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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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2
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Sahm F, Brandner S, Bertero L, Capper D, French PJ, Figarella-Branger D, Giangaspero F, Haberler C, Hegi ME, Kristensen BW, Kurian KM, Preusser M, Tops BBJ, van den Bent M, Wick W, Reifenberger G, Wesseling P. Molecular diagnostic tools for the World Health Organization (WHO) 2021 classification of gliomas, glioneuronal and neuronal tumors; an EANO guideline. Neuro Oncol 2023; 25:1731-1749. [PMID: 37279174 PMCID: PMC10547522 DOI: 10.1093/neuonc/noad100] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Indexed: 06/08/2023] Open
Abstract
In the 5th edition of the WHO CNS tumor classification (CNS5, 2021), multiple molecular characteristics became essential diagnostic criteria for many additional CNS tumor types. For those tumors, an integrated, "histomolecular" diagnosis is required. A variety of approaches exists for determining the status of the underlying molecular markers. The present guideline focuses on the methods that can be used for assessment of the currently most informative diagnostic and prognostic molecular markers for the diagnosis of gliomas, glioneuronal and neuronal tumors. The main characteristics of the molecular methods are systematically discussed, followed by recommendations and information on available evidence levels for diagnostic measures. The recommendations cover DNA and RNA next-generation-sequencing, methylome profiling, and select assays for single/limited target analyses, including immunohistochemistry. Additionally, because of its importance as a predictive marker in IDH-wildtype glioblastomas, tools for the analysis of MGMT promoter methylation status are covered. A structured overview of the different assays with their characteristics, especially their advantages and limitations, is provided, and requirements for input material and reporting of results are clarified. General aspects of molecular diagnostic testing regarding clinical relevance, accessibility, cost, implementation, regulatory, and ethical aspects are discussed as well. Finally, we provide an outlook on new developments in the landscape of molecular testing technologies in neuro-oncology.
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Affiliation(s)
- Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Neuropathology, German Concortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology and Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - David Capper
- Department of Neuropathology, Charité, Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pim J French
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Center, 3015 GD Rotterdam, The Netherlands
| | - Dominique Figarella-Branger
- Aix-Marseille University, APHM, CNRS, INP, Institute Neurophysiopathol, CHU Timone, Service d’Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Austria
| | - Monika E Hegi
- Neuroscience Research Center and Neurosurgery, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Bjarne W Kristensen
- Department of Clinical Medicine and Biotech Research and Innovation Center (BRIC), University of Copenhagen, Denmark
- Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Martin van den Bent
- The Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wolfgang Wick
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, and German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands (P.W.)
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3
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Zappe K, Pühringer K, Pflug S, Berger D, Böhm A, Spiegl-Kreinecker S, Cichna-Markl M. Association between MGMT Enhancer Methylation and MGMT Promoter Methylation, MGMT Protein Expression, and Overall Survival in Glioblastoma. Cells 2023; 12:1639. [PMID: 37371109 DOI: 10.3390/cells12121639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The repair protein O6-methylguanine-DNA methyltransferase (MGMT) is regulated epigenetically, mainly by the methylation of the MGMT promoter. MGMT promoter methylation status has emerged as a prognostic and predictive biomarker for patients with newly diagnosed glioblastoma (GBM). However, a strong negative correlation between MGMT promoter methylation and MGMT protein expression cannot be applied as a rule for all GBM patients. In order to investigate if the DNA methylation status of MGMT enhancers is associated with MGMT promoter methylation, MGMT expression, and the overall survival (OS) of GBM patients, we established assays based on high-resolution melting analysis and pyrosequencing for one intragenic and three intergenic MGMT enhancers. For CpGs in an enhancer located 560 kb upstream of the MGMT promoter, we found a significant negative correlation between the methylation status and MGMT protein levels of GBM samples expressing MGMT. The methylation status of CpGs in the intragenic enhancer (hs696) was strongly negatively correlated with MGMT promoter methylation and was significantly higher in MGMT-expressing GBM samples than in MGMT-non-expressing GBM samples. Moreover, low methylation of CpGs 01-03 and CpGs 09-13 was associated with the longer OS of the GBM patients. Our findings indicate an association between MGMT enhancer methylation and MGMT promoter methylation, MGMT protein expression, and/or OS.
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Affiliation(s)
- Katja Zappe
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Katharina Pühringer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Simon Pflug
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Daniel Berger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Andreas Böhm
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Kepler University Hospital GmbH, Johannes Kepler University, 4040 Linz, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
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4
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Brat DJ, Aldape K, Bridge JA, Canoll P, Colman H, Hameed MR, Harris BT, Hattab EM, Huse JT, Jenkins RB, Lopez-Terrada DH, McDonald WC, Rodriguez FJ, Souter LH, Colasacco C, Thomas NE, Yount MH, van den Bent MJ, Perry A. Molecular Biomarker Testing for the Diagnosis of Diffuse Gliomas. Arch Pathol Lab Med 2022; 146:547-574. [PMID: 35175291 PMCID: PMC9311267 DOI: 10.5858/arpa.2021-0295-cp] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The diagnosis and clinical management of patients with diffuse gliomas (DGs) have evolved rapidly over the past decade with the emergence of molecular biomarkers that are used to classify, stratify risk, and predict treatment response for optimal clinical care. OBJECTIVE.— To develop evidence-based recommendations for informing molecular biomarker testing for pediatric and adult patients with DGs and provide guidance for appropriate laboratory test and biomarker selection for optimal diagnosis, risk stratification, and prediction. DESIGN.— The College of American Pathologists convened an expert panel to perform a systematic review of the literature and develop recommendations. A systematic review of literature was conducted to address the overarching question, "What ancillary tests are needed to classify DGs and sufficiently inform the clinical management of patients?" Recommendations were derived from quality of evidence, open comment feedback, and expert panel consensus. RESULTS.— Thirteen recommendations and 3 good practice statements were established to guide pathologists and treating physicians on the most appropriate methods and molecular biomarkers to include in laboratory testing to inform clinical management of patients with DGs. CONCLUSIONS.— Evidence-based incorporation of laboratory results from molecular biomarker testing into integrated diagnoses of DGs provides reproducible and clinically meaningful information for patient management.
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Affiliation(s)
- Daniel J. Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD
| | - Julia A. Bridge
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE; Cytogenetics, ProPath, Dallas, TX
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| | - Howard Colman
- Department of Neurosurgery and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Meera R. Hameed
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Brent T. Harris
- Department of Neurology and Pathology, MedStar Georgetown University Hospital, Washington, DC
| | - Eyas M. Hattab
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY
| | - Jason T. Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD, Anderson Cancer Center, Houston, TX
| | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Dolores H. Lopez-Terrada
- Departments of Pathology and Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | | | | | | | | | | | | | - Martin J. van den Bent
- Brain Tumor Center at Erasmus MC Cancer Institute University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arie Perry
- Departments of Pathology and Neurological Surgery University of California San Francisco School of Medicine, San Francisco, CA
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5
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Brandner S, McAleenan A, Kelly C, Spiga F, Cheng HY, Dawson S, Schmidt L, Faulkner CL, Wragg C, Jefferies S, Higgins JPT, Kurian KM. MGMT promoter methylation testing to predict overall survival in people with glioblastoma treated with temozolomide: a comprehensive meta-analysis based on a Cochrane Systematic Review. Neuro Oncol 2021; 23:1457-1469. [PMID: 34467991 PMCID: PMC8408882 DOI: 10.1093/neuonc/noab105] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) causes resistance of tumor cells to alkylating agents. It is a predictive biomarker in high-grade gliomas treated with temozolomide, however, there is no consensus on which test method, methylation sites, and cutoff values to use. METHODS We performed a Cochrane Review to examine studies using different techniques to measure MGMT and predict survival in glioblastoma patients treated with temozolomide. Eligible longitudinal studies included (i) adults with glioblastoma treated with temozolomide with or without radiotherapy, or surgery; (ii) where MGMT status was determined in tumor tissue, and assessed by 1 or more technique; and (iii) where overall survival was an outcome parameter, with sufficient information to estimate hazard ratios (HRs). Two or more methods were compared in 32 independent cohorts with 3474 patients. RESULTS Methylation-specific PCR (MSP) and pyrosequencing (PSQ) techniques were more prognostic than immunohistochemistry for MGMT protein, and PSQ is a slightly better predictor than MSP. CONCLUSIONS We cannot draw strong conclusions about use of frozen tissue vs formalin-fixed paraffin-embedded in MSP and PSQ. Also, our meta-analysis does not provide strong evidence about the best CpG sites or threshold. MSP has been studied mainly for CpG sites 76-80 and 84-87 and PSQ at CpG sites ranging from 72 to 95. A cutoff threshold of 9% for CpG sites 74-78 performed better than higher thresholds of 28% or 29% in 2 of the 3 good-quality studies. About 190 studies were identified presenting HRs from survival analysis in patients in which MGMT methylation was measured by 1 technique only.
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Affiliation(s)
- Sebastian Brandner
- Division of Neuropathology and Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Francesca Spiga
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hung-Yuan Cheng
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke’s Hospital, Cambridge, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Bristol Medical School, Brain Tumour Research Centre, Population Health Sciences, University of Bristol, Bristol, UK
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6
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McAleenan A, Kelly C, Spiga F, Kernohan A, Cheng HY, Dawson S, Schmidt L, Robinson T, Brandner S, Faulkner CL, Wragg C, Jefferies S, Howell A, Vale L, Higgins JPT, Kurian KM. Prognostic value of test(s) for O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation for predicting overall survival in people with glioblastoma treated with temozolomide. Cochrane Database Syst Rev 2021; 3:CD013316. [PMID: 33710615 PMCID: PMC8078495 DOI: 10.1002/14651858.cd013316.pub2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Glioblastoma is an aggressive form of brain cancer. Approximately five in 100 people with glioblastoma survive for five years past diagnosis. Glioblastomas that have a particular modification to their DNA (called methylation) in a particular region (the O6-methylguanine-DNA methyltransferase (MGMT) promoter) respond better to treatment with chemotherapy using a drug called temozolomide. OBJECTIVES To determine which method for assessing MGMT methylation status best predicts overall survival in people diagnosed with glioblastoma who are treated with temozolomide. SEARCH METHODS We searched MEDLINE, Embase, BIOSIS, Web of Science Conference Proceedings Citation Index to December 2018, and examined reference lists. For economic evaluation studies, we additionally searched NHS Economic Evaluation Database (EED) up to December 2014. SELECTION CRITERIA Eligible studies were longitudinal (cohort) studies of adults with diagnosed glioblastoma treated with temozolomide with/without radiotherapy/surgery. Studies had to have related MGMT status in tumour tissue (assessed by one or more method) with overall survival and presented results as hazard ratios or with sufficient information (e.g. Kaplan-Meier curves) for us to estimate hazard ratios. We focused mainly on studies comparing two or more methods, and listed brief details of articles that examined a single method of measuring MGMT promoter methylation. We also sought economic evaluations conducted alongside trials, modelling studies and cost analysis. DATA COLLECTION AND ANALYSIS Two review authors independently undertook all steps of the identification and data extraction process for multiple-method studies. We assessed risk of bias and applicability using our own modified and extended version of the QUality In Prognosis Studies (QUIPS) tool. We compared different techniques, exact promoter regions (5'-cytosine-phosphate-guanine-3' (CpG) sites) and thresholds for interpretation within studies by examining hazard ratios. We performed meta-analyses for comparisons of the three most commonly examined methods (immunohistochemistry (IHC), methylation-specific polymerase chain reaction (MSP) and pyrosequencing (PSQ)), with ratios of hazard ratios (RHR), using an imputed value of the correlation between results based on the same individuals. MAIN RESULTS We included 32 independent cohorts involving 3474 people that compared two or more methods. We found evidence that MSP (CpG sites 76 to 80 and 84 to 87) is more prognostic than IHC for MGMT protein at varying thresholds (RHR 1.31, 95% confidence interval (CI) 1.01 to 1.71). We also found evidence that PSQ is more prognostic than IHC for MGMT protein at various thresholds (RHR 1.36, 95% CI 1.01 to 1.84). The data suggest that PSQ (mainly at CpG sites 74 to 78, using various thresholds) is slightly more prognostic than MSP at sites 76 to 80 and 84 to 87 (RHR 1.14, 95% CI 0.87 to 1.48). Many variants of PSQ have been compared, although we did not see any strong and consistent messages from the results. Targeting multiple CpG sites is likely to be more prognostic than targeting just one. In addition, we identified and summarised 190 articles describing a single method for measuring MGMT promoter methylation status. AUTHORS' CONCLUSIONS PSQ and MSP appear more prognostic for overall survival than IHC. Strong evidence is not available to draw conclusions with confidence about the best CpG sites or thresholds for quantitative methods. MSP has been studied mainly for CpG sites 76 to 80 and 84 to 87 and PSQ at CpG sites ranging from 72 to 95. A threshold of 9% for CpG sites 74 to 78 performed better than higher thresholds of 28% or 29% in two of three good-quality studies making such comparisons.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Francesca Spiga
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Hung-Yuan Cheng
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Applied Research Collaboration West (ARC West) , University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomos Robinson
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Amy Howell
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Luke Vale
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Applied Research Collaboration West (ARC West) , University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Kathreena M Kurian
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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7
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Dahlrot RH, Larsen P, Boldt HB, Kreutzfeldt MS, Hansen S, Hjelmborg JB, Kristensen BW. Posttreatment Effect of MGMT Methylation Level on Glioblastoma Survival. J Neuropathol Exp Neurol 2020; 78:633-640. [PMID: 31058280 DOI: 10.1093/jnen/nlz032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) removes temozolomide-induced alkylation, thereby preventing DNA damage and cytotoxicity. We investigated the prognostic effect of different MGMT methylation levels on overall and progression-free survival in 327 patients with primary glioblastoma undergoing standard treatment. We obtained MGMT methylation level in 4 CpG sites using pyrosequencing. The association between MGMT methylation level and survival was investigated using Cox proportional hazards model and an extension to detect time-varying effects. We found an association between MGMT methylation level and overall survival (OS) from around 9 months after the diagnosis, with no association between MGMT methylation level and OS before that. For patients surviving at least 9 months even small increases in MGMT methylation level are significantly beneficial (HR = 0.97, 95% CI [0.96, 0.98]). The predictive ability of MGMT methylation level on OS from 9 months after diagnosis has a Harrel's C of 66%. We conclude that the MGMT methylation level is strongly associated with survival only for patients surviving beyond 9 months with considerable effects for levels much lower than previously reported. Prognostic evaluation of cut-points of MGMT methylation levels and of CpG island site selection should take the time-varying effect on overall survival into account.
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Affiliation(s)
| | - Pia Larsen
- Department of Epidemiology, Biostatistics and Biodemography, University of Southern Denmark
| | | | | | | | - Jacob B Hjelmborg
- Department of Epidemiology, Biostatistics and Biodemography, University of Southern Denmark
| | - Bjarne Winther Kristensen
- Department of Pathology, Odense University Hospital.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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8
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Cell-Free DNA Testing. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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9
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Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-Giménez JL. Epigenetic IVD Tests for Personalized Precision Medicine in Cancer. Front Genet 2019; 10:621. [PMID: 31316555 PMCID: PMC6611494 DOI: 10.3389/fgene.2019.00621] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations play a key role in the initiation and progression of cancer. Therefore, it is possible to use epigenetic marks as biomarkers for predictive and precision medicine in cancer. Precision medicine is poised to impact clinical practice, patients, and healthcare systems. The objective of this review is to provide an overview of the epigenetic testing landscape in cancer by examining commercially available epigenetic-based in vitro diagnostic tests for colon, breast, cervical, glioblastoma, lung cancers, and for cancers of unknown origin. We compile current commercial epigenetic tests based on epigenetic biomarkers (i.e., DNA methylation, miRNAs, and histones) that can actually be implemented into clinical practice.
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Affiliation(s)
- Jesús Beltrán-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Rebeca Osca-Verdegal
- INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Salvador Mena-Mollá
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain.,EpiDisease S.L. Spin-Off of CIBERER (ISCIII), Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain.,INCLIVA Biomedical Research Institute, Valencia, Spain.,Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain.,EpiDisease S.L. Spin-Off of CIBERER (ISCIII), Valencia, Spain
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10
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Johannessen LE, Brandal P, Myklebust TÅ, Heim S, Micci F, Panagopoulos I. MGMT Gene Promoter Methylation Status - Assessment of Two Pyrosequencing Kits and Three Methylation-specific PCR Methods for their Predictive Capacity in Glioblastomas. Cancer Genomics Proteomics 2018; 15:437-446. [PMID: 30343277 DOI: 10.21873/cgp.20102] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/13/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Although methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter predicts response to temozolomide in patients with glioblastoma, no consensus exists as to which assay is best for its detection. MATERIALS AND METHODS Methylation of MGMT promoter was examined by methylation-specific polymerase chain reaction (MSP), quantitative real-time MSP, methylation-sensitive high-resolution melting analysis, and two commercial pyrosequencing (PSQ) kits. Survival was compared among 48 patients with glioblastoma according to assay results. RESULTS Only PSQ and MSP significantly separated patients who benefited from temozolomide, with PSQ being the superior method. For PSQ analysis, the cut-off value that best correlated with prognostic outcome was 7% methylation of MGMT. Median survival in patients with MGMT promoter methylation above this cut-off value was 7.8 months longer compared to those with less than 7% methylation. Two-year overall survival for the two groups was 42% and 7.4%, respectively. CONCLUSION PSQ is the method of choice for MGMT promoter methylation analysis in routine clinical practice.
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Affiliation(s)
- Lene E Johannessen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Tor Åge Myklebust
- Department of Research and Innovation, Møre and Romsdal Hospital Trust, Ålesund, Norway.,Cancer Registry of Norway, Institute of Population-based Cancer Research, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Panagopoulos I, Gorunova L, Leske H, Niehusmann P, Johannessen LE, Staurseth J, Øino N, Meling TR, Heim S, Micci F, Brandal P. Pyrosequencing Analysis of MGMT Promoter Methylation in Meningioma. Cancer Genomics Proteomics 2018; 15:379-385. [PMID: 30194078 DOI: 10.21873/cgp.20096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 06/28/2018] [Accepted: 07/08/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a well-established predictor of response to the DNA-alkylating agent temozolomide in patients with glioblastoma. MATERIALS AND METHODS Pyrosequencing analysis was used to determine the MGMT promoter methylation status in 61 meningiomas, to clarify whether it might have a predictive role. RESULTS Only two tumors (3%) had a mean methylation frequency higher than the cut-off value of 10% for the four CpG sites examined. CONCLUSION The methylation of the MGMT promoter is uncommon, or occurs at a low frequency in meningiomas. There is no convincing rationale to test such tumors for their MGMT methylation status in a clinical setting.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Henning Leske
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Pitt Niehusmann
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Lene E Johannessen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Julie Staurseth
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Nina Øino
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Torstein R Meling
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Neurosurgery, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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