1
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Hsu CL, Chang YS, Li HP. Molecular Diagnosis of Nasopharyngeal Carcinoma: Past and Future. Biomed J 2024:100748. [PMID: 38796105 DOI: 10.1016/j.bj.2024.100748] [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: 03/24/2024] [Revised: 05/01/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor originated from the nasopharynx epithelial cells and has been linked with Epstein-Barr virus (EBV) infection, dietary habits, environmental and genetic factors. It is a common malignancy in Southeast Asia, especially with gender preference among men. Due to its non-specific symptoms, NPC is often diagnosed at a late stage. Thus, the molecular diagnosis of NPC plays a crucial role in early detection, treatment selection, disease monitoring, and prognosis prediction. This review aims to provide a summary of the current state and the latest emerging molecular diagnostic techniques for NPC, including EBV-related biomarkers, gene mutations, liquid biopsy, and DNA methylation. Challenges and potential future directions of NPC molecular diagnosis will be discussed.
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Affiliation(s)
- Cheng-Lung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; School of Medicine, Chang Gung University, Taoyuan 33305, Taiwan.
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan 33305, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33305, Taiwan; Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan.
| | - Hsin-Pai Li
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33305, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan 33305, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan 33305, Taiwan; Department of Microbiology and Immunology, Chang Gung University, Taoyuan 33305, Taiwan.
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2
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Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [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: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
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Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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3
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Javadmanesh A, Mojtabanezhad Shariatpanahi A, Shams Davodly E, Azghandi M, Yassi M, Heidari M, Kerachian M, Kerachian MA. MS-HRM protocol: a simple and low-cost approach for technical validation of next-generation methylation sequencing data. Mol Genet Genomics 2022; 297:1101-1109. [PMID: 35616708 DOI: 10.1007/s00438-022-01906-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 05/05/2022] [Indexed: 11/25/2022]
Abstract
DNA methylation is a fundamental epigenetic process and have a critical role in many biological processes. The study of DNA methylation at a large scale of genomic levels is widely conducted by several techniques that are next-generation sequencing (NGS)-based methods. Methylome data revealed by DNA methylation next-generation sequencing (mNGS), should be always verified by another technique which they usually have a high cost. In this study, we offered a low-cost approach to corroborate the mNGS data. In this regard, mNGS was performed on 6 colorectal cancer (case group) and 6 healthy individual colon tissue (control group) samples. An R-script detected differentially methylated regions (DMRs), was further validated by high resolution melting (MS-HRM) analysis. After analyzing the data, the algorithm found 194 DMRs. Two locations with the highest level of methylation difference were verified by MS-HRM, which their results were in accordance with the mNGS. Therefore, in the present study, we suggested MS-HRM as a simple, accurate and low-cost method, useful for confirming methylation sequencing results.
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Affiliation(s)
- Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | | | - Ehsan Shams Davodly
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Marjan Azghandi
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Maryam Yassi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Mehdi Heidari
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Matin Kerachian
- Faculty of Medicine, McGill University, Montreal, Canada
- Research Institute at McGill University Health Center, Montreal, Canada
| | - Mohammad Amin Kerachian
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
- Cancer Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, 917794-8564, Iran.
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4
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Jakobsen MK, Traynor S, Stæhr M, Duijf PG, Nielsen AY, Terp MG, Pedersen CB, Guldberg P, Ditzel HJ, Gjerstorff MF. The Cancer/Testis Antigen Gene VCX2 Is Rarely Expressed in Malignancies but Can Be Epigenetically Activated Using DNA Methyltransferase and Histone Deacetylase Inhibitors. Front Oncol 2021; 10:584024. [PMID: 33634013 PMCID: PMC7900521 DOI: 10.3389/fonc.2020.584024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/14/2020] [Indexed: 01/25/2023] Open
Abstract
Identification of novel tumor-specific targets is important for the future development of immunotherapeutic strategies using genetically engineered T cells or vaccines. In this study, we characterized the expression of VCX2, a member of the VCX/Y cancer/testis antigen family, in a large panel of normal tissues and tumors from multiple cancer types using immunohistochemical staining and RNA expression data. In normal tissues, VCX2 was detected in the germ cells of the testis at all stages of maturation but not in any somatic tissues. Among malignancies, VCX2 was only found in tumors of a small subset of melanoma patients and thus rarely expressed compared to other cancer/testis antigens such as GAGE and MAGE-A. The expression of VCX2 correlated with that of other VCX/Y genes. Importantly, we found that expression of VCX2 was inversely correlated with promoter methylation and could be activated by treatment with a DNA methyltransferase inhibitor in multiple breast cancer and melanoma cell lines and a breast cancer patient-derived xenograft. The effect could be further potentiated by combining the DNA methyltransferase inhibitor with a histone deacetylase inhibitor. Our results show that the expression of VCX2 can be epigenetically induced in cancer cells and therefore could be an attractive target for immunotherapy of cancer.
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Affiliation(s)
- Mie K Jakobsen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Sofie Traynor
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mette Stæhr
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Pascal G Duijf
- Institute of Health and Biomedical Innovation, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Aaraby Y Nielsen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mikkel G Terp
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Christina B Pedersen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Per Guldberg
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
| | - Morten F Gjerstorff
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
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6
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DNA methylation studies in cattle. J Appl Genet 2021; 62:121-136. [PMID: 33400132 DOI: 10.1007/s13353-020-00604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Investigation of the role of epigenetics in cattle breeding is gaining importance. DNA methylation represents an epigenetic modification which is essential for genomic stability and maintenance of development. Recently, DNA methylation research in cattle has intensified. The studies focus on the definition of methylomes in various organs and tissues in relation to the expression of genes underlying economically important traits, and explore methylome changes under developmental, environmental, disease, and diet influences. The investigations further characterize the methylation patterns of gametes in connection with their quality, and study methylome alterations in the developing naturally or assisted produced zygotes, embryos, and fetuses, considering their viability. A wide array of technologies developed for accurate and precise analysis of DNA methylation patterns is employed for both single-gene and genome-wide studies. Overall, the research is directed towards the identification of single methylation markers or their combinations which may be useful in the selection and breeding of animals to ensure cattle improvement.
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7
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Nast R, Choepak T, Lüder CGK. Epigenetic Control of IFN-γ Host Responses During Infection With Toxoplasma gondii. Front Immunol 2020; 11:581241. [PMID: 33072127 PMCID: PMC7544956 DOI: 10.3389/fimmu.2020.581241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/26/2020] [Indexed: 01/21/2023] Open
Abstract
Host defense against the human pathogen Toxoplasma gondii depends on secretion of interferon (IFN)-γ and subsequent activation of monocytic cells to combat intracellular parasites. Previous studies have shown that T. gondii evades IFN-γ-mediated immunity by secreting the effector TgIST into the host cell where it binds to STAT1, strengthens its DNA binding activity and recruits the Mi-2/NuRD complex to STAT1-responsive promoters. Here we investigated the impact of the host chromatin environment on parasite interference with IFN-γ-induced gene expression. Luciferase reporters under control of primary and secondary IFN-γ response promoters were only inhibited by T. gondii when they were stably integrated into the host genome but not when expressed from a plasmid vector. Absence of CpG islands upstream and/or downstream of the transcriptional start site allowed more vigorous up-regulation by IFN-γ as compared to CpG-rich promoters. Remarkably, it also favored parasite interference with IFN-γ-induced gene expression indicating that nucleosome occupancy at IFN-γ-responsive promoters is important. Promoter DNA of IFN-γ-responsive genes remained largely non-methylated in T. gondii-infected cells, and inhibition of DNA methylation did not impact parasite interference with host responses. IFN-γ up-regulated histone marks H4ac, H3K9ac, and H3K4me3 but down-regulated H3S10p at primary and secondary response promoters. Infection with T. gondii abolished histone modification, whereas total nuclear activities of histone acetyl transferases and histone deacetylases were not altered. Taken together, our study reveals a critical impact of the host chromatin landscape at IFN-γ-activated promoters on their inhibition by T. gondii with a comprehensive blockade of histone modifications at parasite-inactivated promoters.
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Affiliation(s)
- Roswitha Nast
- Institute for Medical Microbiology, University Medical Center Goettingen, Georg-August-University, Göttingen, Germany
| | - Tenzin Choepak
- Institute for Medical Microbiology, University Medical Center Goettingen, Georg-August-University, Göttingen, Germany
| | - Carsten G K Lüder
- Institute for Medical Microbiology, University Medical Center Goettingen, Georg-August-University, Göttingen, Germany
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8
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Bhattacharjee R, Moriam S, Umer M, Nguyen NT, Shiddiky MJA. DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches. Analyst 2018; 143:4802-4818. [PMID: 30226502 DOI: 10.1039/c8an01348a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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9
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Bhattacharjee R, Moriam S, Nguyen NT, Shiddiky MJA. A bisulfite treatment and PCR-free global DNA methylation detection method using electrochemical enzymatic signal engagement. Biosens Bioelectron 2018; 126:102-107. [PMID: 30396016 DOI: 10.1016/j.bios.2018.10.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/09/2023]
Abstract
In this paper we report on a bisulfite treatment and PCR amplification-free method for sensitive and selective quantifying of global DNA methylation. Our method utilizes a three-step strategy that involves (i) initial isolation and denaturation of global DNA using the standard isolation protocol and direct adsorption onto a bare gold electrode via gold-DNA affinity interaction, (ii) selective interrogation of methylation sites in adsorbed DNA via methylation-specific 5mC antibody, and (iii) subsequent signal enhancement using an electrochemical-enzymatic redox cycling reaction. In the redox cycling reaction, glucose oxidase (GOx) is used as an enzyme label, glucose as a substrate and ruthenium complex as a redox mediator. We initially investigated the enzymatic properties of GOx by varying glucose and ruthenium concentration to delineate the redox cyclic mechanism of our assay. Because of the fast electron transfer by ruthenium (Ru) complex and intrinsic signal amplification from GOx label, this method could detect as low as 5% methylation level in 50 ng of total DNA input. Moreover, the use of methylation-specific 5mC antibody conjugated GOx makes this assay relatively highly selective for DNA methylation analysis. The data obtained from the electrochemical response for different levels of methylation showed excellent interassay reproducibility of RSD (relative standard deviation) < 5% for n = 3. We believe that this inexpensive, rapid, and sensitive assay will find high relevance as an alternative method for DNA methylation analysis both in research and clinical platforms.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Sofia Moriam
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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10
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Highly sensitive detection of DNA hypermethylation in melanoma cancer cells. Biosens Bioelectron 2018; 124-125:136-142. [PMID: 30366258 DOI: 10.1016/j.bios.2018.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022]
Abstract
Aberrant hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a promising biomarker for early cancer detection. This methylation status is reflected in the methylation pattern of ctDNA shed from the primary tumor; however, to realize the full clinical utility of ctDNA methylation detection via liquid biopsy for early cancer diagnosis, improvements in the sensitivity and multiplexability of existing technologies must be improved. Additionally, the assay must be cheap and easy to perform in a clinical setting. We report the integration of methylation specific PCR (MSP) to melt curve analysis on giant magnetoresistive (GMR) biosensors to greatly enhance the sensitivity of our DNA hybridization assay for methylation detection. Our GMR sensor is functionalized with synthetic DNA probes that target methylated or unmethylated CpG sites in the MSP amplicon, and measures the difference in melting temperature (Tm) between the two probes (ΔTm), giving an analytical limit of detection down to 0.1% methylated DNA in solution. Additionally, linear regression of ΔTm's for serial dilutions of methylated:unmethylated mixtures allows for quantification of methylation percentage, which could have diagnostic and prognostic utility. Lastly, we performed multiplexed MSP on two different genes, and show the ability of our GMR assay to resolve this mixture, despite their amplicons' overlapping Tm's in standard EvaGreen melt analysis. The multiplexing ability of our assay and its enhanced sensitivity, without necessitating deep sequencing, represent important steps toward realizing an assay for the detection of methylated ctDNA in plasma for early cancer detection in a clinical setting.
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11
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Kirkin AF, Dzhandzhugazyan KN, Guldberg P, Fang JJ, Andersen RS, Dahl C, Mortensen J, Lundby T, Wagner A, Law I, Broholm H, Madsen L, Lundell-Ek C, Gjerstorff MF, Ditzel HJ, Jensen MR, Fischer W. Adoptive cancer immunotherapy using DNA-demethylated T helper cells as antigen-presenting cells. Nat Commun 2018; 9:785. [PMID: 29511178 PMCID: PMC5840134 DOI: 10.1038/s41467-018-03217-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/29/2018] [Indexed: 01/23/2023] Open
Abstract
In cancer cells, cancer/testis (CT) antigens become epigenetically derepressed through DNA demethylation and constitute attractive targets for cancer immunotherapy. Here we report that activated CD4+ T helper cells treated with a DNA-demethylating agent express a broad repertoire of endogenous CT antigens and can be used as antigen-presenting cells to generate autologous cytotoxic T lymphocytes (CTLs) and natural killer cells. In vitro, activated CTLs induce HLA-restricted lysis of tumor cells of different histological types, as well as cells expressing single CT antigens. In a phase 1 trial of 25 patients with recurrent glioblastoma multiforme, cytotoxic lymphocytes homed to the tumor, with tumor regression ongoing in three patients for 14, 22, and 27 months, respectively. No treatment-related adverse effects were observed. This proof-of-principle study shows that tumor-reactive effector cells can be generated ex vivo by exposure to antigens induced by DNA demethylation, providing a novel, minimally invasive therapeutic strategy for treating cancer.
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Affiliation(s)
- Alexei F Kirkin
- Danish Cancer Society Research Center, 2100, Copenhagen, Denmark. .,CytoVac A/S, 2970, Hørsholm, Denmark.
| | - Karine N Dzhandzhugazyan
- Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.,CytoVac A/S, 2970, Hørsholm, Denmark
| | - Per Guldberg
- Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Johnny Jon Fang
- Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.,CytoVac A/S, 2970, Hørsholm, Denmark
| | - Rikke S Andersen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, 5000, Odense, Denmark
| | - Christina Dahl
- Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Jann Mortensen
- Department of Clinical Physiology, Nuclear Medicine and PET, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Tim Lundby
- Department of Clinical Physiology, Nuclear Medicine and PET, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Aase Wagner
- Department of Neuroradiology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Ian Law
- Department of Clinical Physiology, Nuclear Medicine and PET, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Helle Broholm
- Department of Neuropathology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Line Madsen
- Department of Pathology, Aarhus University Hospital, 8000, Aarhus, Denmark
| | | | - Morten F Gjerstorff
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, 5000, Odense, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, 5000, Odense, Denmark.,Department of Oncology, Odense University Hospital, 5000, Odense, Denmark
| | | | - Walter Fischer
- CytoVac A/S, 2970, Hørsholm, Denmark.,Department of Neurosurgery, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
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12
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Abstract
Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays. Bisulfite treatment of the DNA prior to performing MS-HRM ensures a different base composition between methylated and unmethylated DNA, which is used to separate the resulting amplicons by high resolution melting.The high sensitivity of MS-HRM has proven useful for detecting cancer biomarkers in a noninvasive manner in urine from bladder cancer patients, in stool from colorectal cancer patients, and in buccal mucosa from breast cancer patients. MS-HRM is a fast method to diagnose imprinted diseases and to clinically validate results from whole-epigenome studies. The ability to detect few copies of methylated DNA makes MS-HRM a key player in the quest for establishing links between environmental exposure, epigenetic changes, and disease.
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Affiliation(s)
- Dianna Hussmann
- Institute of Biomedicine, Aarhus University, Bartholins Allé 6, Aarhus C, 8000, Denmark
| | - Lise Lotte Hansen
- Institute of Biomedicine, Aarhus University, Bartholins Allé 6, Aarhus C, 8000, Denmark.
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13
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Brandenburg J, Head JA. Effects of in ovo exposure to benzo[k]fluoranthene (BkF) on CYP1A expression and promoter methylation in developing chicken embryos. Comp Biochem Physiol C Toxicol Pharmacol 2018; 204:88-96. [PMID: 29203322 DOI: 10.1016/j.cbpc.2017.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/28/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are toxic environmental pollutants that are potent teratogens. Recent research suggests that early life exposure to PAHs can affect health outcomes later in life. Some of these latent responses may be mediated by epigenetic mechanisms such as DNA methylation. The role of DNA methylation in regulating responses to PAHs in birds is currently unknown. Here, we assess the effect of in ovo exposure to the model PAH, benzo[k]fluoranthene (BkF), on aryl hydrocarbon receptor (AHR) mediated cytochrome P4501A (CYP1A) gene expression and promoter methylation in chicken embryos. Fertilized chicken eggs were injected with BkF (0-100μg/kg) prior to incubation. BkF exposure was associated with an increase in CYP1A4 and CYP1A5 mRNA levels at mid-incubation (embryonic day 10), which dropped to baseline levels towards the end of the incubation period (embryonic day 19). The transient induction in CYP1A expression was accompanied by small but significant increases in CYP1A promoter methylation, which persisted until after shortly after hatching. Methylation within the CYP1A promoter was correlated with levels of CYP1A5, but not CYP1A4 mRNA. Characterization of the role of DNA methylation in the AHR response pathway may increase our understanding of the effects of early life exposure to PAHs in birds.
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Affiliation(s)
- Jonas Brandenburg
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada
| | - Jessica A Head
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
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14
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García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV. Epigenetic biomarkers: Current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 2017; 54:529-550. [PMID: 29226748 DOI: 10.1080/10408363.2017.1410520] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic modifications and regulators represent potential molecular elements which control relevant physiological and pathological features, thereby contributing to the natural history of human disease. These epigenetic modulators can be employed as disease biomarkers, since they show several advantages and provide information about gene function, thus explaining differences among patient endophenotypes. In addition, epigenetic biomarkers can incorporate information regarding the effects of the environment and lifestyle on health and disease, and monitor the effect of applied therapies. Technologies used to analyze these epigenetic biomarkers are constantly improving, becoming much easier to use. Laboratory professionals can easily acquire experience and techniques are becoming more affordable. A high number of epigenetic biomarker candidates are being continuously proposed, making now the moment to adopt epigenetics in the clinical laboratory and convert epigenetic marks into reliable biomarkers. In this review, we describe some current promising epigenetic biomarkers and technologies being applied in clinical practice. Furthermore, we will discuss some laboratory strategies and kits to accelerate the adoption of epigenetic biomarkers into clinical routine. The likelihood is that over time, better markers will be identified and will likely be incorporated into future multi-target assays that might help to optimize its application in a clinical laboratory. This will improve cost-effectiveness, and consequently encourage the development of theragnosis and the application of precision medicine.
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Affiliation(s)
- José Luis García-Giménez
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain.,e EpiDisease S.L. Spin-Off of CIBERER (ISCIII) , Valencia , Spain
| | - Marta Seco-Cervera
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain
| | - Trygve O Tollefsbol
- f Department of Biology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Carlos Romá-Mateo
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
| | - Lorena Peiró-Chova
- b INCLIVA Biomedical Research Institute , Valencia , Spain.,g INCLIVA Biobank , Valencia , Spain
| | - Pablo Lapunzina
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,h Institute of Medical and Molecular Genetics (INGEMM) , IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid , Madrid , Spain
| | - Federico V Pallardó
- a Center for Biomedical Network Research on Rare Diseases (CIBERER) , Institute of Health Carlos III , Valencia , Spain.,b INCLIVA Biomedical Research Institute , Valencia , Spain.,c Department Physiology, School of Medicine and Dentistry , Universitat de València (UV) , Valencia , Spain.,d Epigenetics Research Platform (CIBERER/UV/INCLIVA) , Valencia , Spain
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Rizzi G, Lee JR, Dahl C, Guldberg P, Dufva M, Wang SX, Hansen MF. Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array. ACS NANO 2017; 11:8864-8870. [PMID: 28832112 PMCID: PMC5810360 DOI: 10.1021/acsnano.7b03053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.
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Affiliation(s)
- Giovanni Rizzi
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, South Korea
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
| | - Christina Dahl
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 93405, United States
- Corresponding Authors:.
| | - Mikkel F. Hansen
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
- Corresponding Authors:.
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Hosseini M, Khaki F, Shokri E, Khabbaz H, Dadmehr M, Ganjali MR, Feizabadi M, Ajloo D. Study on the Interaction of the CpG Alternating DNA with CdTe Quantum Dots. J Fluoresc 2017; 27:2059-2068. [PMID: 28842837 DOI: 10.1007/s10895-017-2145-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/18/2017] [Indexed: 12/31/2022]
Abstract
A novel sensitive method for detection of DNA methylation was developed with thioglycollic acid (TGA)-capped CdTe quantum dots (QDs) as fluorescence probes. Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. DNA methylation occurs most often at cytosine-guanine sites (CpG dinucleotides) of gene promoters. The QDs significantly interacted with hybridized unmethylated and methylated DNA. The interaction of CpG rich methylated and unmethylated DNA hybrid with quantum dots as an optical probe has been investigated by fluorescence spectroscopy and electrophoresis assay. The fluorescence intensity of QDs was highly dependent to unmethylated and methylated DNA. Specific site of CpG islands of Adenomatous polyposis coli (APC), a well-studied tumor suppressor gene, was used as the detection target. Under optimum conditions, upon the addition of unmethylated dsDNA, the fluorescence intensity increased in linear range from 1.0 × 10- 10 to 1.0 × 10- 6M with detection limit of 6.2 × 10- 11 M and on the other hand, the intensity of QDs showed no changes with addition of methylated dsDNA. We also demonstrated that the unmethylated and methylated DNA and QDs complexes showed different mobility in electrophoresis assay. This easy and reliable method could distinguish between methylated and unmethylated DNA sequences.
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Affiliation(s)
- Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Freshteh Khaki
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Ehsan Shokri
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Hossein Khabbaz
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mehdi Dadmehr
- Department of Biotechnology, Payame Noor University, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran.,Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Davood Ajloo
- School of Chemistry, Damghan University, Damghan, Iran
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Lazo-de-la-Vega-Monroy ML, Solís-Martínez MO, Romero-Gutiérrez G, Aguirre-Arzola VE, Wrobel K, Wrobel K, Zaina S, Barbosa-Sabanero G. 11 beta-hydroxysteroid dehydrogenase 2 promoter methylation is associated with placental protein expression in small for gestational age newborns. Steroids 2017; 124:60-66. [PMID: 28502862 DOI: 10.1016/j.steroids.2017.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 11/15/2022]
Abstract
Small for gestational age infants have greater risk of developing metabolic diseases in adult life. It has been suggested that low birth weight may result from glucocorticoid excess in utero, a key mechanism in fetal programming. The placental enzyme 11-beta hydroxysteroid dehydrogenase type 2 (11β-HSD2, HSD11B2 gene) acts as a barrier protecting the fetus from maternal corticosteroid deleterious effects. Low placental 11β-HSD2 transcription and activity have been associated with low birth weight, yet the mechanism regulating its protein expression is not fully understood. In the present study we aimed to analyze 11β-HSD2 protein expression in placentas of adequate and small for gestational age (AGA and SGA, respectively) newborns from healthy mothers, and to explore whether 11β-HSD2 protein expression could be modulated by DNA methylation. 11β-HSD2 protein levels were measured by western blot in placental biopsies from term AGA and SGA infants (n=10 per group). DNA methylation was profiled both globally and in the HSD11B2 promoter by liquid chromatography with UV detection and methylation-specific melting curve analysis, respectively. We found lower placental 11β-HSD2 protein expression and higher HSD11B2 promoter methylation in SGA compared to AGA. Promoter methylation was inversely correlated with both protein expression and, importantly, birth weight. No changes in global placental methylation were found. In conclusion, lower 11β-HSD2 protein expression is associated with higher HSD11B2 promoter methylation, correlating with birth weight in healthy pregnancy. Our data support the role of 11β-HSD2 in determining birth weight, providing evidence of its regulation by epigenetic mechanisms, which may affect postnatal metabolic disease risk.
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Affiliation(s)
| | | | | | | | - Katarzyna Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico.
| | - Kazimierz Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico.
| | - Silvio Zaina
- Medical Sciences Department, Health Sciences Division, University of Guanajuato, Leon Campus, Mexico.
| | - Gloria Barbosa-Sabanero
- Medical Sciences Department, Health Sciences Division, University of Guanajuato, Leon Campus, Mexico.
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18
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Optical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 92:668-678. [DOI: 10.1016/j.bios.2016.10.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 11/23/2022]
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19
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Appe AJ, Aggerholm A, Hansen MC, Ebbesen LH, Hokland P, Bentzen HHN, Nyvold CG. Differential expression levels and methylation status of ROBO1 in mantle cell lymphoma and chronic lymphocytic leukaemia. Int J Lab Hematol 2017; 39:e70-e73. [PMID: 28004534 DOI: 10.1111/ijlh.12615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
MESH Headings
- DNA Methylation
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Mantle-Cell/metabolism
- Lymphoma, Mantle-Cell/pathology
- Male
- Neoplasm Proteins/biosynthesis
- Nerve Tissue Proteins/biosynthesis
- Receptors, Immunologic/biosynthesis
- Roundabout Proteins
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Affiliation(s)
- A J Appe
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - A Aggerholm
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - M C Hansen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - L H Ebbesen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - P Hokland
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - H H N Bentzen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - C G Nyvold
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
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Wang H, Ke H, Zheng Y, Lai J, Luo Q, Chen Q. A modified bisulfite conversion method for the detection of DNA methylation. Epigenomics 2017; 9:955-969. [PMID: 28548583 DOI: 10.2217/epi-2016-0174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM Our purpose is to improve the conventional procedures for bisulfite conversion used to detect 5-methylcytosine in DNA. METHODS Impacts of different bisulfite salts, bisulfite conversion temperature, antioxidants and denaturants on DNA conversion and degradation were assessed by methylation-sensitive melt curve analysis. The modified method was tested on different genes and the conversion efficiency was analyzed by bisulfite sequencing. RESULTS We developed a modified bisulfite conversion method that completes this process within 2 h. We demonstrate that high temperature denaturation is the major cause for DNA degradation, and the addition of ethylene glycol dimethyl ether is an effective way to accelerate the bisulfite conversion. The conversion efficiency is comparable to many other commercial kits. CONCLUSION Our modified bisulfite conversion method is simple, cost efficient and less time consuming and is compatible with different genes and samples, thus has a great potential for the future research and clinical applications.
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Affiliation(s)
- Hanze Wang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, 1 Keji Road, College Town, Fuzhou, Fujian 350117, China
| | - Huican Ke
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, 1 Keji Road, College Town, Fuzhou, Fujian 350117, China
| | - Yansong Zheng
- Department of Hepatobiliary Pancreatic Surgery, The First Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Junzhong Lai
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, 1 Keji Road, College Town, Fuzhou, Fujian 350117, China
| | - Qianping Luo
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, 1 Keji Road, College Town, Fuzhou, Fujian 350117, China
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, 1 Keji Road, College Town, Fuzhou, Fujian 350117, China
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Cirilli M, Delfino I, Caboni E, Muleo R. EpiHRMAssay, in tube and in silico combined approach for the scanning and epityping of heterogeneous DNA methylation. Biol Methods Protoc 2017; 2:bpw008. [PMID: 32161783 PMCID: PMC6994072 DOI: 10.1093/biomethods/bpw008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/12/2016] [Accepted: 12/16/2016] [Indexed: 11/18/2022] Open
Abstract
Reliable and cost-effective assays with adequate sensitivity are required to detect the DNA methylation profile in plants for scientific and industrial purposes. The proposed novel assay, named EpiHRMAssay, allows to quantify the overall methylation status at target loci and to enable high-throughput analyses. It combines in tube High Resolution Melting Analysis on bisulphite-treated templates with the in silico prediction of the melting profile of virtual epialleles using uMELTSM software. The predicted melting temperatures (Tm-s) of a set of epialleles characterized by different numbers of methylated cytosines (#mC) or different mC configurations were obtained and used to build calibration models, enabling the quantification of methylation in unknown samples using only the in tube observed melting temperature (Tm-o). EpiHRMAssay was validated by analysing the promoter region of CMT3, DDM1, and ROS1 genes involved in the regulation of methylation/demethylation processes and chromatin remodelling within a population of peach plants. Results demonstrate that EpiHRMAssay is a sensitive and reliable tool for locus-specific large-scale research and diagnostic contexts of the regulative regions of genes, in a broad range of organisms, including mammals. EpiHRMAssay also provides complementary information for the assessment of heterogeneous methylation and can address an array of biological questions on epigenetic regulation for diversity studies and for large-scale functional genomics.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis snc, Viterbo 01100, Italy
| | - Ines Delfino
- Department of Ecological and Biological Sciences, University of Tuscia, L.go dell'Università snc, Viterbo 01100, Italy
| | - Emilia Caboni
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Fruit Tree Research Center, Via di Fioranello, 52, 00134 Rome, Italy
| | - Rosario Muleo
- Department of Agricultural and Forestry Sciences, University of Tuscia, Via S. Camillo de Lellis snc, Viterbo 01100, Italy
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Cheishvili D, Petropoulos S, Christiansen S, Szyf M. Targeted DNA Methylation Analysis Methods. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2017. [DOI: 10.1007/978-1-4939-6743-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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Munch-Petersen HD, Asmar F, Dimopoulos K, Areškevičiūtė A, Brown P, Girkov MS, Pedersen A, Sjö LD, Heegaard S, Broholm H, Kristensen LS, Ralfkiaer E, Grønbæk K. TP53 hotspot mutations are predictive of survival in primary central nervous system lymphoma patients treated with combination chemotherapy. Acta Neuropathol Commun 2016; 4:40. [PMID: 27101868 PMCID: PMC4840983 DOI: 10.1186/s40478-016-0307-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 03/27/2016] [Indexed: 12/18/2022] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is an aggressive variant of diffuse large B-cell lymphoma (DLBCL) confined to the CNS. TP53 mutations (MUT-TP53) were investigated in the context of MIR34A/B/C- and DAPK promoter methylation status, and associated with clinical outcomes in PCNSL patients. In a total of 107 PCNSL patients clinical data were recorded, histopathology reassessed, and genetic and epigenetic aberrations of the p53-miR34-DAPK network studied. TP53 mutational status (exon 5-8), with structural classification of single nucleotide variations according to the IARC-TP53-Database, methylation status of MIR34A/B/C and DAPK, and p53-protein expression were assessed. The 57/107 (53.2 %) patients that were treated with combination chemotherapy +/- rituximab (CCT-treated) had a significantly better median overall survival (OS) (31.3 months) than patients treated with other regimens (high-dose methotrexate/whole brain radiation therapy, 6.0 months, or no therapy, 0.83 months), P < 0.0001. TP53 mutations were identified in 32/86 (37.2 %), among which 12 patients had hotspot/direct DNA contact mutations. CCT-treated patients with PCNSL harboring a hotspot/direct DNA contact MUT-TP53 (n = 9) had a significantly worse OS and progression free survival (PFS) compared to patients with non-hotspot/non-direct DNA contact MUT-TP53 or wild-type TP53 (median PFS 4.6 versus 18.2 or 45.7 months), P = 0.041 and P = 0.00076, respectively. Multivariate Cox regression analysis confirmed that hotspot/direct DNA contact MUT-TP53 was predictive of poor outcome in CCT-treated PCNSL patients, P = 0.012 and P = 0.008; HR: 1.86 and 1.95, for OS and PFS, respectively. MIR34A, MIR34B/C, and DAPK promoter methylation were detected in 53/93 (57.0 %), 80/84 (95.2 %), and 70/75 (93.3 %) of the PCNSL patients with no influence on survival. Combined MUT-TP53 and MIR34A methylation was associated with poor PFS (median 6.4 versus 38.0 months), P = 0.0070. This study suggests that disruption of the p53-pathway by MUT-TP53in hotspot/direct DNA contact codons is predictive of outcome in CCT-treated PCNSL patients, and concomitant MUT-TP53 and MIR34A methylation are associated with poor PFS.
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Chen T, Jia Y, Dong C, Gao J, Mak PI, Martins RP. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device. LAB ON A CHIP 2016; 16:743-752. [PMID: 26781669 DOI: 10.1039/c5lc01533b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis.
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Affiliation(s)
- Tianlan Chen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, University of Macau, Macao, China.
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Stewart L, Evans N, Bexon KJ, van der Meer DJ, Williams GA. Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis. Anal Biochem 2015; 476:36-9. [DOI: 10.1016/j.ab.2015.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/26/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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DNA methylation and histone modifications regulate SOX11 expression in lymphoid and solid cancer cells. BMC Cancer 2015; 15:273. [PMID: 25880212 PMCID: PMC4403777 DOI: 10.1186/s12885-015-1208-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 03/18/2015] [Indexed: 12/12/2022] Open
Abstract
Background The neural transcription factor SOX11 is present at specific stages during embryo development with a very restricted expression in adult tissue, indicating precise regulation of transcription. SOX11 is strongly up-regulated in some malignancies and have a functional role in tumorgenesis. With the aim to explore differences in epigenetic regulation of SOX11 expression in normal versus neoplastic cells, we investigated methylation and histone modifications related to the SOX11 promoter and the possibility to induce re-expression using histone deacetylase (HDAC) or EZH2 inhibitors. Methods The epigenetic regulation of SOX11 was investigated in distinct non-malignant cell populations (n = 7) and neoplastic cell-lines (n = 42) of different cellular origins. DNA methylation was assessed using bisulfite sequencing, methylation-specific melting curve analysis, MethyLight and pyrosequencing. The presence of H3K27me3 was assessed using ChIP-qPCR. The HDAC inhibitors Vorinostat and trichostatin A were used to induce SOX11 in cell lines with no endogenous expression. Results The SOX11 promoter shows a low degree of methylation and strong enrichment of H3K27me3 in non-malignant differentiated cells, independent of cellular origin. Cancers of the B-cell lineage are strongly marked by de novo methylation at the SOX11 promoter in SOX11 non-expressing cells, while solid cancer entities display a more varying degree of SOX11 promoter methylation. The silencing mark H3K27me3 was generally present at the SOX11 promoter in non-expressing cells, and an increased enrichment was observed in cancer cells with a low degree of SOX11 methylation compared to cells with dense methylation. Finally, we demonstrate that the HDAC inhibitors (vorinostat and trichostatin A) induce SOX11 expression in cancer cells with low levels of SOX11 methylation. Conclusions We show that SOX11 is strongly marked by repressive histone marks in non-malignant cells. In contrast, SOX11 regulation in neoplastic tissues is more complex involving both DNA methylation and histone modifications. The possibility to re-express SOX11 in non-methylated tissue is of clinical relevance, and was successfully achieved in cell lines with low levels of SOX11 methylation. In breast cancer patients, methylation of the SOX11 promoter was shown to correlate with estrogen receptor status, suggesting that SOX11 may be functionally re-expressed during treatment with HDAC inhibitors in specific patient subgroups. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1208-y) contains supplementary material, which is available to authorized users.
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Asmar F, Hother C, Kulosman G, Treppendahl MB, Nielsen HM, Ralfkiaer U, Pedersen A, Møller MB, Ralfkiaer E, de Nully Brown P, Grønbæk K. Diffuse large B-cell lymphoma with combined TP53 mutation and MIR34A methylation: Another "double hit" lymphoma with very poor outcome? Oncotarget 2015; 5:1912-25. [PMID: 24722400 PMCID: PMC4039115 DOI: 10.18632/oncotarget.1877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiR34A, B and C have been implicated in lymphomagenesis, but information on their role in normal CD19+ B-cells (PBL-B) and de novo diffuse large B-cell lymphoma (DLBCL) is limited. We show that in normal and activated B-cells miR34A-5p plays a dominant role compared to other miR34 family members. Only miR34A-5p is expressed in PBL-B, and significantly induced in activated B-cells and reactive lymph nodes. In PBL-B, the MIR34A and MIR34B/C promoters are unmethylated, but the latter shows enrichment for the H3K4me3/H3K27me3 silencing mark. Nine de novo DLBCL cases (n=150) carry both TP53 mutation and MIR34A methylation (“double hit”) and these patients have an exceedingly poor prognosis with a median survival of 9.4 months (P<0.0001), while neither TP53 mutation, MIR34A or MIR34B/C promoter methylation alone (“single hit”) influence on survival. The TP53/MIR34A “double-hit” is an independent negative prognostic factor for survival (P=0.0002). In 2 DLBCL-cell lines with both TP53 mutation and promoter methylation of MIR34A, miR34A-5p is upregulated by 5-aza-2'deoxycytidine. Thus, the TP53/MIR34A “double hit” characterizes a very aggressive subgroup of DLBCL, which may be treatable with epigenetic therapy prior to or in combination with conventional immunochemotherapy.
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Affiliation(s)
- Fazila Asmar
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
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Cebola I, Custodio J, Muñoz M, Díez-Villanueva A, Paré L, Prieto P, Aussó S, Coll-Mulet L, Boscá L, Moreno V, Peinado MA. Epigenetics override pro-inflammatory PTGS transcriptomic signature towards selective hyperactivation of PGE2 in colorectal cancer. Clin Epigenetics 2015; 7:74. [PMID: 26207152 PMCID: PMC4512023 DOI: 10.1186/s13148-015-0110-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Misregulation of the PTGS (prostaglandin endoperoxide synthase, also known as cyclooxygenase or COX) pathway may lead to the accumulation of pro-inflammatory signals, which constitutes a hallmark of cancer. To get insight into the role of this signaling pathway in colorectal cancer (CRC), we have characterized the transcriptional and epigenetic landscapes of the PTGS pathway genes in normal and cancer cells. RESULTS Data from four independent series of CRC patients (502 tumors including adenomas and carcinomas and 222 adjacent normal tissues) and two series of colon mucosae from 69 healthy donors have been included in the study. Gene expression was analyzed by real-time PCR and Affymetrix U219 arrays. DNA methylation was analyzed by bisulfite sequencing, dissociation curves, and HumanMethylation450K arrays. Most CRC patients show selective transcriptional deregulation of the enzymes involved in the synthesis of prostanoids and their receptors in both tumor and its adjacent mucosa. DNA methylation alterations exclusively affect the tumor tissue (both adenomas and carcinomas), redirecting the transcriptional deregulation to activation of prostaglandin E2 (PGE2) function and blockade of other biologically active prostaglandins. In particular, PTGIS, PTGER3, PTGFR, and AKR1B1 were hypermethylated in more than 40 % of all analyzed tumors. CONCLUSIONS The transcriptional and epigenetic profiling of the PTGS pathway provides important clues on the biology of the tumor and its microenvironment. This analysis renders candidate markers with potential clinical applicability in risk assessment and early diagnosis and for the design of new therapeutic strategies.
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Affiliation(s)
- Inês Cebola
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
- Current address: Department of Medicine, Imperial College London, London, UK
| | - Joaquin Custodio
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
- Current address: Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
| | - Laia Paré
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona Spain
| | - Patricia Prieto
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona Spain
| | - Llorenç Coll-Mulet
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
| | - Lisardo Boscá
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERESP, Hospitalet de Llobregat, Barcelona Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC, Ctra Can Ruti, Cami de les Escoles, Badalona, 08916 Spain
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Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome. Clin Epigenetics 2014; 6:22. [PMID: 25859283 PMCID: PMC4391486 DOI: 10.1186/1868-7083-6-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/17/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA hypermethylation is reported as a frequent event and prognostic marker in head and neck squamous cell carcinomas (HNSCC). Methylation has been commonly assessed with non-quantitative methodologies, such as methylation-specific PCR (MSP). We investigated previously reported hypermethylated genes with quantitative methodology in oral tongue squamous cell carcinomas (OTSCC). RESULTS The methylation status of 12 genes in 115 OTSCC samples was assessed by one or more of three quantitative analyses: methylation sensitive high resolution melting (MS-HRM), sensitive-melting analysis after real time-methylation specific PCR (SMART-MSP), and bisulfite pyrosequencing. In contrast to much of the literature, either no or infrequent locus-specific methylation was identified by MS-HRM for DAPK1, RASSF1A, MGMT, MLH1, APC, CDH1, CDH13, BRCA1, ERCC1, and ATM. The most frequently methylated loci were RUNX3 (18/108 methylated) and ABO (22/107 methylated). Interrogation of the Cancer Genome Atlas (TCGA) HNSCC cohort confirmed the frequency of significant methylation for the loci investigated. Heterogeneous methylation of RUNX3 (18/108) and ABO (22/107) detected by MS-HRM, conferred significantly worse survival (P = 0.01, and P = 0.03). However, following quantification of methylation levels using pyrosequencing, only four tumors had significant quantities (>15%) of RUNX3 methylation which correlated with a worse patient outcome (P <0.001), while the prognostic significance of ABO hypermethylation was lost. RUNX3 methylation was not prognostic for the TCGA cohort (P = 0.76). CONCLUSIONS We demonstrated the critical need for quantification of methylation levels and its impact on correlative analyses. In OTSCC, we found little evidence of significant or frequent hypermethylation of many loci reported to be commonly methylated. It is likely that previous reports have overestimated the frequency of significant methylation events as a consequence of the use of non-quantitative methodology.
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Dahl C, Abildgaard C, Riber-Hansen R, Steiniche T, Lade-Keller J, Guldberg P. KIT is a frequent target for epigenetic silencing in cutaneous melanoma. J Invest Dermatol 2014; 135:516-524. [PMID: 25178104 DOI: 10.1038/jid.2014.372] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 12/16/2022]
Abstract
The receptor tyrosine kinase KIT and its ligand, stem cell factor (SCF), are essential for the proliferation and survival of normal melanocytes. In melanomas arising on mucosal, acral, and chronically sun-damaged skin, activating KIT mutations have been identified as oncogenic drivers and potent therapeutic targets. Through an initial whole-genome screen for aberrant promoter methylation in melanoma, we identified the KIT promoter as a target for hypermethylation in 43/110 melanoma cell lines, and in 3/12 primary and 11/29 metastatic cutaneous melanomas. Methylation density at the KIT promoter correlated inversely with promoter activity in vitro and in vivo, and the expression of KIT was restored after treatment with the demethylating agent 5-aza-2'-deoxycytidine. Hypermethylation of KIT showed no direct or inverse correlations with well-documented melanoma drivers. Growth of melanoma cells in the presence of SCF led to reduced KIT expression and increased methylation density at the KIT promoter, suggesting that SCF may exert a selection pressure for the loss of KIT. The frequent loss of KIT in cutaneous melanoma by promoter hypermethylation suggests that distinct KIT signaling pathways have opposing roles in the pathogenesis of melanoma subtypes.
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Affiliation(s)
- Christina Dahl
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | | | - Torben Steiniche
- Institute of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, Denmark.
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Metallothionein III (MT3) is a putative tumor suppressor gene that is frequently inactivated in pediatric acute myeloid leukemia by promoter hypermethylation. J Transl Med 2014; 12:182. [PMID: 24962166 PMCID: PMC4082423 DOI: 10.1186/1479-5876-12-182] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/20/2014] [Indexed: 11/14/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is the second most common form of leukemia in children. Aberrant DNA methylation patterns are a characteristic feature in various tumors, including AML. Metallothionein III (MT3) is a tumor suppresser reported to show promoter hypermethylated in various cancers. However, the expression and molecular function of MT3 in pediatric AML is unclear. Methods Eleven human leukemia cell lines and 41 pediatric AML samples and 20 NBM/ITP (Norma bone marrow/Idiopathic thrombocytopenic purpura) control samples were analyzed. Transcription levels of MT3 were evaluated by semi-quantitative and real-time PCR. MT3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BSG). The molecular mechanism of MT3 was investigated by apoptosis assays and PCR array analysis. Results The MT3 promoter was hypermethylated in leukemia cell lines. More CpG’s methylated of MT3 was observed 39.0% pediatric AML samples compared to 10.0% NBM controls. Transcription of MT3 was also significantly decreased in AML samples compared to NBM/ITP controls (P < 0.001); patients with methylated MT3 exhibited lower levels of MT3 expression compared to those with unmethylated MT3 (P = 0.049). After transfection with MT3 lentivirus, proliferation was significantly inhibited in AML cells in a dose-dependent manner (P < 0.05). Annexin V assay showed that apoptosis was significantly upregulated MT3-overexpressing AML cells compared to controls. Real-time PCR array analysis revealed 34 dysregulated genes that may be implicated in MT3 overexpression and apoptosis in AML, including FOXO1. Conclusion MT3 may be a putative tumor suppressor gene in pediatric AML. Epigenetic inactivation of MT3 via promoter hypermethylation was observed in both AML cell lines and pediatric AML samples. Overexpression of MT3 may inhibit proliferation and induce apoptosis in AML cells. FOXO1 was dysregulated in MT3-overexpressing cells, offering an insight into the mechanism of MT3-induced apoptosis. However, further research is required to determine the underlying molecular details.
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Optimizing methodologies for PCR-based DNA methylation analysis. Biotechniques 2014; 55:181-97. [PMID: 24107250 DOI: 10.2144/000114087] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 09/10/2013] [Indexed: 02/07/2023] Open
Abstract
Comprehensive analysis of DNA methylation patterns is critical for understanding the molecular basis of many human diseases. While hundreds of PCR-based DNA methylation studies are published every year, the selection and implementation of appropriate methods for these studies can be challenging for molecular genetics researchers not yet familiar with methylation analysis. Here we review the most commonly used PCR-based DNA methylation analysis techniques: bisulfite sequencing PCR (BSP), methylation specific PCR (MSP), MethyLight, and methylation-sensitive high resolution melting (MS-HRM). We provide critical analysis of the strengths and weaknesses of each approach as well as a series of guidelines to assist in selecting and implementing an appropriate method.
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Chaudhary AG, Hussein IR, Abuzenadah A, Gari M, Bassiouni R, Sogaty S, Lary S, Al-Quaiti M, Al Balwi M, Al Qahtani M. Molecular diagnosis of fragile X syndrome using methylation sensitive techniques in a cohort of patients with intellectual disability. Pediatr Neurol 2014; 50:368-76. [PMID: 24630283 DOI: 10.1016/j.pediatrneurol.2013.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/04/2013] [Accepted: 11/23/2013] [Indexed: 11/26/2022]
Abstract
BACKGROUND Fragile X syndrome, the most common form of inherited intellectual disability, is caused by expansion of CGG trinucleotide repeat at the 5' untranslated region of the FMR1 gene at Xq27. In affected individuals, the CGG repeat expansion leads to hypermethylation and the gene is transcriptionally inactive. Our aim was to identify fragile X syndrome among children with intellectual disability in Saudi Arabia. PATIENTS AND METHODS The study included 63 patients (53 males, 10 females) presented with intellectual disability, 29 normal subjects, and 23 other family members. DNA samples from six patients previously diagnosed with fragile X syndrome by Southern blot technique were used as positive controls. The method was based on bisulfite treatment of DNA followed by two different techniques. The first technique applied polymerase chain reaction amplification using one set of primers specific for amplifying methylated CpG dinucleotide region; another set designed to amplify the unmethylated CGG repeats. The second technique used the methylation-specific melting curve analysis for detection of methylation status of the FMR1 promoter region. RESULTS Molecular testing using methylation sensitive polymerase chain reaction had shown amplified products in all normal subjects using unmethylated but not methylated primers indicating normal alleles, whereas amplified products were obtained using methylated polymerase chain reaction primers in fragile X syndrome-positive samples and in 9 of 53 males, indicating affected individuals. Molecular testing using melting curve analysis has shown a single low melting peak in all normal males and in (44/53) patients indicating unmethylated FMR1 gene, whereas high melting peak indicating methylated gene was observed in the fragile X syndrome-positive samples and in 9 of 53 patients. We found 100% concordance between results of both techniques and the results of Southern blot analysis. Three samples have shown both methylated and unmethylated alleles, indicating possible mosaicism. No female patients or carriers could be detected by both techniques. CONCLUSION The technique can be applied for the rapid screening for fragile X syndrome among patients with intellectual disability. The impact of mosaicism on clinical severity needs further investigation.
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Affiliation(s)
- Adeel G Chaudhary
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Ibtessam R Hussein
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Adel Abuzenadah
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mamdouh Gari
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Randa Bassiouni
- Pediatric Hospital, Ministry of Health, Al Taif, Kingdom of Saudi Arabia
| | | | - Sahira Lary
- Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha Al-Quaiti
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed Al Balwi
- King Abdulaziz Medical City for National Guard Health Affairs, and King Saud bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Al Qahtani
- Faculty of Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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Kristiansen S, Nielsen D, Sölétormos G. Methylated DNA for monitoring tumor growth and regression: how do we get there? Crit Rev Clin Lab Sci 2014; 51:149-59. [PMID: 24611610 DOI: 10.3109/10408363.2014.893279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A wide range of protein cancer biomarkers is currently recommended in international guidelines for monitoring the growth and regression of solid tumors. However, a number of these markers are also present in low concentrations in blood obtained from healthy individuals and from patients with benign diseases. In contrast, evidence has accumulated that suggests that modified methylated DNA is strongly related to the cancer phenotype. The modifications found in modified methylated DNA include a global loss of methylation in the genomes of the tumor cells as well as focal hypermethylation of gene promoters. Because tumor cells naturally secrete DNA and upon cell death leak DNA, modified methylated DNA can be detected in blood, urine, sputum and other body fluids. At present international guidelines do not include recommendations for monitoring modified methylated DNA. The low level of evidence can partly be explained by incomplete collection of serial blood samples, by analytical challenges, and by lack of knowledge of how monitoring studies should be designed and how serial marker data obtained from individual patients should be interpreted. Here, we review the clinical validity and utility of methylated DNA for monitoring the activity of malignant disease.
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Affiliation(s)
- Søren Kristiansen
- Department of Clinical Biochemistry, North Zealand Hospital - Hillerød, University of Copenhagen , Hillerød , Denmark and
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Wojdacz TK. Methylation-sensitive high-resolution melting in the context of legislative requirements for validation of analytical procedures for diagnostic applications. Expert Rev Mol Diagn 2014; 12:39-47. [DOI: 10.1586/erm.11.88] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abstract
Epigenetics has undergone an explosion in the past decade. DNA methylation, consisting of the addition of a methyl group at the fifth position of cytosine (5-methylcytosine, 5-mC) in a CpG dinucleotide, is a well-recognized epigenetic mark with important functions in cellular development and pathogenesis. Numerous studies have focused on the characterization of DNA methylation marks associated with disease development as they may serve as useful biomarkers for diagnosis, prognosis, and prediction of response to therapy. Recently, novel cytosine modifications with potential regulatory roles such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC) have been discovered. Study of the functions of 5-mC and its oxidation derivatives promotes the understanding of the mechanism underlying association of epigenetic modifications with disease biology. In this respect, much has been accomplished in the development of methods for the discovery, detection, and location analysis of 5-mC and its oxidation derivatives. In this review, we focus on the recent advances for the global detection and location study of 5-mC and its oxidation derivatives 5-hmC, 5-foC, and 5-caC.
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40
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Hanson EK, Ballantyne J. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis. F1000Res 2013; 2:281. [PMID: 24715968 PMCID: PMC3976110 DOI: 10.12688/f1000research.2-281.v2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2014] [Indexed: 01/02/2023] Open
Abstract
Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen). The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive, screening of biological evidence.
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Affiliation(s)
- Erin K Hanson
- National Center for Forensic Science, Orlando, FL 32816-2367, USA
| | - Jack Ballantyne
- National Center for Forensic Science, Orlando, FL 32816-2367, USA ; Department of Chemistry, University of Central Florida, Orlando, FL 32816-2366, USA
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Zhang J, Xing B, Song J, Zhang F, Nie C, Jiao L, Liu L, Lv F, Wang S. Associated Analysis of DNA Methylation for Cancer Detection Using CCP-Based FRET Technique. Anal Chem 2013; 86:346-50. [DOI: 10.1021/ac402720g] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jiangyan Zhang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Baoling Xing
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Jinzhao Song
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Feng Zhang
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Chenyao Nie
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lian Jiao
- Department
of Pathology, Changzhou Women and Children Health Hospital, Changzhou 213003, P. R. China
| | - Libing Liu
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fengting Lv
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shu Wang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Organic Solids,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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Xu Z, Wang M, Yin H, Ai S, Wang L, Pang J. A sensitive electrochemical method for DNA methyltransferase assay and inhibitor screening based on DNA methylation-sensitive cleavage. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.09.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Stoccoro A, Karlsson HL, Coppedè F, Migliore L. Epigenetic effects of nano-sized materials. Toxicology 2013; 313:3-14. [DOI: 10.1016/j.tox.2012.12.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/12/2012] [Accepted: 12/03/2012] [Indexed: 12/17/2022]
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Kristensen LS, Treppendahl MB, Grønbæk K. Analysis of epigenetic modifications of DNA in human cells. ACTA ACUST UNITED AC 2013; Chapter 20:Unit20.2. [PMID: 23595599 DOI: 10.1002/0471142905.hg2002s77] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Epigenetics, the study of somatically heritable changes in gene expression not related to changes in the DNA sequence, is a rapidly expanding research field that plays important roles in healthy as well as in diseased cells. DNA methylation and hydroxymethylation are epigenetic modifications found in human cells, which are deeply implicated in normal cellular processes as well as in several major human diseases. Here, a range of different methods for the analyses of DNA methylation and hydroxymethylation at locus-specific and genome-wide scales is described.
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Dahl C, Christensen C, Jönsson G, Lorentzen A, Skjødt ML, Borg Å, Pawelec G, Guldberg P. Mutual exclusivity analysis of genetic and epigenetic drivers in melanoma identifies a link between p14 ARF and RARβ signaling. Mol Cancer Res 2013; 11:1166-78. [PMID: 23851445 DOI: 10.1158/1541-7786.mcr-13-0006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Melanoma genomes contain thousands of alterations including: mutations, copy number alterations, structural aberrations, and methylation changes. The bulk of this variation is stochastic and functionally neutral, with only a small minority representing "drivers" that contribute to the genesis and maintenance of tumors. Drivers are often directly or inversely correlated across tumors, reflecting the molecular and regulatory signaling pathways in which they operate. Here, a profile of genetic and epigenetic drivers in 110 human melanoma cell lines was generated and searched for non-random distribution patterns. Statistically significant mutual exclusivity was revealed among components of each of the p16(INK4A)-CDK4-RB, RAS-RAF-MEK-ERK and PI3K-AKT signaling pathways. In addition, an inverse correlation was observed between promoter hypermethylation of retinoic acid receptor β (RARB) and CDKN2A alterations affecting p14(ARF) (P < 0.0001), suggesting a functional link between RARβ signaling and the melanoma-suppressive activities of p14(ARF). Mechanistically, all-trans retinoic acid (ATRA) treatment increased the expression of p14(ARF) in primary human melanocytes and the steady-state levels of p14(ARF) in these cells were shown to be regulated via RARβ. Furthermore, the ability of ATRA to induce senescence is reduced in p14(ARF)-depleted melanocytes, and we provide proof-of-concept that ATRA can induce irreversible growth arrest in melanoma cells with an intact RARβ-p14(ARF) signaling axis, independent of p16(INK4A) and p53 status. IMPLICATIONS These data highlight the power of mutual exclusivity analysis of cancer drivers to unravel molecular pathways and establish a previously unrecognized cross-talk between RARβ and p14(ARF) with potential implications for melanoma treatment.
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Affiliation(s)
- Christina Dahl
- Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark.
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McGraw S, Shojaei Saadi HA, Robert C. Meeting the methodological challenges in molecular mapping of the embryonic epigenome. Mol Hum Reprod 2013; 19:809-27. [PMID: 23783346 DOI: 10.1093/molehr/gat046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The past decade of life sciences research has been driven by progress in genomics. Many voices are already proclaiming the post-genomics era, in which phenomena other than sequence polymorphism influence gene expression and also explain complex phenotypes. One of these burgeoning fields is the study of the epigenome. Although the mechanisms by which chromatin structure and reorganization as well as cytosine methylation influence gene expression are not fully understood, they are being invoked to explain the now-accepted long-term impact of the environment on gene expression, which appears to be a factor in the development of numerous diseases. Such studies are particularly relevant in early embryonic development, during which waves of epigenetic reprogramming are known to have profound impacts. Since gametes and zygotes are in the process of resetting the genome in order to create embryonic stem cells that will each differentiate to create one of many specific tissue types, this phase of life is now viewed as a window of susceptibility to epigenetic reprogramming errors. Epigenetics could explain the influence of factors such as the nutritional/metabolic status of the mother or the artificial environment of assisted reproductive technologies. However, the peculiar nature of early embryos in addition to their scarcity poses numerous technological challenges that are slowly being overcome. The principal subject of this article is to review the suitability of various current and emerging technological platforms to study oocytes and early embryonic epigenome with more emphasis on studying DNA methylation. Furthermore, the constraint of samples size, inherent to the study of preimplantation embryo development, was put in perspective with the various molecular platforms described.
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Affiliation(s)
- Serge McGraw
- Department of Human Genetics, Montreal Children's Hospital Research Institute, McGill University, Montréal, QC H3Z 2Z3, Canada
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Abstract
The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development have led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter critiques and describes the major approaches to analyzing DNA methylation.
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Dimitrakopoulos L, Vorkas PA, Georgoulias V, Lianidou ES. A closed-tube methylation-sensitive high resolution melting assay (MS-HRMA) for the semi-quantitative determination of CST6 promoter methylation in clinical samples. BMC Cancer 2012; 12:486. [PMID: 23088560 PMCID: PMC3495665 DOI: 10.1186/1471-2407-12-486] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 09/23/2012] [Indexed: 12/12/2022] Open
Abstract
Background CST6 promoter is highly methylated in cancer, and its detection can provide important prognostic information in breast cancer patients. The aim of our study was to develop a Methylation-Sensitive High Resolution Melting Analysis (MS-HRMA) assay for the investigation of CST6 promoter methylation. Methods We designed primers that amplify both methylated and unmethylated CST6 sequences after sodium bisulfate (SB) treatment and used spiked control samples of fully methylated to unmethylated SB converted genomic DNA to optimize the assay. We first evaluated the assay by analyzing 36 samples (pilot training group) and further analyzed 80 FFPES from operable breast cancer patients (independent group). MS-HRMA assay results for all 116 samples were compared with Methylation-Specific PCR (MSP) and the results were comparable. Results The developed assay is highly specific and sensitive since it can detect the presence of 1% methylated CST6 sequence and provides additionally a semi-quantitative estimation of CST6 promoter methylation. CST6 promoter was methylated in 39/80 (48.75%) of FFPEs with methylation levels being very different among samples. MS-HRMA and MSP gave comparable results when all samples were analyzed by both assays. Conclusions The developed MS-HRMA assay for CST6 promoter methylation is closed tube, highly sensitive, cost-effective, rapid and easy-to-perform. It gives comparable results to MSP in less time, while it offers the advantage of additionally providing an estimation of the level of methylation.
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Affiliation(s)
- Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, 15771, Greece
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Epigenetic Methylation of Parathyroid CaR and VDR Promoters in Experimental Secondary Hyperparathyroidism. Int J Nephrol 2012; 2012:123576. [PMID: 23094155 PMCID: PMC3474253 DOI: 10.1155/2012/123576] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/04/2012] [Indexed: 11/25/2022] Open
Abstract
Secondary hyperparathyroidism (s-HPT) in uremia is characterized by decreased expression in the parathyroids of calcium sensing (CaR) and vitamin D receptors (VDR). Parathyroid hormone (PTH) is normalized despite low levels of CaR and VDR after experimental reversal of uremia. The expression of CaR in parathyroid cultures decreases rapidly. Methylation of promoter regions is often detected during epigenetic downregulation of gene expression. Therefore, using an experimental rat model, we examined changes in methylation levels of parathyroid CaR and VDR promoters in vivo and in vitro. Methods. Uremia was induced by 5/6 nephrectomy. Melting temperature profiling of CaR and VDR PCR products after bisulfite treatment of genomic DNA from rat parathyroids was performed. Real-time PCR measured expression of PTH, CaR, VDR, and klotho genes in vitro. Results. Parathyroids from uremic rats had similar low levels of methylation in vivo and in vitro. In culture, a significant downregulation of CaR, VDR, and klotho within two hours of incubation was observed, while housekeeping genes remained stable for 24 hours. Conclusion. In uremic s-HPT and in vitro, no overall changes in methylation levels in the promoter regions of parathyroid CaR and VDR genes were found. Thus, epigenetic methylation of these promoters does not explain decreased parathyroid expression of CaR and VDR genes in uremic s-HPT.
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Olkhov-Mitsel E, Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med 2012; 1:237-60. [PMID: 23342273 PMCID: PMC3544446 DOI: 10.1002/cam4.22] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 12/13/2022] Open
Abstract
DNA methylation, consisting of the addition of a methyl group at the fifth-position of cytosine in a CpG dinucleotide, is one of the most well-studied epigenetic mechanisms in mammals with important functions in normal and disease biology. Disease-specific aberrant DNA methylation is a well-recognized hallmark of many complex diseases. Accordingly, various studies have focused on characterizing unique DNA methylation marks associated with distinct stages of disease development as they may serve as useful biomarkers for diagnosis, prognosis, prediction of response to therapy, or disease monitoring. Recently, novel CpG dinucleotide modifications with potential regulatory roles such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have been described. These potential epigenetic marks cannot be distinguished from 5-methylcytosine by many current strategies and may potentially compromise assessment and interpretation of methylation data. A large number of strategies have been described for the discovery and validation of DNA methylation-based biomarkers, each with its own advantages and limitations. These strategies can be classified into three main categories: restriction enzyme digestion, affinity-based analysis, and bisulfite modification. In general, candidate biomarkers are discovered using large-scale, genome-wide, methylation sequencing, and/or microarray-based profiling strategies. Following discovery, biomarker performance is validated in large independent cohorts using highly targeted locus-specific assays. There are still many challenges to the effective implementation of DNA methylation-based biomarkers. Emerging innovative methylation and hydroxymethylation detection strategies are focused on addressing these gaps in the field of epigenetics. The development of DNA methylation- and hydroxymethylation-based biomarkers is an exciting and rapidly evolving area of research that holds promise for potential applications in diverse clinical settings.
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Affiliation(s)
- Ekaterina Olkhov-Mitsel
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
| | - Bharati Bapat
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
- Department of Pathology, University Health Network, University of TorontoToronto, Ontario, Canada
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