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Manou M, Kanakoglou DS, Loupis T, Vrachnos DM, Theocharis S, Papavassiliou AG, Piperi C. Role of Histone Deacetylases in the Pathogenesis of Salivary Gland Tumors and Therapeutic Targeting Options. Int J Mol Sci 2023; 24:10038. [PMID: 37373187 DOI: 10.3390/ijms241210038] [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: 05/12/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Salivary gland tumors (SGTs) comprise a rare and heterogenous category of benign/malignant neoplasms with progressively increasing knowledge of the molecular mechanisms underpinning their pathogenesis, poor prognosis, and therapeutic treatment efficacy. Emerging data are pointing toward an interplay of genetic and epigenetic factors contributing to their heterogeneity and diverse clinical phenotypes. Post-translational histone modifications such as histone acetylation/deacetylation have been shown to actively participate in the pathobiology of SGTs, further suggesting that histone deacetylating factors (HDACs), selective or pan-HDAC inhibitors (HDACis), might present effective treatment options for these neoplasms. Herein, we describe the molecular and epigenetic mechanisms underlying the pathology of the different types of SGTs, focusing on histone acetylation/deacetylation effects on gene expression as well as the progress of HDACis in SGT therapy and the current status of relevant clinical trials.
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Affiliation(s)
- Maria Manou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios S Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodoros Loupis
- Haematology Research Laboratory, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Dimitrios M Vrachnos
- Haematology Research Laboratory, Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Mat Lazim N, Yousaf A, Abusalah MAH, Sulong S, Mohd Ismail ZI, Mohamud R, Abu-Harirah HA, AlRamadneh TN, Hassan R, Abdullah B. The Epigenesis of Salivary Glands Carcinoma: From Field Cancerization to Carcinogenesis. Cancers (Basel) 2023; 15:cancers15072111. [PMID: 37046772 PMCID: PMC10093474 DOI: 10.3390/cancers15072111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Salivary gland carcinomas (SGCs) are a diverse collection of malignant tumors with marked differences in biological activity, clinical presentation and microscopic appearance. Although the etiology is varied, secondary radiation, oncogenic viruses as well as chromosomal rearrangements have all been linked to the formation of SGCs. Epigenetic modifications may also contribute to the genesis and progression of SGCs. Epigenetic modifications are any heritable changes in gene expression that are not caused by changes in DNA sequence. It is now widely accepted that epigenetics plays an important role in SGCs development. A basic epigenetic process that has been linked to a variety of pathological as well as physiological conditions including cancer formation, is DNA methylation. Transcriptional repression is caused by CpG islands hypermethylation at gene promoters, whereas hypomethylation causes overexpression of a gene. Epigenetic changes in SGCs have been identified, and they have been linked to the genesis, progression as well as prognosis of these neoplasms. Thus, we conduct a thorough evaluation of the currently known evidence on the involvement of epigenetic processes in SGCs.
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Affiliation(s)
- Norhafiza Mat Lazim
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Anam Yousaf
- Department of Molecular Pathology Laboratory, Pakistan Kidney and Liver Institute and Research Centre, Lahore 54000, Pakistan
| | - Mai Abdel Haleem Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Kelantan, Malaysia
| | - Sarina Sulong
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Immunology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Zul Izhar Mohd Ismail
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Anatomy, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Rohimah Mohamud
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Immunology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hashem A. Abu-Harirah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Tareq Nayef AlRamadneh
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Rosline Hassan
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Baharudin Abdullah
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital USM, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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Nikolic N, Carkic J, Jacimovic J, Jakovljevic A, Anicic B, Jezdic Z, Milasin J. Methylation of tumour suppressor genes in benign and malignant salivary gland tumours: a systematic review and meta-analysis. Epigenetics 2022; 17:1661-1676. [PMID: 35287544 PMCID: PMC9620987 DOI: 10.1080/15592294.2022.2052426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The aim of the present systematic review was to critically analyse the relationship between tumour suppressor genes (TSGs) promoter methylation, a potent mechanism of gene silencing, and the development of salivary gland tumours, as well as the possible effect on clinical/histological characteristics. Review protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) database (registration ID CRD42020218511). A comprehensive search of Web of Science, Scopus, PubMed, and Cochrane Central Register of Controlled Trials was performed utilizing relevant key terms, supplemented by a search of grey literature. Newcastle-Ottawa Quality Assessment Scale (NOQAS) was used for the quality assessment of included studies. Sixteen cross-sectional and 12 case-control studies were included in the review, predominantly dealing with methylation in TSGs related to DNA repair, cell cycle, and cell growth regulation and differentiation. Quantitative synthesis could be performed on P16 (inhibitor of cyclin-dependent kinase 4a), RASSF1A (Ras association domain family 1 isoform A) and MGMT (O6-methylguanine DNA methyltransferase) genes only. It showed that P16 and RASSF1A genes were more frequently methylated in salivary gland tumours compared to controls (P = .0002 and P < .0001, respectively), while no significant difference was observed for MGMT. Additionally, P16 did not appear to be related to malignant transformation of pleomorphic adenomas (P = .330). In conclusion, TSG methylation is involved in salivary gland tumour pathogenesis and several genes might play a considerable role. Further studies are needed for a better understanding of complex epigenetic deregulation during salivary gland tumour development and progression.
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Affiliation(s)
- Nadja Nikolic
- University of Belgrade, School of Dental Medicine, Department of Human Genetics, Belgrade, Serbia
- CONTACT Nadja Nikolic University of Belgrade, School of Dental Medicine, Department of Human Genetics, Dr Subotica 1, Belgrade 11 000, Serbia
| | - Jelena Carkic
- University of Belgrade, School of Dental Medicine, Department of Human Genetics, Belgrade, Serbia
| | - Jelena Jacimovic
- University of Belgrade, School of Dental Medicine, Central Library, Belgrade, Serbia
| | - Aleksandar Jakovljevic
- University of Belgrade, School of Dental Medicine, Department of Pathophysiology, Belgrade, Serbia
| | - Boban Anicic
- University of Belgrade, School of Dental Medicine, Clinic for Maxillofacial Surgery, Belgrade, Serbia
| | - Zoran Jezdic
- University of Belgrade, School of Dental Medicine, Clinic for Maxillofacial Surgery, Belgrade, Serbia
| | - Jelena Milasin
- University of Belgrade, School of Dental Medicine, Department of Human Genetics, Belgrade, Serbia
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Tierling S, Jürgens-Wemheuer WM, Leismann A, Becker-Kettern J, Scherer M, Wrede A, Breuskin D, Urbschat S, Sippl C, Oertel J, Schulz-Schaeffer WJ, Walter J. Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics. Clin Epigenetics 2022; 14:26. [PMID: 35180887 PMCID: PMC8857788 DOI: 10.1186/s13148-022-01244-4] [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: 09/02/2021] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Promoter methylation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) is an acknowledged predictive epigenetic marker in glioblastoma multiforme and anaplastic astrocytoma. Patients with methylated CpGs in the MGMT promoter benefit from treatment with alkylating agents, such as temozolomide, and show an improved overall survival and progression-free interval. A precise determination of MGMT promoter methylation is of importance for diagnostic decisions. We experienced that different methods show partially divergent results in a daily routine. For an integrated neuropathological diagnosis of malignant gliomas, we therefore currently apply a combination of methylation-specific PCR assays and pyrosequencing. Results To better rationalize the variation across assays, we compared these standard techniques and assays to deep bisulfite sequencing results in a cohort of 80 malignant astrocytomas. Our deep analysis covers 49 CpG sites of the expanded MGMT promoter, including exon 1, parts of intron 1 and a region upstream of the transcription start site (TSS). We observed that deep sequencing data are in general in agreement with CpG-specific pyrosequencing, while the most widely used MSP assays published by Esteller et al. (N Engl J Med 343(19):1350–1354, 2000. 10.1056/NEJM200011093431901) and Felsberg et al. (Clin Cancer Res 15(21):6683–6693, 2009. 10.1158/1078-0432.CCR-08-2801) resulted in partially discordant results in 22 tumors (27.5%). Local deep bisulfite sequencing (LDBS) revealed that CpGs located in exon 1 are suited best to discriminate methylated from unmethylated samples. Based on LDBS data, we propose an optimized MSP primer pair with 83% and 85% concordance to pyrosequencing and LDBS data. A hitherto neglected region upstream of the TSS, with an overall higher methylation compared to exon 1 and intron 1 of MGMT, is also able to discriminate the methylation status. Conclusion Our integrated analysis allows to evaluate and redefine co-methylation domains within the MGMT promoter and to rationalize the practical impact on assays used in daily routine diagnostics. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01244-4.
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Affiliation(s)
- Sascha Tierling
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.
| | | | - Alea Leismann
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
| | - Julia Becker-Kettern
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - Michael Scherer
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.,Department of Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain
| | - Arne Wrede
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - David Breuskin
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Steffi Urbschat
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Christoph Sippl
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Joachim Oertel
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | | | - Jörn Walter
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
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Head and Neck Cancers Are Not Alike When Tarred with the Same Brush: An Epigenetic Perspective from the Cancerization Field to Prognosis. Cancers (Basel) 2021; 13:cancers13225630. [PMID: 34830785 PMCID: PMC8616074 DOI: 10.3390/cancers13225630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Squamous cell carcinomas affect different head and neck subsites and, although these tumors arise from the same epithelial lining and share risk factors, they differ in terms of clinical behavior and molecular carcinogenesis mechanisms. Differences between HPV-negative and HPV-positive tumors are those most frequently explored, but further data suggest that the molecular heterogeneity observed among head and neck subsites may go beyond HPV infection. In this review, we explore how alterations of DNA methylation and microRNA expression contribute to head and neck squamous cell carcinoma (HNSCC) development and progression. The association of these epigenetic alterations with risk factor exposure, early carcinogenesis steps, transformation risk, and prognosis are described. Finally, we discuss the potential application of the use of epigenetic biomarkers in HNSCC. Abstract Head and neck squamous cell carcinomas (HNSCC) are among the ten most frequent types of cancer worldwide and, despite all efforts, are still diagnosed at late stages and show poor overall survival. Furthermore, HNSCC patients often experience relapses and the development of second primary tumors, as a consequence of the field cancerization process. Therefore, a better comprehension of the molecular mechanisms involved in HNSCC development and progression may enable diagnosis anticipation and provide valuable tools for prediction of prognosis and response to therapy. However, the different biological behavior of these tumors depending on the affected anatomical site and risk factor exposure, as well as the high genetic heterogeneity observed in HNSCC are major obstacles in this pursue. In this context, epigenetic alterations have been shown to be common in HNSCC, to discriminate the tumor anatomical subsites, to be responsive to risk factor exposure, and show promising results in biomarker development. Based on this, this review brings together the current knowledge on alterations of DNA methylation and microRNA expression in HNSCC natural history, focusing on how they contribute to each step of the process and on their applicability as biomarkers of exposure, HNSCC development, progression, and response to therapy.
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Salivary DNA Methylation as an Epigenetic Biomarker for Head and Neck Cancer. Part II: A Cancer Risk Meta-Analysis. J Pers Med 2021; 11:jpm11070606. [PMID: 34206840 PMCID: PMC8304899 DOI: 10.3390/jpm11070606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Aberrant methylation of tumor suppressor genes has been reported as an important epigenetic silencer in head and neck cancer (HNC) pathogenesis. Here, we performed a comprehensive meta-analysis to evaluate the overall and specific impact of salivary gene promoter methylation on HNC risk. The methodological quality was assessed using the Newcastle–Ottawa scale (NOS). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the association and Egger’s and Begg’s tests were applied to detect publication bias. The frequency of salivary DNA promoter methylation was significantly higher in HNC patients than in healthy controls (OR: 8.34 (95% CI = 6.10–11.39; p < 0.01). The pooled ORs showed a significant association between specific tumor-related genes and HNC risk: p16 (3.75; 95% CI = 2.51–5.60), MGMT (5.72; 95% CI = 3.00–10.91), DAPK (5.34; 95% CI = 2.18–13.10), TIMP3 (3.42; 95% CI = 1.99–5.88), and RASSF1A (7.69; 95% CI = 3.88–15.23). Overall, our meta-analysis provides precise evidence on the association between salivary DNA promoter hypermethylation and HNC risk. Thus, detection of promoter DNA methylation in saliva is a potential biomarker for predicting HNC risk.
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Šutić M, Motzek A, Bubanović G, Linke M, Sabol I, Vugrek O, Ozretić P, Brčić L, Seiwerth S, Debeljak Ž, Jakovčević A, Janevski Z, Stančić-Rokotov D, Vukić-Dugac A, Jakopović M, Samaržija M, Zechner U, Knežević J. Promoter methylation status of ASC/TMS1/PYCARD is associated with decreased overall survival and TNM status in patients with early stage non-small cell lung cancer (NSCLC). Transl Lung Cancer Res 2019; 8:1000-1015. [PMID: 32010578 PMCID: PMC6976376 DOI: 10.21037/tlcr.2019.12.08] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death worldwide, with 5-year overall survival less than 15%. Therefore, it is essential to find biomarkers for early detection and prognosis. Aberrant DNA methylation is a common feature of human cancers and its utility is already recognized in cancer management. The aim of this study was to explore the diagnostic and prognostic value of the promoter methylation status of the ASC/TMS1/PYCARD and MyD88 genes, key adaptor molecules in the activation of the innate immune response and apoptosis pathways. METHODS A total of 50 non-small cell lung cancer (NSCLC) patients were enrolled in the study. Methylation of bisulphite converted DNA was quantified by pyrosequencing in fresh frozen malignant tissues and adjacent non-malignant tissues. Associations between methylation and lung function, tumor grade and overall survival were evaluated using receiver-operating characteristics (ROC) analysis and statistical tests of hypothesis. RESULTS Methylation level of tested genes is generally low but significantly decreased in tumor tissues (ASC/TMS1/PYCARD, P<0.0001; MyD88, P<0.0002), which correlates with increased protein expression. Three CpG sites were identified as promising diagnostic marker candidates; CpG11 (-63 position) in ASC/TMS1/PYCARD and CpG1 (-253 position) and 2 (-265 position) in MyD88. The association study showed that the methylation status of the ASC/TMS1 CpG4 site (-34 position) in malignant and non-malignant tissues is associated with the overall survival (P=0.019) and the methylation status of CpG8 site (-92 position) is associated with TNM-stage (P=0.011). CONCLUSIONS The methylation status of the ASC/TMS1/PYCARD and MyD88 promoters are promising prognostic biomarker candidates. However, presented results should be considered as a preliminary and should be confirmed on the larger number of the samples.
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Affiliation(s)
- Maja Šutić
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Antje Motzek
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Gordana Bubanović
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Matthias Linke
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ivan Sabol
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Oliver Vugrek
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Petar Ozretić
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
| | - Luka Brčić
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Sven Seiwerth
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Željko Debeljak
- Institute of Clinical Laboratory Diagnostics, University Hospital Osijek, Osijek, Croatia
- Faculty of Medicine, Department of Pharmacology, JJ Strossmayer University of Osijek, Osijek, Croatia
| | - Antonija Jakovčević
- Department of Pathology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Zoran Janevski
- Department of Thoracic Surgery Jordanovac, Clinical Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Dinko Stančić-Rokotov
- Department of Thoracic Surgery Jordanovac, Clinical Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Andrea Vukić-Dugac
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Miroslav Samaržija
- Department for Respiratory Diseases, Clinic for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ulrich Zechner
- Institute for Human Genetics, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jelena Knežević
- Ruđer Bošković Institute, Division for Molecular Medicine, Zagreb, Croatia
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Wen G, Wang H, Zhong Z. Associations of RASSF1A, RARβ, and CDH1 promoter hypermethylation with oral cancer risk: A PRISMA-compliant meta-analysis. Medicine (Baltimore) 2018; 97:e9971. [PMID: 29538221 PMCID: PMC5882397 DOI: 10.1097/md.0000000000009971] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Oral tumor is a heterogeneous group of tumors, in which it has several different histopathological and molecular features. Recently, genetic and epigenetic alterations are often detected in the development of oral cancer. Gene promoter hypermethylation leads to the silencing of cancer related genes without changes of genes sequence. To clarify the effect of RAS association domain family protein 1a (RASSF1A), retinoic acid receptor beta (RARβ), and E-cadherin (CDH1) promoter hypermethylation on the risk of oral cancer, we performed this meta-analysis. METHODS PubMed, Web of Science, Embase, and Chinese National Knowledge Infrastructure (CNKI) databases were retrieved to identify eligible articles. Stata 12.0 software was used to analyze extracted data of the included articles. Odds ratios (ORs) with the corresponding 95% confidence interval (95% CI) were calculated to evaluate the associations of RASSF1A, RARβ, and CDH1 promoter hypermethylation with oral cancer risk. RESULTS Around 23 literatures with 29 studies were included in the final meta-analysis, in which 12 studies were about RASSF1A promoter methylation, 4 studies were about RARβ promoter methylation, and 13 studies were about CDH1 promoter methylation. Overall, the results of this meta-analysis showed that there were significant associations between RASSF1A, RARβ, and CDH1 promoter hypermethylation and oral cancer risk (RASSF1A, OR = 11.8, 95% CI = 6.14-22.66; RARβ, OR = 20.35, 95% CI = 5.64-73.39; CDH1, OR = 13.46, 95% CI = 5.31-34.17). In addition, we found that RASSF1A promoter hypermethylation exerted higher frequency in the tongue tumor than other site tumor in mouth (RASSF1A, tongue tumor vs other site tumor in mouth, unmethylation vs methylation, OR = 0.65, 95%CI = 0.44-0.98). CONCLUSION RASSF1A, RARβ, and CDH1 promoter hypermethylation might significantly increase the risk of oral cancer.
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Affiliation(s)
- Guohong Wen
- School of Public Health and Management, Chongqing Medical University, Chongqing
- Medical Records and Statistics Room of Nanchong Central Hospital
| | - Huadong Wang
- School of Public Health and Management, Chongqing Medical University, Chongqing
- Oral and Maxillofacial Surgery of Nanchong Central Hospital, NanChong City, SiChuan Province, China
| | - Zhaohui Zhong
- School of Public Health and Management, Chongqing Medical University, Chongqing
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Current Insights into Oral Cancer Epigenetics. Int J Mol Sci 2018; 19:ijms19030670. [PMID: 29495520 PMCID: PMC5877531 DOI: 10.3390/ijms19030670] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/30/2022] Open
Abstract
Epigenetic modifications have emerged into one of the cancer hallmarks, replacing the concept of malignant pathologies as being solely genetic-based conditions. The epigenetic landscape is responsible for normal development but also for the heterogeneity among tissues in terms of gene expression patterns. Dysregulation in these mechanisms has been associated with disease stage, and increased attention is now granted to cancer in order to take advantage of these modifications in terms of novel therapeutic strategies or diagnosis/prognosis tools. Oral cancer has also been subjected to epigenetic analysis with numerous studies revealing that the development and progression of this malignancy are partially induced by an altered epigenetic substrate together with genetic alterations and prolonged exposure to environmental risk factors. The present review summarizes the most important epigenetic modifications associated with oral cancer and also their potential to be used as new therapeutic targets.
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Qiao B, Zhang Z, Li Y. Association of MGMT promoter methylation with tumorigenesis features in patients with ovarian cancer: A systematic meta-analysis. Mol Genet Genomic Med 2017; 6:69-76. [PMID: 29195029 PMCID: PMC5823672 DOI: 10.1002/mgg3.349] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Background The MGMT is a key tumor suppressor gene and aberrant promoter methylation has been reported in many cancers. However, the relationship between MGMT promoter methylation and ovarian cancer remains controversial. This meta‐analysis was first conducted to estimate the clinical significance of MGMT promoter methylation in ovarian carcinoma. Methods Literature search was performed in the PubMed, Embase, EBSCO and Cochrane Library databases. The pooled odds ratio (OR) and their corresponding 95% confidence interval (95% CI) were summarized. Results Final 10 studies with 910 ovarian tissue samples were included in this meta‐analysis. MGMT promoter methylation was significantly higher in ovarian cancer than in normal ovarian tissues (OR = 4.13, 95% CI = 2.32–7.33, p < .001). The MGMT had a similar methylation status in cancer versus benign lesions and low malignant potential (LMP) samples (OR = 2.01, 95% CI = 0.67–6.04, p = .212; OR = 1.42, 95% CI = 0.46–4.40, p = .543; respectively). MGMT promoter methylation was correlated with pathological types in which it was significantly lower in serous cancer than in nonserous cancer (OR = 0.29, 95% CI = 0.14–0.59, p = .001). The methylation of the MGMT promoter was not associated with clinical stage and tumor grade (OR = 1.46, 95% CI = 0.71–3.02, p = .301; OR = 1.13, 95% CI = 0.51–2.46, p = .767; respectively). Conclusions MGMT promoter methylation may be correlated with the tumorigenesis of ovarian cancer. It was associated with tumor histotypes, but not correlated with clinical stage and tumor grade. More prospective studies with lager sample sizes are necessary in the future.
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Affiliation(s)
- Baoli Qiao
- Department of Gynaecology and Obstetrics, Beijing Chao-Yang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhenyu Zhang
- Department of Gynaecology and Obstetrics, Beijing Chao-Yang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yanfang Li
- Department of Gynaecology and Obstetrics, Beijing Chao-Yang Hospital Affiliated to Capital Medical University, Beijing, China
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Jayaprakash C, Radhakrishnan R, Ray S, Satyamoorthy K. Promoter methylation of MGMT in oral carcinoma: A population-based study and meta-analysis. Arch Oral Biol 2017; 80:197-208. [DOI: 10.1016/j.archoralbio.2017.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/02/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022]
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12
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Martínez-Baños D, Sánchez-Hernández B, Jiménez G, Barrera-Lumbreras G, Barrales-Benítez O. Global methylation and promoter-specific methylation of the P16, SOCS-1, E-cadherin, P73 and SHP-1 genes and their expression in patients with multiple myeloma during active disease and remission. Exp Ther Med 2017; 13:2442-2450. [PMID: 28565861 DOI: 10.3892/etm.2017.4274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/21/2016] [Indexed: 01/22/2023] Open
Abstract
Tumor suppressor gene promoter CpG island methylation is a well-recognized mechanism in cancer pathogenesis, but its role in multiple myeloma (MM) is controversial. The present study investigated the methylation status and expression of P16, suppressor of cytokine signaling 1 (SOCS-1), P73, E-cadherin and Src homology region 2 domain-containing phosphatase 1 (SHP-1), as well as global methylation in patients with MM during active disease and remission. Bone marrow samples were obtained from 43 patients at the Multiple Myeloma Clinic, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (Mexico City, Mexico) during active disease and remission. Methylation-specific polymerase chain reaction and ELISA were performed on bisulfite-treated or untreated DNA to determine promoter-specific or genomic methylation, respectively. Gene expression was measured using reverse-transcription polymerase chain reaction. The results indicated that SOCS-1 methylation occurred more frequently during active disease than remission [29 vs. 3.2% (P=0.021)] and was associated with more advanced forms of the disease [international staging system (ISS) 3, 16.67% vs. ISS 1, 8.3% (P=0.037)]. SHP-1 methylation during active disease was associated with a lower probability of survival at 39-month follow up (median), 52.5 vs. 87.5% (P=0.025). The percentage of methylation was associated with active disease at remission, but this was not significant. Global hypomethylation at remission was a negative predictor factor for overall survival (OS). The results indicated that methylated P16, SOCS-1 and SHP-1 were associated with clinical variables of poor prognosis in MM, likewise the persistence of global hypomethylation at remission. The negative impact on OS of global hypomethylation at remission must be confirmed in a larger sample. Future studies are necessary to investigate whether patients with global hypermethylation at remission should receive more aggressive treatments to improve their OS.
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Affiliation(s)
- Déborah Martínez-Baños
- Department of Hematology and Oncology, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Tlalpan 14080, Mexico
| | - Beatríz Sánchez-Hernández
- Department of Genetics, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Tlalpan 14080, Mexico
| | - Guadalupe Jiménez
- Department of Hematology and Oncology, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Tlalpan 14080, Mexico
| | - Georgina Barrera-Lumbreras
- Department of Hematology and Oncology, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Tlalpan 14080, Mexico
| | - Olga Barrales-Benítez
- Department of Hematology and Oncology, National Institute of Medical Science and Nutrition Salvador Zubiran, Mexico City, Tlalpan 14080, Mexico
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Matsui S, Kagara N, Mishima C, Naoi Y, Shimoda M, Shimomura A, Shimazu K, Kim SJ, Noguchi S. Methylation of the SEPT9_v2 promoter as a novel marker for the detection of circulating tumor DNA in breast cancer patients. Oncol Rep 2016; 36:2225-35. [PMID: 27499429 DOI: 10.3892/or.2016.5004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/25/2016] [Indexed: 01/11/2023] Open
Abstract
The aim of the present study was to evaluate the promoter methylation status of SEPT9_v2 in breast cancer and to detect this methylated gene in circulating tumor DNA (ctDNA) in plasma. Bisulfite sequencing was performed with a next generation sequencer. Methylation of the SEPT9_v2 promoter was found in 67% (8/12) of breast cancer cell lines and 53% (10/19) of breast tumor tissue, but not in normal breast tissue (0/19). A clear inverse correlation was observed between the expression of SEPT9_v2 mRNA and the methylation index (MI) both in cell lines and breast cancer tissues. The MI of SEPT9_v2 was significantly higher in non-basal subtype of breast cancer (13.0%, n=84) than in basal subtype (3.0%, n=23) (P<0.0001). Methylated SEPT9_v2 ctDNA in plasma was detected in 11% (9/82) of primary breast cancer patients and 52% (26/50) of metastatic breast cancer patients, but not in the healthy controls (0/51). These results indicate that SEPT9_v2 promoter hypermethylation, which silences the expression of SEPT9_v2 mRNA, is observed in a significant proportion of breast tumors, and that methylated SEPT9_v2 may serve as a novel tumor marker for breast cancer.
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Affiliation(s)
- Saki Matsui
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Naofumi Kagara
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Chieko Mishima
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yasuto Naoi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Masafumi Shimoda
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Atsushi Shimomura
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kenzo Shimazu
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Seung Jin Kim
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Shinzaburo Noguchi
- Department of Breast and Endocrine Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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14
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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15
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Kim Y, Jin D, Lee BB, Cho EY, Han J, Shim YM, Kim DH. RARβ2 hypermethylation is associated with poor recurrence-free survival in never-smokers with adenocarcinoma of the lung. Clin Epigenetics 2015; 7:32. [PMID: 25806093 PMCID: PMC4371724 DOI: 10.1186/s13148-015-0066-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/27/2015] [Indexed: 12/16/2022] Open
Abstract
Background This study was aimed at investigating if the effect of RARβ2 hypermethylation on recurrence-free survival (RFS) in non-small cell lung cancer (NSCLC) depends on one’s smoking status and specific interacting proteins. Results We retrospectively analyzed the expressions of five proteins using immunohistochemistry in archival formalin-fixed and paraffin-embedded tissues from 578 NSCLC patients who had undergone surgical resection from 1994 through 2004. Promoter methylation of RARβ2 was assessed by bisulfite pyrosequencing. Recurrence was found in 268 (46%) of 578 NSCLCs with a median follow-up period of 4.8 years. Overexpression of β-catenin, c-MET, cyclin D1, and EGFR occurred in 55%, 72%, 51%, and 41% of the patients, respectively. E-cadherin expression was negative in 62% of the patients, and RARβ2 hypermethylation was found in 37%. The abnormal expression of c-MET (P = 0.002) and EGFR (P = 0.001) was found to be highly prevalent in never-smokers. RARβ2 hypermethylation was significantly associated with poor recurrence-free survival (RFS) in 128 never-smokers with adenocarcinoma (P = 0.01) For parsimonious model building, the five proteins were clustered into three groups (β-catenin and E-cadherin; c-MET; cyclin D1 and EGFR) by an unsupervised hierarchical clustering and were included in a multivariate analysis. Cox proportional hazard analysis showed that RARβ2 hypermethylation was significantly associated with poor RFS in 128 never-smokers with adenocarcinoma (adjusted hazard ratio [HR] = 2.19, 95% confidence interval [CI] = 1.28 to 3.47; P = 0.009), after adjusting for interacting proteins. Conclusions The present study suggests that RARβ2 hypermethylation may be an independent prognostic factor of RFS in never-smokers with adenocarcinoma of the lung.
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Affiliation(s)
- Yujin Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, #300 Chunchun-dong, Jangan-Ku, Kyunggido, Suwon 440-746 South Korea
| | - DongHao Jin
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, #300 Chunchun-dong, Jangan-Ku, Kyunggido, Suwon 440-746 South Korea
| | - Bo Bin Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, #300 Chunchun-dong, Jangan-Ku, Kyunggido, Suwon 440-746 South Korea
| | - Eun Yoon Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, #50 Ilwon-dong, Kangnam-Ku, Seoul 135-710 South Korea
| | - Joungho Han
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, #50 Ilwon-dong, Kangnam-Ku, Seoul 135-710 South Korea
| | - Young Mog Shim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, #50 Ilwon-dong, Kangnam-Ku, Seoul 135-710 South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, #300 Chunchun-dong, Jangan-Ku, Kyunggido, Suwon 440-746 South Korea.,Samsung Biomedical Research Institute, Rm B155, #50 Ilwon-dong, Kangnam-Ku, Seoul 135-710 South Korea
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Kim JS, Kim SY, Lee M, Kim SH, Kim SM, Kim EJ. Radioresistance in a human laryngeal squamous cell carcinoma cell line is associated with DNA methylation changes and topoisomerase II α. Cancer Biol Ther 2015; 16:558-66. [PMID: 25719218 DOI: 10.1080/15384047.2015.1017154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Accumulating evidence suggests that changes in methylation patterns may help mediate the sensitivity or resistance of cancer cells to ionizing radiation. The present study provides evidence for the involvement of radioresistance-induced DNA methylation changes in tumor radioresistance. We established radioresistant laryngeal cancer cells via long-term fractionated irradiation, and examined differences in DNA methylation between control and radioresistant laryngeal cancer cells. Interestingly, we found that the promoter-CpG islands of 5 previously identified radioresistance-related genes (TOPO2A, PLXDC2, ETNK2, GFI1, and IL12B) were significantly altered in the radioresistant laryngeal cancer cells. Furthermore, the demethylation of these gene promoters with a DNA methyltransferase inhibitor (5-aza-2'-deoxycytidine) increased their transcription levels. Treatment with 5-aza-2'-deoxycytidine also sensitized the radioresistant laryngeal cancer cells to irradiation, indicating that changes in DNA methylation contributed to their radioresistance. Of the tested genes, the expression and activity levels of TOPO2A were tightly associated with the radioresistant phenotype in our system, suggesting that the hypermethylation of TOPO2A might be involved in this radioresistance. Collectively, our data suggest that radiation-induced epigenetic changes can modulate the radioresistance of laryngeal cancer cells, and thus may prove useful as prognostic indicators for radiotherapy.
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Affiliation(s)
- Jae-Sung Kim
- a Division of Radiation Cancer Research; Korea Institute of Radiological & Medical Sciences ; Seoul , Korea
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17
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Leung TW, Liu SS, Leung RCY, Chu MMY, Cheung ANY, Ngan HYS. HPV 16 E2 binding sites 1 and 2 become more methylated than E2 binding site 4 during cervical carcinogenesis. J Med Virol 2015; 87:1022-33. [PMID: 25648229 DOI: 10.1002/jmv.24129] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2014] [Indexed: 02/01/2023]
Abstract
E2 protein binding to the four E2 binding sites (E2BSs) at the long control region of Human Papillomavirus (HPV) 16/18 genome may exert either transcriptional activation/repression on E6 and E7 oncoproteins. Methylation status at the E2BSs may affect the relative binding of E2 protein to them. In this study, methylation percentage at E2BS 1, 2 (promoter-proximal), and 4 (promoter-distal) were assessed by pyrosequencing and compared among HPV 16/18-positive cervical cancer, high-grade, and low-grade Cervical Intraepithelial Neoplasia, Atypical Squamous Cells of Undetermined Significance, and normal cervical epithelium. HPV 16 E2BS1&2 were more methylated than HPV 16 E2BS4 in cervical cancer whereas in cervical premalignant lesions and normal epithelium, HPV 16 E2BS1&2 were less methylated than HPV 16 E2BS4. HPV 18 E2BS1&2 remained more methylated than E2BS4 in all histological groups. HPV 16 E2BS1&2 methylation increased from high-grade lesions to cervical cancer (P < 0.001). HPV 16 E2BS4 methylation increased from low-grade to high-grade premalignant lesions (P = 0.041). Both HPV 18 E2BS1&2 and E2BS4 methylation increased from low-grade to high-grade Cervical Intraepithelial Neoplasia (P = 0.019 and 0.001 respectively) and further increased form high-grade lesions to cervical cancer (P < 0.001 and 0.005 respectively). Conclusively, HPV 16 E2BS1&2 (for transcriptional repression of E6/E7 oncoproteins) became more heavily methylated than E2BS4 (for transcriptional activation of E6/E7) in cervical cancer, favouring the differential binding of E2 protein to E2BS4. Increasing methylation at HPV 16/18 E2BSs are potentially useful adjunctive molecular markers for predicting progression from low-grade to high-grade cervical premalignant lesions and from high-grade lesions to cervical cancer.
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Affiliation(s)
- Tsin-Wah Leung
- Department of Obstetrics & Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
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18
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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: 18] [Impact Index Per Article: 1.8] [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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Exposures in early life: associations with DNA promoter methylation in breast tumors. J Dev Orig Health Dis 2014; 4:182-90. [PMID: 25054684 DOI: 10.1017/s2040174412000694] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
There is evidence that epigenetic changes occur early in breast carcinogenesis. We hypothesized that early-life exposures associated with breast cancer would be associated with epigenetic alterations in breast tumors. In particular, we examined DNA methylation patterns in breast tumors in association with several early-life exposures in a population-based case-control study. Promoter methylation of E-cadherin, p16 and RAR-β2 genes was assessed in archived tumor blocks from 803 cases with real-time methylation-specific PCR. Unconditional logistic regression was used for case-case comparisons of those with and without promoter methylation. We found no differences in the prevalence of DNA methylation of the individual genes by age at menarche, age at first live birth and weight at age 20. In case-case comparisons of premenopausal breast cancer, lower birth weight was associated with increased likelihood of E-cadherin promoter methylation (OR = 2.79, 95% CI, 1.15-6.82, for ⩽2.5 v. 2.6-2.9 kg); higher adult height with RAR-β2 methylation (OR = 3.34, 95% CI, 1.19-9.39, for ⩾1.65 v. <1.60 m); and not having been breastfed with p16 methylation (OR = 2.75, 95% CI, 1.14-6.62). Among postmenopausal breast cancers, birth order was associated with increased likelihood of p16 promoter methylation. Being other than first in the birth order was inversely associated with likelihood of ⩾1 of the three genes being methylated for premenopausal breast cancers, but positively associated with methylation in postmenopausal women. These results suggest that there may be alterations in methylation associated with early-life exposures that persist into adulthood and affect breast cancer risk.
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Scesnaite A, Jarmalaite S, Mueller M, Agaimy A, Zenk J, Hartmann A, Iro H, Peters B, Schwarz S, Schneider-Stock R. Prognostic value of O-6-methylguanine-DNA methyltransferase loss in salivary gland carcinomas. Head Neck 2013; 36:1258-67. [PMID: 25201059 DOI: 10.1002/hed.23445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 03/12/2013] [Accepted: 08/01/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The purpose of this study was to determine the prognostic value of O-6-methylguanine-DNA methyltransferase (MGMT) inactivation in a group of 286 patients with salivary gland carcinoma and matched histologically normal tissues. METHODS MGMT promoter methylation was studied in 36 patients with salivary gland carcinoma and 19 histologically matched normal tissues by pyrosequencing. MGMT protein expression was examined in 286 patients with salivary gland carcinomas and histologically matched normal tissues by immunohistochemistry on tissue microarrays. The results were correlated to demographic, clinicopathologic parameters, and disease follow-up data. RESULTS MGMT hypermethylation was significantly (p = .021) associated with the protein loss. MGMT loss was found in 39.2% of salivary gland carcinomas and was predominant in aggressive tumors (poorly differentiated, grade III, regional lymph node involved). MGMT loss significantly (p = .004) predicted poor clinical outcome of salivary gland carcinomas and defined high-risk subgroups in clinically favorable tumor groups. CONCLUSION We suggest that immunohistochemical evaluation of nuclear MGMT protein might serve as a tool for the prediction of overall survival in patients with salivary gland carcinoma.
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Affiliation(s)
- Asta Scesnaite
- Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania
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21
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Gauchotte G, Lacomme S, Brochin L, Tournier B, Cahn V, Monhoven N, Piard F, Klein M, Martinet N, Rochette-Egly C, Vignaud JM. Retinoid acid receptor expression is helpful to distinguish between adenoma and well-differentiated carcinoma in the thyroid. Virchows Arch 2013; 462:619-32. [DOI: 10.1007/s00428-013-1419-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/26/2013] [Accepted: 04/22/2013] [Indexed: 11/24/2022]
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Malouf GG, Brugières L, Le Deley MC, Faivre S, Fabre M, Paradis V, Aerts I, Le Tourneau C, Dreyer C, Branchereau S, Belghiti J, Raymond E. Pure and mixed fibrolamellar hepatocellular carcinomas differ in natural history and prognosis after complete surgical resection. Cancer 2012; 118:4981-90. [PMID: 22415897 DOI: 10.1002/cncr.27520] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 11/16/2011] [Accepted: 12/20/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND The purpose of the current study was to describe pure and mixed fibrolamellar hepatocellular carcinoma (FL-HCC). METHODS Consecutive patients with pure and mixed FL-HCC were identified from a central pathological review using Edmondson's criteria. Clinical, pathological, and epigenetic characteristics of patients who underwent curative surgery were evaluated. Overall and disease-free survival as well as patterns of disease recurrence were examined. Methylation levels of L1 retrotransposon (LINE-1) repetitive elements and Ras association domain family 1A gene (RASSF1) promoter were also assessed using pyrosequencing. RESULTS Forty of 53 patients with a median age of 22 years (range, 9 years-;65 years) met the criteria for analysis. Central pathological review found that 30 patients (75%) had pure and 10 patients (25%) had mixed FL-HCC. Pure FL-HCC typically occurred in patients aged < 30 years. These patients often presented with lymph node metastasis at the time of diagnosis and frequently experienced extrahepatic recurrences (n = 16). Conversely, mixed FL-HCC appeared to resemble to classic HCC, occurring in patients aged > 40 years and frequently involving the liver as the primary site of disease recurrence. With a median follow-up of 7.8 years, the median overall survival from the time of diagnosis in all patients was 6.4 years (range, 3.2 years-12 years). Multivariate analysis found that the risk of death was increased in patients with higher American Joint Committee on Cancer disease stages (P = .003) and those with mixed FL-HCC (P = .03). Methylation analysis of LINE-1 repetitive elements and RASSF1 promoter revealed different methylation levels between pure and mixed FL-HCC, suggesting a different epigenetic background. CONCLUSIONS Pure and mixed FL-HCC display distinct clinical presentations and epigenetic backgrounds leading to different prognoses and as such may be regarded as separate clinical entities.
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Affiliation(s)
- Gabriel G Malouf
- Department of Medical Oncology, Beaujon University Hospital, Clichy, France
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Mascolo M, Siano M, Ilardi G, Russo D, Merolla F, De Rosa G, Staibano S. Epigenetic disregulation in oral cancer. Int J Mol Sci 2012; 13:2331-2353. [PMID: 22408457 PMCID: PMC3292026 DOI: 10.3390/ijms13022331] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 01/10/2023] Open
Abstract
Squamous cell carcinoma of the oral region (OSCC) is one of the most common and highly aggressive malignancies worldwide, despite the fact that significant results have been achieved during the last decades in its detection, prevention and treatment. Although many efforts have been made to define the molecular signatures that identify the clinical outcome of oral cancers, OSCC still lacks reliable prognostic molecular markers. Scientific evidence indicates that transition from normal epithelium to pre-malignancy, and finally to oral carcinoma, depends on the accumulation of genetic and epigenetic alterations in a multistep process. Unlike genetic alterations, epigenetic changes are heritable and potentially reversible. The most common examples of such changes are DNA methylation, histone modification, and small non-coding RNAs. Although several epigenetic changes have been currently linked to OSCC initiation and progression, they have been only partially characterized. Over the last decade, it has been demonstrated that especially aberrant DNA methylation plays a critical role in oral cancer. The major goal of the present paper is to review the recent literature about the epigenetic modifications contribution in early and later phases of OSCC malignant transformation; in particular we point out the current evidence of epigenetic marks as novel markers for early diagnosis and prognosis as well as potential therapeutic targets in oral cancer.
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Affiliation(s)
- Massimo Mascolo
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
| | - Maria Siano
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
| | - Gennaro Ilardi
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
| | - Daniela Russo
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
| | - Francesco Merolla
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
| | - Gaetano De Rosa
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
- Centro di Riferimento Oncologico di Basilicata (C.R.O.B.) Oncology Research Center of Basilicata, Rionero in Vulture, Potenza 85028, Italy
| | - Stefania Staibano
- Department of Biomorphological and Functional Sciences, Pathology Section, University of Naples “Federico II”, Naples 80131, Italy; E-Mails: (M.M.); (M.S.); (G.I.); (D.R.); (F.M.); (G.D.R.)
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Tao MH, Marian C, Shields PG, Nie J, McCann SE, Millen A, Ambrosone C, Hutson A, Edge SB, Krishnan SS, Xie B, Winston J, Vito D, Russell M, Nochajski TH, Trevisan M, Freudenheim JL. Alcohol consumption in relation to aberrant DNA methylation in breast tumors. Alcohol 2011; 45:689-99. [PMID: 21168302 DOI: 10.1016/j.alcohol.2010.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 11/26/2010] [Accepted: 11/27/2010] [Indexed: 02/06/2023]
Abstract
The mechanism for the observed association of alcohol consumption breast cancer risk is not known; understanding that mechanism could improve understanding of breast carcinogenesis and optimize prevention strategies. Alcohol may impact breast malignancies or tumor progression by altering DNA methylation. We examined promoter methylation of three genes, the E-cadherin, p16, and retinoic acid-binding receptor-β2 (RAR-β2) genes in archived breast tumor tissues from participants in a population-based case-control study. Real time methylation-specific PCR was performed on 803 paraffin-embedded samples, and lifetime alcohol consumption was queried. Unordered polytomous and unconditional logistic regression were used to derive adjusted odds ratios (ORs) and 95% confidence intervals (CIs). RAR-β2 methylation was not associated with drinking. Among premenopausal women, alcohol consumption was also not associated with promoter methylation for E-cadherin and p16 genes. In case-case comparisons of postmenopausal breast cancer, compared with lifetime never drinkers, promoter methylation likelihood was increased for higher alcohol intake for E-cadherin (OR=2.39; 95% CI, 1.15-4.96), in particular for those with estrogen receptor-negative tumors (OR=4.13; 95% CI, 1.16-14.72), and decreased for p16 (OR=0.52; 95% CI, 0.29-0.92). There were indications that the association with p16 was stronger for drinking at younger ages. Methylation was also associated with drinking intensity independent of total consumption for both genes. We found alcohol consumption was associated with DNA methylation in postmenopausal breast tumors, suggesting that the association of alcohol and breast cancer may be related, at least in part, to altered methylation, and may differ by drinking pattern.
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Lee SH, Hwang TS, Koh YC, Kim WY, Han HS, Kim WS, Ko YS, Lim SD. A Consideration of MGMTGene Promotor Methylation Analysis for Glioblastoma Using Methylation-Specific Polymerase Chain Reaction and Pyrosequencing. KOREAN JOURNAL OF PATHOLOGY 2011. [DOI: 10.4132/koreanjpathol.2011.45.1.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sang Hwa Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Tae Sook Hwang
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Young-Cho Koh
- Department of Neurosurgery, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Wook Youn Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Hye Seung Han
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Young Sin Ko
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - So Dug Lim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
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Quantitative promoter methylation differentiates carcinoma ex pleomorphic adenoma from pleomorphic salivary adenoma. Br J Cancer 2010; 103:1846-51. [PMID: 21063414 PMCID: PMC3008600 DOI: 10.1038/sj.bjc.6605953] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background: Potential epigenetic biomarkers for malignant transformation to carcinoma ex pleomorphic adenoma (Ca ex PSA) have been sought previously with and without specific comparison with the benign variant, pleomorphic salivary adenoma (PSA). Previous analysis has been limited by a non-quantitative approach. We sought to demonstrate quantitative promoter methylation across a panel of tumour suppressor genes (TSGs) in both Ca ex PSA and PSA. Methods: Quantitative methylation-specific real-time polymerase chain reaction (qMSP) analysis of p16INK4A, CYGB, RASSF1, RARβ, human telomerase reverse transcriptase (hTERT), Wilms’ tumour 1 (WT1) and TMEFF2 gene promoters was undertaken on bisulphite-converted DNA, previously extracted from archival fixed tissue specimens of 31 Ca ex PSA and an unrelated cohort of 28 PSA. All target regions examined had formerly been shown to be hypermethylated in salivary and/or mucosal head and neck malignancies. Results: The qMSP demonstrated abnormal methylation of at least one target in 20 out of 31 (64.5%) Ca ex PSA and 2 out of 28 (7.1%) PSA samples (P<0.001). RASSF1 was the single gene promoter for which methylation is shown to be a statistically significant predictor of malignant disease (P<0.001) with a sensitivity of 51.6% and a specificity of 92.9%. RARβ, TMEFF2 and CYGB displayed no apparent methylation, while a combinatory epigenotype based on p16, hTERT, RASSF1 and WT1 was associated with a significantly higher chance of detecting malignancy in any positive sample (odds ratio: 24, 95% CI: 4.7–125, P<0.001). Conclusions: We demonstrate the successful application of qMSP to a large series of historical Ca ex PSA samples and report on a panel of TSGs with significant differences in their methylation profiles between benign and malignant variants of pleomorphic salivary adenoma. qMSP analysis could be developed as a useful clinical tool to differentiate between Ca ex PSA and its benign precursor.
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p15INK4b methylation correlates with thrombocytopenia, blast percentage, and survival in myelodysplastic syndromes in a dose dependent manner: Quantitation using pyrosequencing study. Leuk Res 2010; 34:718-22. [DOI: 10.1016/j.leukres.2009.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/02/2009] [Accepted: 09/06/2009] [Indexed: 11/19/2022]
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Durr ML, Mydlarz WK, Shao C, Zahurak ML, Chuang AY, Hoque MO, Westra WH, Liegeois NJ, Califano JA, Sidransky D, Ha PK. Quantitative methylation profiles for multiple tumor suppressor gene promoters in salivary gland tumors. PLoS One 2010; 5:e10828. [PMID: 20520817 PMCID: PMC2877085 DOI: 10.1371/journal.pone.0010828] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 04/27/2010] [Indexed: 11/25/2022] Open
Abstract
Background Methylation profiling of tumor suppressor gene (TSGs) promoters is quickly becoming a powerful diagnostic tool for the early detection, prognosis, and even prediction of clinical response to treatment. Few studies address this in salivary gland tumors (SGTs); hence the promoter methylation profile of various TSGs was quantitatively assessed in primary SGT tissue to determine if tumor-specific alterations could be detected. Methodology DNA isolated from 78 tumor and 17 normal parotid gland specimens was assayed for promoter methylation status of 19 TSGs by fluorescence-based, quantitative methylation-specific PCR (qMSP). The data were utilized in a binary fashion as well as quantitatively (using a methylation quotient) allowing for better profiling and interpretation of results. Principal Findings The average number of methylation events across the studied genes was highest in salivary duct carcinoma (SDC), with a methylation value of 9.6, compared to the normal 4.5 (p<0.0003). There was a variable frequency and individual methylation quotient detected, depending on the TSG and the tumor type. When comparing normal, benign, and malignant SGTs, there was a statistically significant trend for increasing methylation in APC, Mint 1, PGP9.5, RAR-β, and Timp3. Conclusions/Significance Screening promoter methylation profiles in SGTs showed considerable heterogeneity. The methylation status of certain markers was surprisingly high in even normal salivary tissue, confirming the need for such controls. Several TSGs were found to be associated with malignant SGTs, especially SDC. Further study is needed to evaluate the potential use of these associations in the detection, prognosis, and therapeutic outcome of these rare tumors.
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Affiliation(s)
- Megan L. Durr
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Wojciech K. Mydlarz
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Chunbo Shao
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Marianna L. Zahurak
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Alice Y. Chuang
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Mohammad O. Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - William H. Westra
- Department of Pathology, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Nanette J. Liegeois
- Department of Oncology, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
- Milton J. Dance, Jr. Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
| | - Patrick K. Ha
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institution, Baltimore, Maryland, United States of America
- Milton J. Dance, Jr. Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- * E-mail:
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Taioli E, Ragin C, Wang XH, Chen J, Langevin SM, Brown AR, Gollin SM, Garte S, Sobol RW. Recurrence in oral and pharyngeal cancer is associated with quantitative MGMT promoter methylation. BMC Cancer 2009; 9:354. [PMID: 19807915 PMCID: PMC2763008 DOI: 10.1186/1471-2407-9-354] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 10/06/2009] [Indexed: 12/12/2022] Open
Abstract
Background Biomarkers that predict clinical response, tumor recurrence or patient survival are severely lacking for most cancers, particularly for oral and pharyngeal cancer. This study examines whether gene-promoter methylation of tumor DNA correlates with survival and recurrence rates in a population of patients with oral or pharyngeal cancer. Methods The promoter methylation status of the DNA repair gene MGMT and the tumor suppressor genes CDKN2A and RASSF1 were evaluated by methylation-specific PCR in 88 primary oral and pharyngeal tumors and correlated with survival and tumor recurrence. Quantitative MGMT methylation was also assessed. Results 29.6% of the tumors presented with MGMT methylation, 11.5% with CDKN2A methylation and 12.1% with RASSF1 methylation. MGMT promoter methylation was significantly associated with poorer overall and disease-free survival. No differences in methylation status of MGMT and RASSF1 with HPV infection, smoking or drinking habits were observed. A significant inverse trend with the amount of MGMT methylation and overall and disease-free survival was observed (ptrend = 0.002 and 0.001 respectively). Conclusion These results implicate MGMT promoter methylation as a possible biomarker for oral and pharyngeal cancer prognosis. The critical role of MGMT in DNA repair suggests that defective DNA repair may be correlative in the observed association between MGMT promoter methylation and tumor recurrence. Follow-up studies should include further quantitative MSP-PCR measurement, global methylation profiling and detailed analysis of downstream DNA repair genes regulated by promoter methylation.
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Affiliation(s)
- Emanuela Taioli
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
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Vasilatos SN, Broadwater G, Barry WT, Baker JC, Lem S, Dietze EC, Bean GR, Bryson AD, Pilie PG, Goldenberg V, Skaar D, Paisie C, Torres-Hernandez A, Grant TL, Wilke LG, Ibarra-Drendall C, Ostrander JH, D'Amato NC, Zalles C, Jirtle R, Weaver VM, Seewaldt VL. CpG island tumor suppressor promoter methylation in non-BRCA-associated early mammary carcinogenesis. Cancer Epidemiol Biomarkers Prev 2009; 18:901-14. [PMID: 19258476 DOI: 10.1158/1055-9965.epi-08-0875] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Only 5% of all breast cancers are the result of BRCA1/2 mutations. Methylation silencing of tumor suppressor genes is well described in sporadic breast cancer; however, its role in familial breast cancer is not known. METHODS CpG island promoter methylation was tested in the initial random periareolar fine-needle aspiration sample from 109 asymptomatic women at high risk for breast cancer. Promoter methylation targets included RARB (M3 and M4), ESR1, INK4a/ARF, BRCA1, PRA, PRB, RASSF1A, HIN-1, and CRBP1. RESULTS Although the overall frequency of CpG island promoter methylation events increased with age (P<0.0001), no specific methylation event was associated with age. In contrast, CpG island methylation of RARB M4 (P=0.051), INK4a/ARF (P=0.042), HIN-1 (P=0.044), and PRA (P=0.032), as well as the overall frequency of methylation events (P=0.004), was associated with abnormal Masood cytology. The association between promoter methylation and familial breast cancer was tested in 40 unaffected premenopausal women in our cohort who underwent BRCA1/2 mutation testing. Women with BRCA1/2 mutations had a low frequency of CpG island promoter methylation (15 of 15 women had <or=4 methylation events), whereas women without a mutation showed a high frequency of promoter methylation events (24 of 25 women had 5-8 methylation events; P<0.0001). Of women with a BRCA1/2 mutation, none showed methylation of HIN-1 and only 1 of 15 women showed CpG island methylation of RARB M4, INK4a/ARF, or PRB promoters. CONCLUSIONS This is the first evidence of CpG island methylation of tumor suppressor gene promoters in non-BRCA1/2 familial breast cancer.
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Affiliation(s)
- Shauna N Vasilatos
- Department of Medicine, Duke University Medical Center, Box 2628, Durham, NC 27710, USA
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Abstract
Pyrosequencing is a real-time DNA sequencing method. It is based on the transformation of pyrophosphates, released during DNA elongation by DNA polymerase, into measurable light. During DNA elongation, a single pyrophosphate molecule is released following incorporation of a single nucleotide. In the pyrosequencing reaction, released pyrophosphates are then rapidly converted by sulfurylase to adenosine triphosphate, which in turn is utilized by luciferase to produce light. Within standardized conditions, this reaction is accomplished in a few milliseconds and the light produced can be registered with a CCD camera. Therefore, it becomes possible to quantitatively measure the nucleotides incorporated. This approach has been automated in different platforms and can be used for a wide variety of applications, such as single-nucleotide polymorphism (SNP) genotyping, DNA sequencing, loss of heterozygosity analysis, and CpG methylation studies. Here we describe the entire process, focusing our attention on SNP genotyping, and giving examples of some other applications.
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Affiliation(s)
- Jose Luis Royo
- Department of Structural Genomics, Neocodex SL, Seville, Spain
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Tränkenschuh W, Puls F, Christgen M, Albat C, Heim A, Poczkaj J, Fleming P, Kreipe H, Lehmann U. Calcium influx and the Ca2+-calmodulin complex are involved in interferon-gamma-induced expression of HLA class II molecules on HL-60 cells. Proc Natl Acad Sci U S A 1988; 5:e13688. [PMID: 21060828 PMCID: PMC2966398 DOI: 10.1371/journal.pone.0013688] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 10/05/2010] [Indexed: 11/24/2022] Open
Abstract
Background Gene silencing due to aberrant DNA methylation is a frequent event in hepatocellular carcinoma (HCC) and also in hepatocellular adenoma (HCA). However, very little is known about epigenetic defects in fibrolamellar carcinoma (FLC), a rare variant of hepatocellular carcinoma that displays distinct clinical and morphological features. Methodology/Principal Findings We analyzed the methylation status of the APC, CDH1, cyclinD2, GSTπ1, hsa-mir-9-1, hsa-mir-9-2, and RASSF1A gene in a series of 15 FLC and paired normal liver tissue specimens by quantitative high-resolution pyrosequencing. Results were compared with common HCC arising in non-cirrhotic liver (n = 10). Frequent aberrant hypermethylation was found for the cyclinD2 (19%) and the RASSF1A (38%) gene as well as for the microRNA genes mir-9-1 (13%) and mir-9-2 (33%). In contrast to common HCC the APC and CDH1 (E-cadherin) genes were found devoid of any DNA methylation in FLC, whereas the GSTπ1 gene showed comparable DNA methylation in tumor and surrounding tissue at a moderate level. Changes in global DNA methylation level were measured by analyzing methylation status of the highly repetitive LINE-1 sequences. No evidence of global hypomethylation could be found in FLCs, whereas HCCs without cirrhosis showed a significant reduction in global methylation level as described previously. Conclusions FLCs display frequent and distinct gene-specific hypermethylation in the absence of significant global hypomethylation indicating that these two epigenetic aberrations are induced by different pathways and that full-blown malignancy can develop in the absence of global loss of DNA methylation. Only quantitative DNA methylation detection methodology was able to identify these differences.
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Affiliation(s)
| | - Florian Puls
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Matthias Christgen
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Cord Albat
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Albert Heim
- Institute of Virology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Jeanette Poczkaj
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Peer Fleming
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
- * E-mail:
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