signaling were accompanied by p,p'-DDT-specific decrease in the levels of estrogen receptors i.e. ESR1 and/or GPER1 depending on sex. In contrast, o,p'-DDT did not induce depressive-like effects and exhibited quite distinct pattern of biochemical alterations that was related to aryl hydrocarbon receptor (AHR), its nuclear translocator ARNT, and ESR2. Exposure to o,p'-DDT increased AHR expression in male and female brains, and reduced expression levels of ARNT and ESR2 in the female brains. The evolution of p,p'-DDT-induced depressive-like behavior was preceded by attenuation of Htr1a and Gper1/GPER1 expression as observed in the 7-day-old mouse pups. Because p,p'-DDT caused sex- and age-independent attenuation of GPER1, we suggest that impairment of GPER1 signaling plays a key role in the propagation of DDT-induced depressive-like symptoms.
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Affiliation(s)
- Malgorzata Kajta
- Department of Experimental Neuroendocrinology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland.
| | - Agnieszka Wnuk
- Department of Experimental Neuroendocrinology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Joanna Rzemieniec
- Department of Experimental Neuroendocrinology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Ewa Litwa
- Department of Experimental Neuroendocrinology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Wladyslaw Lason
- Department of Experimental Neuroendocrinology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Agnieszka Zelek-Molik
- Department of Brain Biochemistry, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Irena Nalepa
- Department of Brain Biochemistry, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Zofia Rogóż
- Department of Pharmacology, Institute of Pharmacology, Polish Academy of Sciences, Smetna Street 12, 31-343 Krakow, Poland
| | - Adam Grochowalski
- Department of Analytical Chemistry, Krakow University of Technology, Warszawska Street 24, 31-155 Krakow, Poland
| | - Anna K Wojtowicz
- Department of Animal Biotechnology, Faculty of Animal Sciences, University of Agriculture, Redzina Street 1B, 30-248 Krakow, Poland
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Fachet C, Quarino L, Karnas KJ. High resolution melt curve analysis based on methylation status for human semen identification. Forensic Sci Med Pathol 2016; 13:86-91. [DOI: 10.1007/s12024-016-9825-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 11/24/2022]
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17
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Naghitorabi M, Mohammadi-Asl J, Sadeghi HMM, Rabbani M, Jafarian-Dehkordi A, Javanmard SH. Quantitation of CDH1 promoter methylation in formalin-fixed paraffin-embedded tissues of breast cancer patients using differential high resolution melting analysis. Adv Biomed Res 2016; 5:91. [PMID: 27308263 PMCID: PMC4908786 DOI: 10.4103/2277-9175.183139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND E-cadherin (CDH1) plays an important role in cell-cell adhesion of epithelial tissues. Loss of E-cadherin expression can lead to loss of tissue integrity, metastasis, and cancer progression. Also loss of E-cadherin expression might be related to aberrant promoter methylation of the CDH1 gene. Many studies have been performed on CDH1 promoter methylation, especially in breast cancer. Although most of the studies have used qualitative methods for methylation analysis, this study is designed to quantitatively investigate CDH1 promoter methylation in breast cancer and its correlation with patients' clinicopathological features. MATERIALS AND METHODS Using differential high resolution melting analysis (D-HRMA), the methylation level of the CDH1 gene promoter was quantified in 98 breast cancer formalin-fixed paraffin-embedded (FFPE) tissues and also 10 fresh frozen normal breast tissues. RESULTS All samples were detected to be methylated at the CDH1 promoter region. About 74.5% of the breast cancer samples were hypermethylated with an average methylation level of around 60%, while 25.5% of the patients were methylated with the mean methylation level of about 33%, and 90% of the normal samples had a mean methylation level of about 18%. Statistical analyses represented a significant correlation between CDH1 promoter methylation and cancer progression hallmarks, such as, clinical stage, nodal involvement, tumor size, and histological grade. CONCLUSION In summary, quantitation of CDH1 promoter methylation can serve as a diagnostic and prognostic tool in breast cancer. Also D-HRMA can be used as a fast and reliable method for quantitation of promoter methylation.
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Affiliation(s)
- Mojgan Naghitorabi
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Mohammadi-Asl
- Cancer, Petroleum and Environmental Pollutants Research Centre, Ahvaz Jundishapur University of Medical sciences, Ahvaz, Iran
| | | | - Mohammad Rabbani
- Department of Pharmaceutical Biotechnology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Jafarian-Dehkordi
- Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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18
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High-resolution melt analysis of DNA methylation to discriminate semen in biological stains. Anal Biochem 2016; 494:40-5. [DOI: 10.1016/j.ab.2015.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 12/29/2022]
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Tanaka S, Hosokawa M, Ueda K, Iwakawa S. Effects of Decitabine on Invasion and Exosomal Expression of miR-200c and miR-141 in Oxaliplatin-Resistant Colorectal Cancer Cells. Biol Pharm Bull 2015; 38:1272-9. [PMID: 26179333 DOI: 10.1248/bpb.b15-00129] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of decitabine (DAC), a DNA methyltransferase (DNMT) inhibitor, on metastasis and exosomal expression of microRNAs were examined in SW620/OxR cells, a human colorectal cancer (CRC) cell line (SW620) with acquired resistance to oxaliplatin. This cell line shows an invasive phenotype by epithelial-mesenchymal transition. Two CRC cell lines, SW480, derived from primary CRC, and SW620, derived from lymph node metastasis, which were obtained from the same patient, as well as SW620/OxR, were also used in the present study. Cytarabine (Ara-C), a non-DNMT-inhibiting cytidine analog, was used as negative control of DAC. No significant difference was observed in the invasion abilities of SW480 cells treated with DAC or Ara-C. On the other hand, invasion ability was suppressed by treatment with DAC in SW620 and SW620/OxR cells. Up-regulated expression of E-cadherin, microRNA-200c (miR-200c), and miR-141 following DAC treatment indicated the acquisition of epithelial cell-like characteristics in SW620 and SW620/OxR cells. Exosomal expression levels of miR-200c and miR-141 were also up-regulated by DAC treatment in SW620 and SW620/OxR but not in SW480 cells. This increase in exosomal miRNA expression negatively correlated with invasion ability. These results suggest that DNA demethylation treatment caused acquisition of epithelial cell-like characteristics in SW620 and SW620/OxR cells. Furthermore, the observed increased exosomal expression of miR-200c and miR-141 may be an indicator or biomarker candidate for mesenchymal-epithelial transition of CRC cells.
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Affiliation(s)
- Shota Tanaka
- Department of Pharmaceutics, Kobe Pharmaceutical University
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Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis. Expert Rev Mol Med 2015; 17:e13. [PMID: 26132880 PMCID: PMC4836209 DOI: 10.1017/erm.2015.11] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1
boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed
X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200)
females. XCI skewing has been also linked to abnormal X-linked gene expression with the
broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2
CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA),
including 3 sites that could not be analysed with previously used EpiTYPER system. The
method was applied for detection of skewed XCI in FM females and in different types of
SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40),
and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y
chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM
females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X
chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant
correlation with the EpiTYPER reference method in FM males and females
(P < 0.0001) and SCAs (P < 0.05). In
conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with
diagnostic utility.
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Capper RL, Jin YK, Lundgren PB, Peplow LM, Matz MV, van Oppen MJH. Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples. BMC Genet 2015; 16:62. [PMID: 26070466 PMCID: PMC4465018 DOI: 10.1186/s12863-015-0222-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Background The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs. Conclusions Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxana L Capper
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Young K Jin
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. .,Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Petra B Lundgren
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Mikhail V Matz
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data. BMC Bioinformatics 2014; 15 Suppl 12:S6. [PMID: 25474268 PMCID: PMC4243086 DOI: 10.1186/1471-2105-15-s12-s6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
DNA methylation is a common epigenetic marker that regulates gene expression. A robust and cost-effective way for measuring whole genome methylation is Methyl-CpG binding domain-based capture followed by sequencing (MBDCap-seq). In this study, we proposed BIMMER, a Hidden Markov Model (HMM) for differential Methylation Regions (DMRs) identification, where HMMs were proposed to model the methylation status in normal and cancer samples in the first layer and another HMM was introduced to model the relationship between differential methylation and methylation statuses in normal and cancer samples. To carry out the prediction for BIMMER, an Expectation-Maximization algorithm was derived. BIMMER was validated on the simulated data and applied to real MBDCap-seq data of normal and cancer samples. BIMMER revealed that 8.83% of the breast cancer genome are differentially methylated and the majority are hypo-methylated in breast cancer.
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Batista AR, Gianni D, Ventosa M, Coelho AV, Almeida MR, Sena-Esteves M, Saraiva MJ. Gene therapy approach to FAP: in vivo influence of T119M in TTR deposition in a transgenic V30M mouse model. Gene Ther 2014; 21:1041-50. [DOI: 10.1038/gt.2014.86] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/16/2014] [Accepted: 08/06/2014] [Indexed: 11/09/2022]
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Millares L, Rosell A, Setó L, Sanz J, Andreo F, Monsó E. Variability in the measurement of the methylation status of lung cancer-related genes in bronchial secretions. Oncol Rep 2014; 32:1435-40. [PMID: 25069886 DOI: 10.3892/or.2014.3364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/12/2014] [Indexed: 11/06/2022] Open
Abstract
Assessment of the methylation status of genes related to the development of lung cancer (LC) in bronchial secretions has been proposed as a biomarker for early detection. Several techniques are available to detect gene methylation, and the method chosen may have an effect on the results. A cross-sectional study was conducted in which the methylation status of DAPK, CDKN2A (p16) and RASSF1A genes in sputum and bronchial washing (BW) from subjects at risk for LC was analyzed. The methylation results of both samples were compared, considering BW as the reference. Results obtained by methylation-sensitive PCR (MSP) were validated by methylation-sensitive high-resolution melting (MS-HRM). The methylation results obtained in sputum and BW samples did not show statistically significant differences for any of the three genes analyzed in 65 subjects (McNemar test>0.05). Concordant results between sputum and BW were found in 40 patients for DAPK (61%), in 52 patients for p16 (80%) and in 63 patients for RASSF1 (97%). More methylated samples were found in BW, however, and sputum sensitivities and specificities for the identification of methylation status were 44 and 72% for DAPK gene, 21 and 94% for p16 and 100 and 98% for RASSF1A, respectively. When MSP results were validated by MS-HRM, DAPK and p16 gene samples methylated by MSP appeared to be unmethylated by MS-HRM. One sample showing methylation of RASSF1A gene also showed methylation when tested following MS-HRM procedure. Sputum and BW samples may be considered equally valid for the identification of methylated genes in bronchial secretions. The low sensitivity of sputum for the assessment of the methylation status of DAPK and p16 genes, however, suggests that the analysis of two or more sputum samples, or of a BW obtained semi-invasively, would be needed to attain higher reliability, together with the use of confirmatory techniques for positive results.
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Affiliation(s)
| | - Antoni Rosell
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Laia Setó
- Fundació Parc Taulí, Sabadell/Badalona, Spain
| | - José Sanz
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Felipe Andreo
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
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Xiao Z, Li B, Wang G, Zhu W, Wang Z, Lin J, Xu A, Wang X. Validation of methylation-sensitive high-resolution melting (MS-HRM) for the detection of stool DNA methylation in colorectal neoplasms. Clin Chim Acta 2014; 431:154-63. [PMID: 24518356 DOI: 10.1016/j.cca.2014.01.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/18/2014] [Accepted: 01/26/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown. METHODS First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed. RESULTS The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (P<0.001, R(2)=0.957) and VIM (P<0.001, R(2)=0.954). CONCLUSIONS MS-HRM shows potential for CRC screening.
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Affiliation(s)
- Zhujun Xiao
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Bingsheng Li
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Gastroenterology, Huizhou First Hospital, Huizhou 516003, China
| | - Guozhen Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Weisi Zhu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Zhongqiu Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Jinfeng Lin
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China
| | - Angao Xu
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Huizhou Medicine Institute, Huizhou 516003, China.
| | - Xinying Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Gastroenterology, Guangzhou 510515, China.
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High resolution melting analysis of deletion/insertion polymorphisms: A new method for the detection and quantification of mixed chimerism in allogeneic stem cell transplantation. Mol Cell Probes 2014; 28:19-24. [DOI: 10.1016/j.mcp.2013.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 09/11/2013] [Accepted: 09/11/2013] [Indexed: 11/23/2022]
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Athamanolap P, Shin DJ, Wang TH. Droplet Array Platform for High-Resolution Melt Analysis of DNA Methylation Density. ACTA ACUST UNITED AC 2013; 19:304-12. [PMID: 24114798 DOI: 10.1177/2211068213507923] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Indexed: 11/16/2022]
Abstract
High-resolution melting (HRM) has garnered significant interest as an analytical technique for a number of applications, including DNA methylation detection, due to its inherent sensitivity and robustness. In this study, we describe a miniaturized assay platform for quantitative methylation density analysis using a microfluidic droplet array cartridge. We demonstrate that the DNA methylation level of the RASSF1A promoter can be directly analyzed using HRM. PCR products were generated by amplifying bisulfite-treated DNA with varying CpG densities using CpG island-flanking primer sets. Subsequent HRM analysis on the miniaturized droplet platform shows distinct melting curve profiles associated with methylation levels, which was verified using a conventional benchtop PCR-HRM system. The characteristic melting temperature (Tm) of the PCR products was used to directly quantify the respective levels of DNA methylation density. Our approach provides a key advantage over current gold standard methods such as methylation-specific PCR (MSP), which are incapable of providing specific information regarding the overall methylation density of the target genes. The miniaturized platform establishes a practical approach to methylation density profiling from multiple DNA samples with a potential application in point-of-care diagnostics.
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Affiliation(s)
- Pornpat Athamanolap
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Dong Jin Shin
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD, USA
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Uzawa K, Baba T, Uchida F, Yamatoji M, Kasamatsu A, Sakamoto Y, Ogawara K, Shiiba M, Bukawa H, Tanzawa H. Circulating tumor-derived mutant mitochondrial DNA: a predictive biomarker of clinical prognosis in human squamous cell carcinoma. Oncotarget 2013; 3:670-7. [PMID: 22832574 PMCID: PMC3443250 DOI: 10.18632/oncotarget.523] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
While circulating tumor-derived molecules have been identified in a variety of malignant tumors, it is sometimes difficult to detect the molecular targets due to the lower serum concentration. We report that evaluation of circulating tumor-derived mitochondrial DNA (mtDNA) seems to have novel efficiency for detecting tumoral micrometastasis. In murine xenografting human oral cancer cells, human mtDNAs could be quantitatively detected from multiple organs and blood samples whereas human nucleic DNAs could not. We also determined if this mtDNA blood test was relevant for patients with oral cancer with no histologic evidence of tumoral cells in their surgical margins. For this, mtDNA from normal and tumorous tissues and serum mtDNA obtained pre and postoperatively was examined at three different regions including the displacement loop, 12S-rRNA, and 16S-rRNA. All recurring patients had significantly higher amounts of mutant mtDNAs in the tumoral tissues compared with the non-recurring group. More importantly, on the blood test with the cut-off point by receiver operating characteristic (ROC) curve analysis, while the vast majority of serum mtDNA samples obtained postoperatively in the recurring cases maintained significantly higher amounts of mutant mtDNAs, the non-recurring cases did not, and they showed good prognosis. This is the first report of this approach for managing patients after resection of oral tumors, and may have substantial diagnostic potential for other tumoral types.
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Affiliation(s)
- Katsuhiro Uzawa
- Department of Clinical Molecular Biology, Graduate School of Medicine, Chiba University, Chiba, Japan.
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Quantitative evaluation of DNMT3B promoter methylation in breast cancer patients using differential high resolution melting analysis. Res Pharm Sci 2013; 8:167-75. [PMID: 24019826 PMCID: PMC3764668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
DNA methylation plays an important role in carcinogenesis through epigenetic silencing of tumor suppressor genes. Aberrant methylation usually results from changes in the activity of DNA methyltransferases (DNMTs). Some studies show that the overexpression of the DNMTs may lead to aberrant methylation of tumor suppressor genes. Also the overexpression of DNMTs may be related to methylation status of their genes. Due to limited number of studies on DNMT3B promoter methylation, this study was performed to quantitatively measure the methylation level of DNMT3B gene in archival formalin fixed paraffin embedded (FFPE) tissues from breast cancer patients. Using differential high resolution melting analysis (D-HRMA) technology, the methylation level of DNMT3B gene promoter was quantified in 98 breast cancer FFPE tissues and also 10 fresh frozen normal tissue samples. Statistical analyses used for analyzing the correlation between the methylation and clinical variables. All the normal samples were found to be methylated at the DNMT3B promoter (the average methylation level 3.34%). Patients were identified as hypo-methylated (mean methylation level 0.8%), methylated (mean methylation level 2.48%) and hyper-methylated (mean methylation level 10.5%). Statistical analysis showed a significant correlation between the methylation status and the sample type, cancer type and tumor size. Also the methylation level was significantly associated with histologic grade. It is concluded that quantification of DNMT3B promoter methylation might be used as a reliable and sensitive diagnostic and prognostic tool in breast cancer. Also D-HRMA is demonstrated as a rapid and cost effective method for quantitative evaluation of promoter methylation.
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Vinci S, Gelmini S, Mancini I, Malentacchi F, Pazzagli M, Beltrami C, Pinzani P, Orlando C. Genetic and epigenetic factors in regulation of microRNA in colorectal cancers. Methods 2012; 59:138-46. [PMID: 22989523 DOI: 10.1016/j.ymeth.2012.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 08/27/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023] Open
Abstract
Studies on miRNA profiling revealed that a large number of them are significantly deregulated in human cancers. The molecular mechanisms of this deregulation are not totally clarified, even if genetics and epigenetics are frequently involved. Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the human genome. A SNP into miRNA gene might affect the transcription of primary miRNA, its processing and miRNA-mRNA interaction. We investigated the distribution of sequence variants of miR-146a, miR-196a2, miR-499 and miR-149 in colorectal cancer (CRC) and their effect on miRNA expression. Each variant was identified with HRM. For miR-499 we demonstrated a significant reduction of its expression in CRC connected to a specific genotype. To evaluate the epigenetic effects on miRNA genes in CRC, we investigated the influence of DNA methylation on miR-34b, miR-34c and miR-9-1 expression. We aimed to verify the relationship between the methylation status of these miRNA genes and their relative expression in tumor samples. For the quantification of DNA methylation we adopted a method based on Differential High Resolution Melting (D-HRM).
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Affiliation(s)
- Serena Vinci
- Clinical Biochemistry, Dept. of Clinical Physiopathology, University of Florence, Italy
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31
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Slaats GG, Reinius LE, Alm J, Kere J, Scheynius A, Joerink M. DNA methylation levels within the CD14 promoter region are lower in placentas of mothers living on a farm. Allergy 2012; 67:895-903. [PMID: 22564189 DOI: 10.1111/j.1398-9995.2012.02831.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Epigenetic regulation has been suggested to be a link between environmental intrauterine exposures and development of asthma and allergy. The placenta is an essential part of the intrauterine environment. We have previously found the innate immune receptor CD14 to be differentially expressed on the mRNA level in placentas in relation to lifestyle and parental allergen sensitization. We here hypothesized that the promoter region of CD14 may be subject to differential DNA methylation and therefore a link between intrauterine exposure and mRNA expression. METHODS Ninety-four placentas from the ALADDIN (Assessment of Lifestyle and Allergic Disease During Infancy) study were investigated. We used methylation-sensitive high-resolution melting (MS-HRM) analysis to semi-quantitatively analyze the DNA methylation of the promoter region of CD14 in 36 placentas known to have different CD14 mRNA expression. EpiTYPER was used to validate the MS-HRM data and to analyze an additional 58 placentas selected on mothers living on a farm or not. RESULTS MS-HRM analysis on 36 placenta samples revealed a relation between methylation of the CD14 promoter region with the level of CD14 mRNA expression. The MS-HRM and EpiTYPER data correlated highly significantly. EpiTYPER analysis of the additional 58 placentas demonstrated that DNA methylation in the CD14 promoter was significantly lower in placentas of mothers living on a farm compared with mothers not living on a farm. CONCLUSION Our data suggest that epigenetic regulation of CD14 in placenta might be involved in the protective effect of 'living on a farm', with regard to allergy development.
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Affiliation(s)
| | - Lovisa E. Reinius
- Department of Biosciences and Nutrition; Karolinska Institutet; Stockholm; Sweden
| | - Johan Alm
- Department of Clinical Science and Education; Karolinska Institutet, Södersjukhuset, Sachs' Children's Hospital; Stockholm; Sweden
| | | | - Annika Scheynius
- Department of Medicine Solna; Translational Immunology Unit, Karolinska Institutet; Stockholm; Sweden
| | - Maaike Joerink
- Department of Medicine Solna; Translational Immunology Unit, Karolinska Institutet; Stockholm; Sweden
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32
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Hypermethylation in bladder cancer: biological pathways and translational applications. Tumour Biol 2012; 33:347-61. [PMID: 22274923 DOI: 10.1007/s13277-011-0310-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/28/2011] [Indexed: 12/18/2022] Open
Abstract
A compelling body of evidences sustains the importance of epigenetic mechanisms in the development and progression of cancer. Assessing the epigenetic component of bladder tumors is strongly improving our understanding of their biology and clinical behavior. In terms of DNA methylation, cancer cells show genome-wide hypomethylation and site-specific CpG island promoter hypermethylation. In the context of other epigenetic alterations, this review will focus on the hypermethylation of CpG islands in promoter regions, as the most widely described epigenetic modification in bladder cancer. CpG islands hypermethylation is believed to be critical in the transcriptional silencing and regulation of tumor suppressor and crucial cancer genes involved in the major molecular pathways controlling bladder cancer development and progression. In particular, several biological pathways of frequently methylated genes include cell cycle, DNA repair, apoptosis, and invasion, among others. Furthermore, translational aspects of bladder cancer methylomes described to date will be discussed towards their potential application as bladder cancer biomarkers. Several tissue methylation signatures and individual candidates have been evidenced, that could potentially stratify tumors histopathologically, and discriminate patients in terms of their clinical outcome. Tumor methylation profiles could also be detected in urinary specimens showing a promising role as non-invasive markers for cancer diagnosis towards an early detection and potentially for the surveillance of bladder cancer patients in a near future. However, the epigenomic exploration of bladder cancer has only just begun. Genome-scale DNA methylation profiling studies will further highlight the relevance of the epigenetic component to gain knowledge of bladder cancer biology and identify those profiles and candidates better correlating with clinical behavior.
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33
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Newman M, Blyth BJ, Hussey DJ, Jardine D, Sykes PJ, Ormsby RJ. Sensitive quantitative analysis of murine LINE1 DNA methylation using high resolution melt analysis. Epigenetics 2012; 7:92-105. [PMID: 22274612 DOI: 10.4161/epi.7.1.18815] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We present here the first high resolution melt (HRM) assay to quantitatively analyze differences in murine DNA methylation levels utilizing CpG methylation of Long Interspersed Elements-1 (LINE1 or L1). By calculating the integral difference in melt temperature between samples and a methylated control, and biasing PCR primers for unmethylated CpGs, the assay demonstrates enhanced sensitivity to detect changes in methylation in a cell line treated with low doses of 5-aza-2'-deoxycytidine (5-aza). The L1 assay was confirmed to be a good marker of changes in DNA methylation of L1 elements at multiple regions across the genome when compared with total 5-methyl-cytosine content, measured by Liquid Chromatography-Mass Spectrometry (LC-MS). The assay design was also used to detect changes in methylation at other murine repeat elements (B1 and Intracisternal-A-particle Long-terminal Repeat elements). Pyrosequencing analysis revealed that L1 methylation changes were non-uniform across the CpGs within the L1-HRM target region, demonstrating that the L1 assay can detect small changes in CpG methylation among a large pool of heterogeneously methylated DNA templates. Application of the assay to various tissues from Balb/c and CBA mice, including previously unreported peripheral blood (PB), revealed a tissue hierarchy (from hypermethylated to hypomethylated) of PB > kidney > liver > prostate > spleen. CBA mice demonstrated overall greater methylation than Balb/c mice, and male mice demonstrated higher tissue methylation compared with female mice in both strains. Changes in DNA methylation have been reported to be an early and fundamental event in the pathogenesis of many human diseases, including cancer. Mouse studies designed to identify modulators of DNA methylation, the critical doses, relevant time points and the tissues affected are limited by the low throughput nature and exorbitant cost of many DNA methylation assays. The L1 assay provides a high throughput, inexpensive and sensitive screening tool for identifying and characterizing DNA methylation changes to L1 elements at multiple regions across the genome.
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Affiliation(s)
- Michelle Newman
- Haematology and Genetic Pathology, Flinders University and Medical Centre, Bedford Park, Adelaide, SA Australia
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Tse MY, Ashbury JE, Zwingerman N, King WD, Taylor SA, Pang SC. A refined, rapid and reproducible high resolution melt (HRM)-based method suitable for quantification of global LINE-1 repetitive element methylation. BMC Res Notes 2011; 4:565. [PMID: 22204640 PMCID: PMC3284418 DOI: 10.1186/1756-0500-4-565] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 12/28/2011] [Indexed: 12/28/2022] Open
Abstract
Background The methylation of DNA is recognized as a key mechanism in the regulation of genomic stability and evidence for its role in the development of cancer is accumulating. LINE-1 methylation status represents a surrogate measure of genome-wide methylation. Findings Using high resolution melt (HRM) curve analysis technology, we have established an in-tube assay that is linear (r > 0.9986) with a high amplification efficiency (90-105%), capable of discriminating between partcipant samples with small differences in methylation, and suitable for quantifying a wide range of LINE-1 methylation levels (0-100%)--including the biologically relevant range of 50-90% expected in human DNA. We have optimized this procedure to perform using 2 μg of starting DNA and 2 ng of bisulfite-converted DNA for each PCR reaction. Intra- and inter-assay coefficients of variation were 1.44% and 0.49%, respectively, supporting the high reproducibility and precision of this approach. Conclusions In summary, this is a completely linear, quantitative HRM PCR method developed for the measurement of LINE-1 methylation. This cost-efficient, refined and reproducible assay can be performed using minimal amounts of starting DNA. These features make our assay suitable for high throughput analysis of multiple samples from large population-based studies.
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Affiliation(s)
- M Yat Tse
- Department of Anatomy and Cell Biology, Queen's University, Kingston, ON, Canada.
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35
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Azhikina T, Kozlova A, Skvortsov T, Sverdlov E. Heterogeneity and degree of TIMP4, GATA4, SOX18, and EGFL7 gene promoter methylation in non-small cell lung cancer and surrounding tissues. Cancer Genet 2011; 204:492-500. [PMID: 22018271 DOI: 10.1016/j.cancergen.2011.07.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/28/2011] [Accepted: 07/21/2011] [Indexed: 12/19/2022]
Abstract
We used methylation-sensitive high resolution melting analysis to assess methylation of CpG islands within the promoters of the TIMP4, GATA4, SOX18, and EGFL7 genes in samples of non-small cell lung cancer and surrounding apparently normal tissue and noncancerous lung tissues. We found that the promoter methylation was heterogeneous in both tumor and surrounding normal tissue. This is in contrast to healthy lung tissue, where the promoters were normally either non- or hypomethylated, and the heterogeneity of methylation was low. An increased heterogeneity of methylation in the normal tissues surrounding the tumor may suggest an early start of epigenetic processes preceding genetic and morphologic changes and can be used as a biomarker of early cancerization events. This analysis is an easy and sensitive tool for studying epigenetic heterogeneity and could be used in clinical practice.
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Affiliation(s)
- Tatyana Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow.
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36
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Zhu Q, Jin Z, Yuan Y, Lu Q, Ge D, Zong M. Impact of MTHFR gene C677T polymorphism on Bcl-2 gene methylation and protein expression in colorectal cancer. Scand J Gastroenterol 2011; 46:436-45. [PMID: 21128871 DOI: 10.3109/00365521.2010.537682] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To investigate the impact of MTHFR C677T polymorphism on Bcl-2 gene promoter CpG island (CGI) methylation and Bcl-2 protein expression. MATERIAL AND METHODS MTHFR polymorphisms of 86 sporadic colorectal cancer (CRC) patients and 100 healthy volunteers were analyzed by PCR-based restriction fragment length polymorphism, and Bcl-2 promoter CGI methylation in 86 CRC tissues and 86 paired nonneoplastic adjacent tissues was determined by methylation-specific PCR. Bcl-2 oncoprotein expression in 70 CRC tissues and paired nonneoplastic adjacent tissues was detected by immunohistochemistry. RESULTS The frequency of MTHFR 677 T allele and combined variant genotypes (677CT + TT) in CRC patients was significantly higher than that in healthy controls (p = 0.023 and p = 0.035, respectively), and there is a significant association between 677TT or 677(CT + TT) genotypes and CRC (OR = 2.534, p = 0.045 and OR = 1.888, p = 0.035, respectively). The frequency of methylated Bcl-2 promoter CGI in tumor tissues was significantly lower than that in nonneoplastic adjacent tissues (p = 0.014). The frequency of methylated Bcl-2 promoter CGI in CRC tissues of the individuals with CC genotype was significantly higher than that of those with CT/TT genotypes (p = 0.018), there was significant distribution difference of C and T alleles between individuals with methylated and unmethylated Bcl-2 promoter CGI in colorectal cancer tissues (p = 0.023). Bcl-2 promoter hypomethylation was significantly correlated with Bcl-2 oncoprotein expression in colorectal cancer tissues (r = 0.558, p < 0.001). CONCLUSION Bcl-2 promoter is hypomethylated in colorectal cancer tissue, and there is a significant correlation between MTHFR 677 TT or CT/TT genotypes and CRC or Bcl-2 promoter CGI methylation/oncoprotein expression in CRC.
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Affiliation(s)
- Qinghui Zhu
- Experimental Center for Medical Science Research of Teaching Hospital of Jiangsu University, Shanghai People's Hospital of Putuo District, Shanghai, PR China.
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37
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Anuj SN, Whiley DM, Kidd TJ, Ramsay KA, Bell SC, Syrmis MW, Grimwood K, Wainwright CE, Nissen MD, Sloots TP. Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis. Clin Microbiol Infect 2011; 17:1403-8. [PMID: 21129101 DOI: 10.1111/j.1469-0691.2010.03439.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.
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Affiliation(s)
- S N Anuj
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Qld, Australia.
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Mader E, Ruzicka J, Schmiderer C, Novak J. Quantitative high-resolution melting analysis for detecting adulterations. Anal Biochem 2010; 409:153-5. [PMID: 20946863 DOI: 10.1016/j.ab.2010.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 10/01/2010] [Accepted: 10/01/2010] [Indexed: 11/17/2022]
Abstract
Admixtures of different plant species are a common problem in raw materials for medicinal use. Two exemplary assays were developed to admixtures in Helleborus niger with high-resolution melting analysis. HRM proved to be a very sensitive tool in detecting admixtures, able to detect a ratio of 1:1000 with unknown species, and of 1:200,000 with Veratrum nigrum. The example proves the ability of HRM for quantification in multiplex PCR. The method is not limited to detecting adulterations. It can also be used to quantify a specific target by integrating a second amplicon in the assay as internal standard.
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Affiliation(s)
- Eduard Mader
- Institute for Applied Botany, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Wien, Austria.
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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40
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Rapid determination of AKAP12 promoter methylation levels in peripheral blood using methylation-sensitive high resolution melting (MS-HRM) analysis: application in colorectal cancer. Clin Chim Acta 2010; 411:940-6. [PMID: 20227403 DOI: 10.1016/j.cca.2010.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 03/01/2010] [Accepted: 03/03/2010] [Indexed: 01/09/2023]
Abstract
BACKGROUND Colorectal cancer is the third most common form of cancer and hypermethylation has been shown to increase the risk of developing this disease. DNA hypermethylation in the A kinase anchor protein 12 (AKAP12/Gravin) promoter region and the accompanied underexpression of it has been noted in a variety of human cancers. METHODS We applied methylation-specific high resolution melting (MS-HRM) technology to detect quantitatively A kinase anchor protein 12 (AKAP12/Gravin) methylation in peripheral blood from 100 colorectal cancer patients and 50 healthy volunteers and in 3 colorectal cancer cell lines. RESULTS In this study 48 of the 100 colorectal cancer samples (48%) were found to be methylated at the AKAP12 promoter region. AKAP12 methylation was significantly higher in the colorectal cancer samples with differentiation (p=0.03). We also compared the results generated by MS-HRM with a traditional methylation-specific PCR (MSP) assay. We found that intra-assay variability ranged from 6.14 to 9.90% and inter-assay variability ranged from 14.5 to 17.2%. The AKAP12 MS-HRM assay was able to reproducibly detect 1% methylated DNA, whereas the MSP method was unable to detect less than 5% methylation. CONCLUSIONS We demonstrate the utility of quantitative AKAP12 MS-HRM analysis of promoter methylation in peripheral blood samples. AKAP12 MS-HRM quantitative methods with excellent detection capabilities have many promising applications in the research and diagnosis of colorectal cancer.
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