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Liu J, Huang B, Ding F, Li Y. Environment factors, DNA methylation, and cancer. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:7543-7568. [PMID: 37715840 DOI: 10.1007/s10653-023-01749-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023]
Abstract
Today, the rapid development of science and technology and the rapid change in economy and society are changing the way of life of human beings and affecting the natural, living, working, and internal environment on which human beings depend. At the same time, the global incidence of cancer has increased significantly yearly, and cancer has become the number one killer that threatens human health. Studies have shown that diet, living habits, residential environment, mental and psychological factors, intestinal flora, genetics, social factors, and viral and non-viral infections are closely related to human cancer. However, the molecular mechanisms of the environment and cancer development remain to be further explored. In recent years, DNA methylation has become a key hub and bridge for environmental and cancer research. Some environmental factors can alter the hyper/hypomethylation of human cancer suppressor gene promoters, proto-oncogene promoters, and the whole genome, causing low/high expression or gene mutation of related genes, thereby exerting oncogenic or anticancer effects. It is expected to develop early warning markers of cancer environment based on DNA methylation, thereby providing new methods for early detection of cancers, diagnosis, and targeted therapy. This review systematically expounds on the internal mechanism of environmental factors affecting cancer by changing DNA methylation, aiming to help establish the concept of cancer prevention and improve people's health.
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Affiliation(s)
- Jie Liu
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Binjie Huang
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Feifei Ding
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China
| | - Yumin Li
- Department of General Surgery, Second Hospital of Lanzhou University, Lan Zhou, China.
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lan Zhou, China.
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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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Fielding D, Hartel G, Pass D, Davis M, Brown M, Dent A, Agnew J, Dickie G, Ware RS, Hodge R. Volatile organic compound breath testing detects in-situ squamous cell carcinoma of bronchial and laryngeal regions and shows distinct profiles of each tumour. J Breath Res 2020; 14:046013. [PMID: 33021204 DOI: 10.1088/1752-7163/abb18a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Volatile organic compound (VOC) breath testing of lung and head and neck squamous cell carcinoma (SCC) has been widely studied, however little is known regarding VOC profiles of in-situ SCC. A prospective study of VOC in patients with histologically proven SCC, either in-situ or advanced, and controls. Breath samples were analysed using the E-nose Cyranose ®320 and by gas chromatography/mass spectroscopy. Predictive models were developed using bootstrap forest using all 32 sensors. Data from 55 participants was analysed: 42 SCC cases comprising 20 bronchial (10 in-situ, 10 advanced) and 22 laryngeal (12 in-situ, 10 advanced), and 13 controls. There were 32 (76%) male SCC cases with mean age 63.6 (SD = 9.5) compared with 11 (85%) male controls with mean age 61.9 (SD = 10.1). Predictive models for in situ cases had good sensitivity and specificity compared to controls (overall, 95% and 69%; laryngeal, 100% and 85%; bronchial, 77% and 80%). When distinguishing in-situ and advanced tumours, sensitivity and specificity 82% and 75% respectively. For different tumour types (bronchial versus advanced laryngeal) sensitivity and specificity were 100% and 80% respectively. VOCs isolated from in-situ cancers included some previously demonstrated in advanced cancers and some novel VOCs. In-situ bronchial and laryngeal cancer can be detected by VOC analysis. Distinction from normal controls and between the two tumour types could allow screening in high risk groups for these curable lesions.
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Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
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Epidemiological Trends in Gastrointestinal Cancers in China: An Ecological Study. Dig Dis Sci 2019; 64:532-543. [PMID: 30350242 DOI: 10.1007/s10620-018-5335-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND In recent decades, the patterns and trends of gastrointestinal (GI) cancer epidemics in Chinese population have been changing. AIMS To present the epidemiological trends and geographic distributions of four major GI cancers (esophageal cancer, stomach cancer, liver cancer and colorectal cancer) in China from 2010 to 2014. METHODS It used standardized data extracted from the National Central Cancer Registry database. RESULTS The age-standardized incidence rates (ASIR) of esophageal cancer decreased from 16.7 to 12.2 per 100,000 and the age-standardized mortality rates (ASMR) decreased from 12.0 to 8.8 per 100,000. The ASIR and the ASMR of stomach cancer dropped from 23.7 to 19.5 per 100,000 and from 16.6 to 13.3 per 100,000. The ASIR of liver cancer fell from 21.4 to 17.8 per 100,000 and its ASMR fell from 18.4 per 100,000 to 15.3 per 100,000. The ASIR of colorectal cancer increased from 16.1 to 17.5 per 100,000, whereas the ASMR fluctuated between 7.6 and 7.9 per 100,000. Moreover, the incidence and mortality of each cancer differed between males and females, urban and rural residence, as well as various regions. CONCLUSION From 2010 to 2014, esophageal cancer, stomach cancer and liver cancer showed downward trend, while the ASIR of colorectal cancer slightly rose and its ASMR presented stable.
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Boscolo-Rizzo P, Furlan C, Lupato V, Polesel J, Fratta E. Novel insights into epigenetic drivers of oropharyngeal squamous cell carcinoma: role of HPV and lifestyle factors. Clin Epigenetics 2017; 9:124. [PMID: 29209433 PMCID: PMC5704592 DOI: 10.1186/s13148-017-0424-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/18/2017] [Indexed: 12/22/2022] Open
Abstract
In the last years, the explosion of high throughput sequencing technologies has enabled epigenome-wide analyses, allowing a more comprehensive overview of the oropharyngeal squamous cell carcinoma (OPSCC) epigenetic landscape. In this setting, the cellular pathways contributing to the neoplastic phenotype, including cell cycle regulation, cell signaling, DNA repair, and apoptosis have been demonstrated to be potential targets of epigenetic alterations in OPSCC. Of note, it has becoming increasingly clear that HPV infection and OPSCC lifestyle risk factors differently drive the epigenetic machinery in cancer cells. Epigenetic changes, including DNA methylation, histone modifications, and non-coding RNA expression, can be used as powerful and reliable tools for early diagnosis of OPSCC patients and improve prognostication. Since epigenetic changes are dynamic and reversible, epigenetic enzymes may also represent suitable targets for the development of more effective OPSCC therapeutic strategies. Thus, this review will focus on the main known epigenetic modifications that can occur in OPSCC and their exploitation as potential biomarkers and therapeutic targets. Furthermore, we will address epigenetic alterations to OPSCC risk factors, with a particular focus on HPV infection, tobacco exposure, and heavy alcohol consumption.
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Affiliation(s)
- Paolo Boscolo-Rizzo
- Department of Neurosciences, ENT Clinic and Regional Center for Head and Neck Cancer, Treviso Regional Hospital, University of Padova, Treviso, Italy
| | - Carlo Furlan
- Division of Radiotherapy, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Valentina Lupato
- Unit of Otolaryngology, General Hospital “S. Maria degli Angeli”, Pordenone, Italy
| | - Jerry Polesel
- Unit of Cancer Epidemiology, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico, IRCCS-National Cancer Institute, Aviano, PN Italy
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Kim M, Na H, Kasai H, Kawai K, Li YS, Yang M. Comparison of Blueberry ( Vaccinium spp.) and Vitamin C via Antioxidative and Epigenetic Effects in Human. J Cancer Prev 2017; 22:174-181. [PMID: 29018782 PMCID: PMC5624458 DOI: 10.15430/jcp.2017.22.3.174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 01/06/2023] Open
Abstract
Background Chemopreventive effects and the underlying mechanisms of blueberry (Vaccinium spp.) are not clearly understood in human. We hypothesized blueberry would work via antioxidative and epigenetic modulation, which is similar to vitamin C. Methods We performed a pilot and non-inferiority study in healthy young women (n = 12), who consumed vitamin C (1 g/d) or 240 mL of blueberry juice (total polyphenols 300 mg and proanthocyanidin 76 mg/d) for 2 weeks. We analyzed 8-hydroxydeoxyguanosine (8-OHdG) and malondialdehyde (MDA) levels in their urine, and global and specific DNA methylation at the NAD(P)H quinone oxidoreductase 1 (NQO1), methylenetetrahydrofolate reductase (MTHFR), or DNA methyltransferase 1 (DNMT1) genes in their blood. Results Urinary 8-OHdG levels were reduced by blueberry consumption rather than by vitamin C. The methylation (%) of the MTHFR was significantly decreased in blueberry-consumers and the antioxidant-susceptible subgroup, whose urinary MDA levels were decreased by the intervention. We also found a positive correlation between changes of urinary 8-OHdG and of DNA methylation at the MTHFR or the DNMT1 (P < 0.05). However, the genetic polymorphism of the MTHFR (C677T in exon 4) did not affect any above markers. Conclusions Blueberry juice shows similar anti-oxidative or anti-premutagenic activity to vitamin C and the potential as a methylation inhibitor for the MTHFR and the DNMT1 in human.
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Affiliation(s)
- Minju Kim
- Research Center for Cell Fate Control and College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Hyunkyung Na
- Research Center for Cell Fate Control and College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Hiroshi Kasai
- Department of Environmental Oncology and Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kazuaki Kawai
- Department of Environmental Oncology and Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Yun-Shan Li
- Department of Environmental Oncology and Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Mihi Yang
- Research Center for Cell Fate Control and College of Pharmacy, Sookmyung Women's University, Seoul, Korea
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Expression patterns for nicotinic acetylcholine receptor subunit genes in smoking-related lung cancers. Oncotarget 2017; 8:67878-67890. [PMID: 28978081 PMCID: PMC5620221 DOI: 10.18632/oncotarget.18948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/17/2017] [Indexed: 01/03/2023] Open
Abstract
Cigarette smoking is associated with increased risk for all histologic types of lung cancer, but why the strength of this association is stronger for squamous cell carcinoma than adenocarcinoma of the lung (SQC-L, ADC-L) is not fully understood. Because nicotine and tobacco-specific nitrosamines contribute to carcinogenesis by activating nicotinic acetylcholine receptors (nAChRs) on lung tumors and epithelial cells, we investigated whether differential expression of nAChR subtypes in these tumors could explain their different association with smoking. Expression of nAChR subunit genes in paired tumor and non-tumor lung specimens from 40 SQC-L and 38 ADC-L patients was analyzed by quantitative PCR. Compared to normal lung, both tumors share: i) transcriptional dysregulation of CHRNA3/CHRNA5/CHRNB4 (α3, α5, β4 subunits) at the chromosomal locus that predisposes to lung cancer; and ii) decreased expression of CHRFAM7A (dupα7 subunit); this last subunit negatively modulates α7-nAChR activity in oocytes. In contrast, CHRNA7 (α7 subunit) expression was increased in SQC-L, particularly in smokers and non-survivors, while CHRNA4 (α4 subunit) expression was decreased in ADC-L. Thus, over-representation of cancer-stimulating α7-nAChR in SQC-L, also potentiated by smoking, and under-representation of cancer-inhibiting α4β2-nAChR in ADC-L could explain the different tobacco influences on the tumorigenic process in each cancer type.
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Hosoda K, Yashima K, Tamoto A, Yamamoto S, Kawata S, Ikebuchi Y, Matsumoto K, Kawaguchi K, Harada K, Murawaki Y, Isomoto H. Expression of methylation-modulated tumor-related genes in endoscopically resected early esophageal squamous neoplasia. Oncol Lett 2017; 14:737-742. [PMID: 28693228 PMCID: PMC5494775 DOI: 10.3892/ol.2017.6196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 03/28/2017] [Indexed: 02/06/2023] Open
Abstract
Smoking and alcohol consumption are major risk factors for the development of esophageal squamous cell carcinoma (ESCC). Recent studies have demonstrated that smoking and alcohol consumption may be associated with altered DNA methylation in human cancer development. The aim of the present study was to evaluate methylation-modulated protein expression of tumor-related genes (TRGs) in the early stages of esophageal squamous neoplasia (ESN). ESN tissue samples (n=141) comprising 19 cases of low-grade intraepithelial neoplasia (LGIN), 70 of high-grade intraepithelial neoplasia/carcinoma in situ (HGIN/CIS) and 52 of invasive cancer, were endoscopically resected. The methylation-modulated protein expression of 5 TRGs [fragile histidine triad (FHIT), E-cadherin, MutL homolog 1 (MLH1) /MutS homolog 2 (MSH2) and cyclooxygenase-2 (COX-2)] as well as p53 was examined with immunohistochemistry, and their expression was compared with patient clinicopathological characteristics. Reduced or loss of FHIT, E-cadherin, MLH1/MSH2 and COX-2 expression was detected in 26.3 (5/19), 5.3 (1/19), 0 (0/19) and 63.2% (12/19) of LGIN cases, 61.4 (43/70), 18.6 (13/70), 7.1 (5/70) and 65.7% (46/70) of HGIN/CIS cases, and 78.8 (41/52), 50.0 (26/52), 11.5 (6/52) and 59.6% (31/52) of invasive cancer cases, respectively. Reduced or absent expression of FHIT and E-cadherin was significantly associated with neoplastic progression (FHIT, P=0.0007; E-cadherin, P=0.00014). The mean number of TRGs (FHIT, E-cadherin, MLH1/MSH2, and COX-2) that exhibited reduced or absent expression in LGIN, HGIN/CIS and invasive cancer specimens was 1.12±0.61, 1.66±0.93 and 2.09±0.96, respectively, demonstrating a significant stepwise increment from LGIN to HGIN/CIS and then to invasive cancer (P<0.05). p53 overexpression was frequently detected in ESN with head and neck carcinomas. However p53 overexpression was not significantly associated with ESN progression. An increase in the number of the 5 TRG proteins with reduced or loss of expression in the early stages of esophageal tumorigenesis was demonstrated, and their decreased expression was observed to be associated with tumor progression. Therefore, smoking and alcohol drinking may be associated with not only carcinogenesis but also the progression of ESN.
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Affiliation(s)
- Kohei Hosoda
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kazuo Yashima
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Akihiro Tamoto
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Sohei Yamamoto
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Soichiro Kawata
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Yuichiro Ikebuchi
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kazuya Matsumoto
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Koichiro Kawaguchi
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kenichi Harada
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Yoshikazu Murawaki
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Hajime Isomoto
- Division of Medicine and Clinical Science, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
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Lopomo A, Ricciardi R, Maestri M, De Rosa A, Melfi F, Lucchi M, Mussi A, Coppedè F, Migliore L. Gene-Specific Methylation Analysis in Thymomas of Patients with Myasthenia Gravis. Int J Mol Sci 2016; 17:E2121. [PMID: 27999265 PMCID: PMC5187921 DOI: 10.3390/ijms17122121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022] Open
Abstract
Thymomas are uncommon neoplasms that arise from epithelial cells of the thymus and are often associated with myasthenia gravis (MG), an autoimmune disease characterized by autoantibodies directed to different targets at the neuromuscular junction. Little is known, however, concerning epigenetic changes occurring in thymomas from MG individuals. To further address this issue, we analyzed DNA methylation levels of genes involved in one-carbon metabolism (MTHFR) and DNA methylation (DNMT1, DNMT3A, and DNMT3B) in blood, tumor tissue, and healthy thymic epithelial cells from MG patients that underwent a surgical resection of a thymic neoplasm. For the analyses we applied the methylation-sensitive high-resolution melting technique. Both MTHFR and DNMT3A promoters showed significantly higher methylation in tumor tissue with respect to blood, and MTHFR also showed significantly higher methylation levels in tumor tissue respect to healthy adjacent thymic epithelial cells. Both DNMT1 and DNMT3B promoter regions were mostly hypomethylated in all the investigated tissues. The present study suggests that MTHFR methylation is increased in thymomas obtained from MG patients; furthermore, some degrees of methylation of the DNMT3A gene were observed in thymic tissue with respect to blood.
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Affiliation(s)
- Angela Lopomo
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
| | - Roberta Ricciardi
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Michelangelo Maestri
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Anna De Rosa
- Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Franca Melfi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Marco Lucchi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Alfredo Mussi
- Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
| | - Lucia Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy.
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Ho V, Ashbury JE, Taylor S, Vanner S, King WD. Gene-specific DNA methylation of DNMT3B and MTHFR and colorectal adenoma risk. Mutat Res 2015; 782:1-6. [PMID: 26485042 DOI: 10.1016/j.mrfmmm.2015.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/08/2015] [Accepted: 09/26/2015] [Indexed: 12/12/2022]
Abstract
DNA methyltransferase 3B (DNMT3B) and methylenetetrahydrofolate reductase (MTHFR) are genes which encode enzymes critical to one-carbon metabolism. Polymorphisms in these genes have been implicated in colorectal cancer etiology; however, epigenetic modifications such as gene-specific DNA methylation also affect gene expression. DNA methylation of DNMT3B and MTHFR was quantified in blood leukocytes using Sequenom EpiTYPER® among 272 participants undergoing a screening colonoscopy. DNA methylation was quantified in 66 and 28CpG sites of DNMT3B and MTHFR respectively, and conceptualized using two approaches. First, measures representing average methylation across all CpG sites were created. Second, unsupervised principal component (PC) analysis was used to identify summary variables representing methylation around the transcription start site and in the gene-coding area for both DNMT3B and MTHFR. Logistic regression was used to compare methylation levels between participants diagnosed with colorectal adenoma(s) versus those with a normal colonoscopy via the estimation of odds ratios (ORs) and 95% confidence intervals (95% CIs) for the risk of colorectal adenomas. No association was observed between average DNA methylation of either DNMT3B or MTHFR and colorectal adenoma risk. For DNMT3B, increasing DNA methylation of CpG sites in the gene-coding area was associated with a higher risk of colorectal adenomas (OR=1.34; 95% CI: 1.01-1.79 per SD). This research provides preliminary evidence that methylation of DNMT3B may have functional significance with respect to colorectal adenomas, precursors to the vast majority of colorectal cancers.
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Affiliation(s)
- Vikki Ho
- Department of Public Health Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada.
| | - Janet E Ashbury
- Department of Public Health Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Sherryl Taylor
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Stephen Vanner
- Gastrointestinal Diseases Research Unit (GIDRU), Queen's University, Kingston, Ontario K7L3N6, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario K7L3N6, Canada
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Ho V, Ashbury JE, Taylor S, Vanner S, King WD. Quantification of gene-specific methylation of DNMT3B and MTHFR using sequenom EpiTYPER®. Data Brief 2015; 6:39-46. [PMID: 26759827 PMCID: PMC4683340 DOI: 10.1016/j.dib.2015.11.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/09/2015] [Accepted: 11/16/2015] [Indexed: 11/29/2022] Open
Abstract
Among 272 patients undergoing a screening colonoscopy, DNA methylation of DNMT3B and MTHFR, genes encoding enzymes critical to one-carbon metabolism, was quantified in blood leukocytes using Sequenom EpiTYPER®. DNA methylation was quantified in 66 and 28 CpG sites of DNMT3B and MTHFR respectively, and conceptualized using two approaches. First, measures representing average methylation across all CpG sites were created. Second, unsupervised principal component (PC) analysis was used as a pattern derivation and data-reduction approach, to develop two summary variables (PC1 and PC2). These two summary variables represented methylation around the transcription start site (PC1) and in the gene-coding area (PC2) for both DNMT3B and MTHFR. The data contained in this article presents the variation of methylation levels for individual CpG sites within the DNMT3B and MTHFR genes and possible correlations uncovered using PC analysis. The data are related to the research article “Gene-specific DNA methylation of DNMT3B and MTHFR and colorectal adenoma risk” in Mutation Research – Fundamental and Molecular Mechanisms of Mutagenesis.
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Affiliation(s)
- Vikki Ho
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
| | - Janet E Ashbury
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
| | - Sherryl Taylor
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Stephen Vanner
- Gastrointestinal Diseases Research Unit (GIDRU), Queen's University, Kingston, Ontario, Canada K7L3N6
| | - Will D King
- Department of Public Health Sciences, Queen's University Kingston, Ontario, Canada K7L3N6
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Choudhury JH, Ghosh SK. Promoter Hypermethylation Profiling Identifies Subtypes of Head and Neck Cancer with Distinct Viral, Environmental, Genetic and Survival Characteristics. PLoS One 2015; 10:e0129808. [PMID: 26098903 PMCID: PMC4476679 DOI: 10.1371/journal.pone.0129808] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Epigenetic and genetic alteration plays a major role to the development of head and neck squamous cell carcinoma (HNSCC). Consumption of tobacco (smoking/chewing) and human papilloma virus (HPV) are also associated with an increase the risk of HNSCC. Promoter hypermethylation of the tumor suppression genes is related with transcriptional inactivation and loss of gene expression. We investigated epigenetic alteration (promoter methylation of tumor-related genes/loci) in tumor tissues in the context of genetic alteration, viral infection, and tobacco exposure and survival status. METHODOLOGY The study included 116 tissue samples (71 tumor and 45 normal tissues) from the Northeast Indian population. Methylation specific polymerase chain reaction (MSP) was used to determine the methylation status of 10 tumor-related genes/loci (p16, DAPK, RASSF1, BRAC1, GSTP1, ECAD, MLH1, MINT1, MINT2 and MINT31). Polymorphisms of CYP1A1, GST (M1 & T1), XRCC1and XRCC2 genes were studied by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and multiplex-PCR respectively. PRINCIPAL FINDINGS Unsupervised hierarchical clustering analysis based on methylation pattern had identified two tumor clusters, which significantly differ by CpG island methylator phenotype (CIMP), tobacco, GSTM1, CYP1A1, HPV and survival status. Analyzing methylation of genes/loci individually, we have found significant higher methylation of DAPK, RASSF1, p16 and MINT31 genes (P = 0.031, 0.013, 0.031 and 0.015 respectively) in HPV (+) cases compared to HPV (-). Furthermore, a CIMP-high and Cluster-1 characteristic was also associated with poor survival. CONCLUSIONS Promoter methylation profiles reflecting a correlation with tobacco, HPV, survival status and genetic alteration and may act as a marker to determine subtypes and patient outcome in HNSCC.
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Affiliation(s)
- Javed Hussain Choudhury
- Molecular Medicine Laboratory, Department of Biotechnology,Assam University, Silchar, Pin-788011, Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology,Assam University, Silchar, Pin-788011, Assam, India
- * E-mail:
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13
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Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
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Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
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14
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Guerrero-Preston R, Michailidi C, Marchionni L, Pickering CR, Frederick MJ, Myers JN, Yegnasubramanian S, Hadar T, Noordhuis MG, Zizkova V, Fertig E, Agrawal N, Westra W, Koch W, Califano J, Velculescu VE, Sidransky D. Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer. Epigenetics 2014; 9:1031-46. [PMID: 24786473 PMCID: PMC4143405 DOI: 10.4161/epi.29025] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tumor suppressor genes (TSGs) are commonly inactivated by somatic mutation and/or promoter methylation; yet, recent high-throughput genomic studies have not identified key TSGs inactivated by both mechanisms. We pursued an integrated molecular analysis based on methylation binding domain sequencing (MBD-seq), 450K Methylation arrays, whole exome sequencing, and whole genome gene expression arrays in primary head and neck squamous cell carcinoma (HNSCC) tumors and matched uvulopalatopharyngoplasty tissue samples (UPPPs). We uncovered 186 downregulated genes harboring cancer specific promoter methylation including PAX1 and PAX5 and we identified 10 key tumor suppressor genes (GABRB3, HOXC12, PARP15, SLCO4C1, CDKN2A, PAX1, PIK3AP1, HOXC6, PLCB1, and ZIC4) inactivated by both promoter methylation and/or somatic mutation. Among the novel tumor suppressor genes discovered with dual mechanisms of inactivation, we found a high frequency of genomic and epigenomic alterations in the PAX gene family of transcription factors, which selectively impact canonical NOTCH and TP53 pathways to determine cell fate, cell survival, and genome maintenance. Our results highlight the importance of assessing TSGs at the genomic and epigenomic level to identify key pathways in HNSCC, deregulated by simultaneous promoter methylation and somatic mutations.
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Affiliation(s)
- Rafael Guerrero-Preston
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA; Department of Obstetrics and Gynecology; University of Puerto Rico School of Medicine; Río Piedras, Puerto Rico
| | - Christina Michailidi
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA
| | - Luigi Marchionni
- Department of Oncology Biostatistics; Johns Hopkins University; School of Medicine; Baltimore, MD USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery; University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Mitchell J Frederick
- Department of Head and Neck Surgery; University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery; University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | | | - Tal Hadar
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA
| | - Maartje G Noordhuis
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA; Department of Otorhinolaryngology-Head and Neck Surgery; University of Groningen; University Medical Center; Groningen, The Netherlands
| | - Veronika Zizkova
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA; Laboratory of Molecular Pathology and Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Elana Fertig
- Division of Biostatistics and Bioinformatics; Department of Oncology; Sidney Kimmel Comprehensive Cancer Center; Baltimore, MD USA
| | - Nishant Agrawal
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA; Sidney Kimmel Comprehensive Cancer Center; Johns Hopkins University; Baltimore, MD USA
| | - William Westra
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA
| | - Wayne Koch
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA
| | - Joseph Califano
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA; Milton J. Dance Head and Neck Center; Greater Baltimore Medical Center; Baltimore, MD USA
| | - Victor E Velculescu
- Sidney Kimmel Comprehensive Cancer Center; Johns Hopkins University; Baltimore, MD USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery; Johns Hopkins University; School of Medicine; Baltimore, MD USA
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15
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Koestler DC, Li J, Baron JA, Tsongalis GJ, Butterly LF, Goodrich M, Lesseur C, Karagas MR, Marsit CJ, Moore JH, Andrew AS, Srivastava A. Distinct patterns of DNA methylation in conventional adenomas involving the right and left colon. Mod Pathol 2014; 27:145-55. [PMID: 23868178 PMCID: PMC3880603 DOI: 10.1038/modpathol.2013.104] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/05/2013] [Accepted: 05/11/2013] [Indexed: 12/17/2022]
Abstract
Recent studies have shown two distinct non-CIMP methylation clusters in colorectal cancer, raising the possibility that DNA methylation, involving non-CIMP genes, may play a role in the conventional adenoma-carcinoma pathway. A total of 135 adenomas (65 left colon and 70 right colon) were profiled for epigenome-wide DNA methylation using the Illumina HumanMethylation450 BeadChip. A principal components analysis was performed to examine the association between variability in DNA methylation and adenoma location. Linear regression and linear mixed effects models were used to identify locus-specific differential DNA methylation in adenomas of right and left colon. A significant association was present between the first principal component and adenoma location (P=0.007), even after adjustment for subject age and gender (P=0.009). A total of 168 CpG sites were differentially methylated between right- and left-colon adenomas and these loci demonstrated enrichment of homeobox genes (P=3.0 × 10(-12)). None of the 168 probes were associated with CIMP genes. Among CpG loci with the largest difference in methylation between right- and left-colon adenomas, probes associated with PRAC (prostate cancer susceptibility candidate) gene showed hypermethylation in right-colon adenomas whereas those associated with CDX2 (caudal type homeobox transcription factor 2) showed hypermethylation in left-colon adenomas. A subgroup of left-colon adenomas enriched for current smokers (OR=6.1, P=0.004) exhibited a methylation profile similar to right-colon adenomas. In summary, our results indicate distinct patterns of DNA methylation, independent of CIMP genes, in adenomas of the right and left colon.
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Affiliation(s)
- Devin C Koestler
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Jing Li
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - John A Baron
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Lynn F Butterly
- Department of Gastroenterology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Martha Goodrich
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Corina Lesseur
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Margaret R Karagas
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jason H Moore
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Genetics, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Angeline S Andrew
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
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Sun YV, Smith AK, Conneely KN, Chang Q, Li W, Lazarus A, Smith JA, Almli LM, Binder EB, Klengel T, Cross D, Turner ST, Ressler KJ, Kardia SLR. Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans. Hum Genet 2013; 132:1027-37. [PMID: 23657504 PMCID: PMC3744600 DOI: 10.1007/s00439-013-1311-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 05/01/2013] [Indexed: 12/31/2022]
Abstract
Cigarette smoking is an environmental risk factor for many chronic diseases, and disease risk can often be managed by smoking control. Smoking can induce cellular and molecular changes, including epigenetic modification, but the short- and long-term epigenetic modifications caused by cigarette smoking at the gene level have not been well understood. Recent studies have identified smoking-related DNA methylation (DNAm) sites in Caucasians. To determine whether the same DNAm sites associate with smoking in African Americans, and to identify novel smoking-related DNAm sites, we conducted a methylome-wide association study of cigarette smoking using a discovery sample of 972 African Americans, and a replication sample of 239 African Americans with two array-based methods. Among 15 DNAm sites significantly associated with smoking after correction for multiple testing in our discovery sample, 5 DNAm sites are replicated in an independent cohort, and 14 sites in the replication sample have effects in the same direction as in the discovery sample. The top two smoking-related DNAm sites in F2RL3 (factor II receptor-like 3) and GPR15 (G-protein-coupled receptor 15) observed in African Americans are consistent with previous findings in Caucasians. The associations between the replicated DNAm sites and smoking remain significant after adjusting for genetic background. Despite the distinct genetic background between African Americans and Caucasians, the DNAm from the two ethnic groups shares common associations with cigarette smoking, which suggests a common molecular mechanism of epigenetic modification influenced by environmental exposure.
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Affiliation(s)
- Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE #3049, Atlanta, GA, 30322, USA.
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Epigenetic, genetic and environmental interactions in esophageal squamous cell carcinoma from northeast India. PLoS One 2013; 8:e60996. [PMID: 23596512 PMCID: PMC3626640 DOI: 10.1371/journal.pone.0060996] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/05/2013] [Indexed: 12/11/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) develops as a result of complex epigenetic, genetic and environmental interactions. Epigenetic changes like, promoter hypermethylation of multiple tumour suppressor genes are frequent events in cancer, and certain habit-related carcinogens are thought to be capable of inducing aberrant methylation. However, the effects of environmental carcinogens depend upon the level of metabolism by carcinogen metabolizing enzymes. As such key interactions between habits related factors and carcinogen metabolizing gene polymorphisms towards modulating promoter methylation of genes are likely. However, this remains largely unexplored in ESCC. Here, we studied the interaction of various habits related factors and polymorphism of GSTM1/GSTT1 genes towards inducing promoter hypermethylation of multiple tumour suppressor genes. Methodology/Principal Findings The study included 112 ESCC cases and 130 age and gender matched controls. Conditional logistic regression was used to calculate odds ratios (OR) and multifactor dimensionality reduction (MDR) was used to explore high order interactions. Tobacco chewing and smoking were the major individual risk factors of ESCC after adjusting for all potential confounding factors. With regards to methylation status, significantly higher methylation frequencies were observed in tobacco chewers than non chewers for all the four genes under study (p<0.01). In logistic regression analysis, betel quid chewing, alcohol consumption and null GSTT1 genotypes imparted maximum risk for ESCC without promoter hypermethylation. Whereas, tobacco chewing, smoking and GSTT1 null variants were the most important risk factors for ESCC with promoter hypermethylation. MDR analysis revealed two predictor models for ESCC with promoter hypermethylation (Tobacco chewing/Smoking/Betel quid chewing/GSTT1 null) and ESCC without promoter hypermethylation (Betel quid chewing/Alcohol/GSTT1) with TBA of 0.69 and 0.75 respectively and CVC of 10/10 in both models. Conclusion Our study identified a possible interaction between tobacco consumption and carcinogen metabolizing gene polymorphisms towards modulating promoter methylation of tumour suppressor genes in ESCC.
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