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Hazarika G, Kalita MJ, Kalita S, Das PP, Dutta K, Lahkar L, Rajkonwar A, Idris MG, Khamo V, Kusre G, Medhi S. Epigenetic Modulation of DDIT3 and MGMT Expression Acts Synergistically with Resistance to Imatinib towards CML Disease Progression: A Hospital based Study. Asian Pac J Cancer Prev 2023; 24:4059-4069. [PMID: 38156838 PMCID: PMC10909112 DOI: 10.31557/apjcp.2023.24.12.4059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION Imatinib Mesylate is an authenticated drug that aids in the treatment of Chronic Myeloid Leukaemia and Philadelphia patients which is recognized as a BCR-ABL tyrosine kinase inhibitor. Indeed, DNA Methylation occupies a key role in the stability of chromosomes. OBJECTIVE Changes in the methylation status of genes may impart to the advancement of Chronic Myeloid Leukaemia. The present investigation aims to assess the role of expression analysis and methylation status of DDIT3 and MGMT genes in imatinib-resistant and nonresistant cases. METHODS The Imatinib resistance was screened through RFLP. In this case maximum number of patients were recorded in the chronic phase belonging to the age group 40-59 and the accelerated and blast phase is more common in elderly patients showing the progressive nature of the disease with age. Hemoglobin and platelet count are found to be higher in cases where WBC count was minimal. A history of long-term alcohol consumption is found to be associated with the progression of the disease. RESULTS The maximum level of expression of the DDIT3 gene was recorded in the chronic phase regardless of upstream (67.8%) and downstream (57.9%) regulation. The highest MGMT expression regulation was also observed in the case of chronic phase in both upstream (78.9%) and downstream (44%) regulation. Further, the MGMT gene showed the highest methylation of 6.6% and DDIT3 showed 3.3% in CML cases. CONCLUSION In the present study notable depletion of survivality was established in the Imatinib resistance patients manifesting genetic malfunction of BCR-ABL transcripts among the North East Indian inhabitants and advocating for the expansion of the disease.
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Affiliation(s)
- Gautam Hazarika
- Department of Anatomy, Assam Medical College &Hospital, Dibrugarh, (Assam) India.
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
| | - Manash Jyoti Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
| | - Simanta Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
- Multi-disciplinary Research Unit, DMC, India.
| | - Partha Pratim Das
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
- Multi-disciplinary Research Unit, FAAMCH, India.
| | - Kalpajit Dutta
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
| | - Lipika Lahkar
- Department. of Botany, Silapathar College, Dhemaji, (Assam) India.
| | - Anjanjyoti Rajkonwar
- Department of Anatomy, Assam Medical College &Hospital, Dibrugarh, (Assam) India.
| | | | - Vinotsale Khamo
- Department of Pathology, Naga Hospital Authority, Kohima, (Nagaland) India.
| | - Giriraj Kusre
- Department of Anatomy, Assam Medical College &Hospital, Dibrugarh, (Assam) India.
| | - Subhash Medhi
- Department of Bioengineering & Technology, Gauhati University, Guwahati, (Assam) India.
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Ramazi S, Daddzadi M, Sahafnejad Z, Allahverdi A. Epigenetic regulation in lung cancer. MedComm (Beijing) 2023; 4:e401. [PMID: 37901797 PMCID: PMC10600507 DOI: 10.1002/mco2.401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/31/2023] Open
Abstract
Lung cancer is indeed a major cause of cancer-related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non-small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.
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Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Meadeh Daddzadi
- Department of BiotechnologyFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Zahra Sahafnejad
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Abdollah Allahverdi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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Vera-Chang MN, Danforth JM, Stuart M, Goodarzi AA, Brand M, Richardson RB. Profound DNA methylomic differences between single- and multi-fraction alpha irradiations of lung fibroblasts. Clin Epigenetics 2023; 15:174. [PMID: 37891670 PMCID: PMC10612361 DOI: 10.1186/s13148-023-01564-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/05/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alpha (α)-radiation is a ubiquitous environmental agent with epigenotoxic effects. Human exposure to α-radiation at potentially harmful levels can occur repetitively over the long term via inhalation of naturally occurring radon gas that accumulates in enclosed spaces, or as a result of a single exposure from a nuclear accident. Alterations in epigenetic DNA methylation (DNAm) have been implicated in normal aging and cancer pathogenesis. Nevertheless, the effects of aberrations in the methylome of human lung cells following exposure to single or multiple α-irradiation events on these processes remain unexplored. RESULTS We performed genome-wide DNAm profiling of human embryonic lung fibroblasts from control and irradiated cells using americium-241 α-sources. Cells were α-irradiated in quadruplicates to seven doses using two exposure regimens, a single-fraction (SF) where the total dose was given at once, and a multi-fraction (MF) method, where the total dose was equally distributed over 14 consecutive days. Our results revealed that SF irradiations were prone to a decrease in DNAm levels, while MF irradiations mostly increased DNAm. The analysis also showed that the gene body (i.e., exons and introns) was the region most altered by both the SF hypomethylation and the MF hypermethylation. Additionally, the MF irradiations induced the highest number of differentially methylated regions in genes associated with DNAm biomarkers of aging, carcinogenesis, and cardiovascular disease. The DNAm profile of the oncogenes and tumor suppressor genes suggests that the fibroblasts manifested a defensive response to the MF α-irradiation. Key DNAm events of ionizing radiation exposure, including changes in methylation levels in mitochondria dysfunction-related genes, were mainly identified in the MF groups. However, these alterations were under-represented, indicating that the mitochondria undergo adaptive mechanisms, aside from DNAm, in response to radiation-induced oxidative stress. CONCLUSIONS We identified a contrasting methylomic profile in the lung fibroblasts α-irradiated to SF compared with MF exposures. These findings demonstrate that the methylome response of the lung cells to α-radiation is highly dependent on both the total dose and the exposure regimen. They also provide novel insights into potential biomarkers of α-radiation, which may contribute to the development of innovative approaches to detect, prevent, and treat α-particle-related diseases.
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Affiliation(s)
- Marilyn N Vera-Chang
- Radiobiology and Health Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada
| | - John M Danforth
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marilyne Stuart
- Environment and Waste Technologies Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada
| | - Aaron A Goodarzi
- Departments of Biochemistry and Molecular Biology and Oncology, Cumming School of Medicine, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marjorie Brand
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada
| | - Richard B Richardson
- Radiobiology and Health Branch, Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, K0J 1J0, Canada.
- McGill Medical Physics Unit, Cedars Cancer Centre-Glen Site, Montreal, QC, H4A 3J1, Canada.
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Mohammed F, Baydaa Abed Hussein A, Ahmed T. Evaluation of Methylation Panel in the Promoter Region of p16INK4a , RASSF1A, and MGMT as a Biomarker in Sputum for Lung Cancer. ARCHIVES OF RAZI INSTITUTE 2022; 77:1075-1081. [PMID: 36618318 PMCID: PMC9759213 DOI: 10.22092/ari.2022.357985.2131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 01/10/2023]
Abstract
Lung cancer is the most common cause of cancer death in the world. Effective early detection and appropriate medications can help treat this deadly cancer. Therefore, early detection of lung cancer is of utmost importance, especially in screening high-risk populations (such as smokers) with an urgent need to identify new biomarkers. The present study aimed to demonstrate the potential of using the panel of DNA methylation as a biomarker for the early diagnosis of lung cancer from sputum samples. The methylated promoter of p16INK4a , RASSF1A, and MGMT genes was estimated by the methylation-specific polymerase chain reaction in a sample of 84 lung cancer patients (65 smokers and 19 non-smokers). Based on the results, p16INK4a promoter methylation was significantly associated with smoking habit and lung cancer progression in terms of histological grading and patient staging. The sensitivity and specificity of the p16INK4a gene as a biomarker for lung cancer were 71% and 90%, respectively. The methylated promoter of RASSF1A was less sensitive (48%) as a biomarker for lung cancer with 83%. The results demonstrated a strong association between promoter methylation of RASSF1A and late stages of lung cancer (P=0.0007). The sensitivity of the MGMT gene as a biomarker for lung cancer was 61% with high specificity (92%), compared to other candidate genes in this study. The epigenetic alteration in the promoter region of p16INK4a , RASSF1A, and MGMT genes is highly associated with cancer cell development. It is suggested that the use of these candidate biomarkers can be used as an adjunct to computed tomography screening to diagnose patients at high risk for lung cancer after validation.
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Affiliation(s)
- F Mohammed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
| | - A Baydaa Abed Hussein
- Department of Sciences, College of Basic Education, University of Misan, Maysan, Iraq
| | - T Ahmed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
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5
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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Nooreldeen R, Bach H. Current and Future Development in Lung Cancer Diagnosis. Int J Mol Sci 2021; 22:8661. [PMID: 34445366 PMCID: PMC8395394 DOI: 10.3390/ijms22168661] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths in North America and other developed countries. One of the reasons lung cancer is at the top of the list is that it is often not diagnosed until the cancer is at an advanced stage. Thus, the earliest diagnosis of lung cancer is crucial, especially in screening high-risk populations, such as smokers, exposure to fumes, oil fields, toxic occupational places, etc. Based on the current knowledge, it looks that there is an urgent need to identify novel biomarkers. The current diagnosis of lung cancer includes different types of imaging complemented with pathological assessment of biopsies, but these techniques can still not detect early lung cancer developments. In this review, we described the advantages and disadvantages of current methods used in diagnosing lung cancer, and we provide an analysis of the potential use of body fluids as carriers of biomarkers as predictors of cancer development and progression.
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Affiliation(s)
| | - Horacio Bach
- Division of Infectious Diseases, Faculty of Medicine, The University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
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Yalcin D, Otu HH. An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200724145835] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Epigenetic repression mechanisms play an important role in gene
regulation, specifically in cancer development. In many cases, a CpG island’s (CGI) susceptibility
or resistance to methylation is shown to be contributed by local DNA sequence features.
Objective:
To develop unbiased machine learning models–individually and combined for different
biological features–that predict the methylation propensity of a CGI.
Methods:
We developed our model consisting of CGI sequence features on a dataset of 75
sequences (28 prone, 47 resistant) representing a genome-wide methylation structure. We tested
our model on two independent datasets that are chromosome (132 sequences) and disease (70
sequences) specific.
Results:
We provided improvements in prediction accuracy over previous models. Our results
indicate that combined features better predict the methylation propensity of a CGI (area under the
curve (AUC) ~0.81). Our global methylation classifier performs well on independent datasets
reaching an AUC of ~0.82 for the complete model and an AUC of ~0.88 for the model using select
sequences that better represent their classes in the training set. We report certain de novo motifs
and transcription factor binding site (TFBS) motifs that are consistently better in separating prone
and resistant CGIs.
Conclusion:
Predictive models for the methylation propensity of CGIs lead to a better
understanding of disease mechanisms and can be used to classify genes based on their tendency to
contain methylation prone CGIs, which may lead to preventative treatment strategies. MATLAB®
and Python™ scripts used for model building, prediction, and downstream analyses are available
at https://github.com/dicleyalcin/methylProp_predictor.
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Affiliation(s)
- Dicle Yalcin
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
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Evaluation of Methylation Profiles of An Epidermal Growth Factor Receptor Gene in a Head and Neck Squamous Cell Carcinoma Patient Group. Balkan J Med Genet 2021; 23:65-72. [PMID: 33816074 PMCID: PMC8009575 DOI: 10.2478/bjmg-2020-0025] [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] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey, and 48 unrelated healthy volunteers from different geographic regions of Turkey, were included in this study. Methylation status of the promoter region of the EGFR gene was detected by methylation-specific-polymerase chain reaction (MS-PCR). The correlation between EGFR gene promoter methylation profiles and clinical characteristics were examined using the χ2 test. Methylation was observed in 79.0% of HNSCC patients, whereas this ratio was 90.0% in healthy individuals. The results show that promoter region methylation of the EGFR gene was not associated with HNSCC development in the studied Turkish patient group. In addition, the methylation status of the EGFR gene promoter was not found to be related to age, gender or tumor stage.
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Wang W, Zhang Y, Peng Y, Jin KZ, Li YL, Liang Y, Tan HY, Yu XJ, Zhou ZW, Chen J. A Ki-67 Index to Predict Treatment Response to the Capecitabine/Temozolomide Regimen in Neuroendocrine Neoplasms: A Retrospective Multicenter Study. Neuroendocrinology 2021; 111:752-763. [PMID: 32668427 DOI: 10.1159/000510159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/14/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The efficacy of the capecitabine/temozolomide (CAPTEM) regimen has been demonstrated in metastatic neuroendocrine neoplasms (NENs), but because of varying response rates among the patients, biomarkers to predict its response are greatly needed. Here, we investigated the clinical utility of a Ki-67 index to predict the CAPTEM regimen objective responses and select patients who could benefit from this regimen. METHODS Metastatic NENs patients treated with the CAPTEM regimen from 4 high-volume medical centers were selected and grouped in a training and validation cohort. The classification and regression tree (CART) was generated to identify the optimal threshold of Ki-67 for stratifying the patients into different Ki-67 range groups based on their response to the CAPTEM regimen. RESULTS AND CONCLUSIONS The overall response rate (ORR) and disease control rate of the entire cohort (N = 151) were 26.5 and 76.2%, respectively, with a median progression-free survival (PFS) of 12.0 months. CART analysis showed that patients in the Ki-67 range group 10-40% demonstrated a significantly higher ORR than those in Ki-67 >40 and <10% groups (p < 0.001 in the training cohort and p = 0.036 in the validation cohort). Response to the CAPTEM regimen was not influenced by the expression of O6-methylguanine-DNA methyltransferase or primary tumor location. Multivariate analysis identified the Ki-67 index as the only independent prognostic factor for overall survival (p = 0.031) and PFS (p = 0.006). The proposed Ki-67 index was externally validated and could be used to clinically identify suitable metastatic NENs patients who could achieve an optimal cytoreduction using the CAPTEM regimen.
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Affiliation(s)
- Wei Wang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ying Peng
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai-Zhou Jin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yuan-Liang Li
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Yao Liang
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huang-Ying Tan
- Department of Integrative Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Xian-Jun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhi-Wei Zhou
- Department of Gastric Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China,
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Li Y, Zhang T, Zhang H, Wang X, Liu X, Huang Q, Li L. Clinical Significance of P16 Gene Methylation in Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:133-142. [PMID: 32949396 DOI: 10.1007/978-981-15-4494-1_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of death from cancer in China. The lack of early screening technologies makes most patients to be diagnosed at advanced stages with a poor prognosis which often miss the best treatment opportunities. Thus, identifying biomarkers for minimally invasive detection and prognosis of early stage disease is urgently needed. Genetic and epigenetic alterations that promote tumorigenesis and metastasis exist in multiple cancers. These aberrant alterations usually represent early events in cancer progression suggesting their potential applications as a biomarker for cancer prediction. Studies have shown that DNA methylation is one of the key factors in progression of lung cancer. P16 promoter methylation is one of the most common epigenetic change plays a key role in lung cancer. In this review, we highlight the p16 gene methylation and its clinical significance in lung cancer.
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Affiliation(s)
- Yanjun Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Tingting Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Hui Zhang
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Xiangdong Wang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Xiaozhuan Liu
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China.,Zhengzhou University People's Hospital, Zhengzhou, Henan, China.,Henan University People's Hospital, Zhengzhou, Henan, China
| | - Qihong Huang
- Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Li Li
- Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, Zhengzhou, Henan, China. .,Zhengzhou University People's Hospital, Zhengzhou, Henan, China. .,Henan University People's Hospital, Zhengzhou, Henan, China. .,Department of Scientific Research and Discipline Construction, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
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Bond DR, Uddipto K, Enjeti AK, Lee HJ. Single-cell epigenomics in cancer: charting a course to clinical impact. Epigenomics 2020; 12:1139-1151. [PMID: 32790506 DOI: 10.2217/epi-2020-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of global epigenetic dysregulation. Mutations in epigenetic regulators are common events in multiple cancer types and epigenetic therapies are emerging as a treatment option in several malignancies. A major challenge for the clinical management of cancer is the heterogeneous nature of this disease. Cancers are composed of numerous cell types and evolve over time. This heterogeneity confounds decisions regarding treatment and promotes disease relapse. The emergence of single-cell epigenomic technologies has introduced the exciting possibility of linking genetic and transcriptional heterogeneity in the context of cancer biology. The next challenge is to leverage these tools for improved patient outcomes. Here we consider how single-cell epigenomic technologies may address the current challenges faced by cancer clinicians.
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Affiliation(s)
- Danielle R Bond
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Kumar Uddipto
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Newcastle, Waratah 2298, New South Wales, Australia.,School of Medicine & Public Health, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia.,NSW Health Pathology - Hunter, New Lambton Heights 2305, New South Wales, Australia
| | - Heather J Lee
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
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Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21155425. [PMID: 32751497 PMCID: PMC7432919 DOI: 10.3390/ijms21155425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modification is considered a major mechanism of the inactivation of tumor suppressor genes that finally contributes to carcinogenesis. LIM homeobox transcription factor 1α (LMX1A) is one of the LIM-homeobox-containing genes that is a critical regulator of growth and differentiation. Recently, LMX1A was shown to be hypermethylated and functioned as a tumor suppressor in cervical cancer, ovarian cancer, and gastric cancer. However, its role in lung cancer has not yet been clarified. In this study, we used public databases, methylation-specific PCR (MSP), reverse transcription PCR (RT-PCR), and bisulfite genomic sequencing to show that LMX1A was downregulated or silenced due to promoter hypermethylation in lung cancers. Treatment of lung cancer cells with the demethylating agent 5-aza-2'-deoxycytidine restored LMX1A expression. In the lung cancer cell lines H23 and H1299, overexpression of LMX1A did not affect cell proliferation but suppressed colony formation and invasion. These suppressive effects were reversed after inhibition of LMX1A expression in an inducible expression system in H23 cells. The quantitative RT-PCR (qRT-PCR) data showed that LMX1A could modulate epithelial mesenchymal transition (EMT) through E-cadherin (CDH1) and fibronectin (FN1). NanoString gene expression analysis revealed that all aberrantly expressed genes were associated with processes related to cancer progression, including angiogenesis, extracellular matrix (ECM) remodeling, EMT, cancer metastasis, and hypoxia-related gene expression. Taken together, these data demonstrated that LMX1A is inactivated through promoter hypermethylation and functions as a tumor suppressor. Furthermore, LMX1A inhibits non-small cell lung cancer (NSCLC) cell invasion partly through modulation of EMT, angiogenesis, and ECM remodeling.
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Ratna MG, Nugrahaningsih DAA, Sholikhah EN, Dwianingsih EK, Malueka RG. The association between PON1 and GSTM1 genetic variation with methylation of p16 gene promoter among Javanese farmers exposed to pesticides at Magelang Regency, Central Java, Indonesia. Heliyon 2020; 6:e03993. [PMID: 32478190 PMCID: PMC7248662 DOI: 10.1016/j.heliyon.2020.e03993] [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: 08/12/2019] [Revised: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 12/08/2022] Open
Abstract
Occupational exposure to pesticides leads to the development of cancer. Aberrant DNA methylation plays a crucial role in cancer. The manifestation of the carcinogenic effect of pesticides could be determined by the variation of genes encoding enzyme, including PON1 Q192R and GSTM1. The goal of this study was to find out polymorphism of PON1 Q192R and methylation of p16 gene promoter, and their correlation on Javanese farmers in the agricultural area of Ngablak Subdistrict, Magelang Regency, Central Java. Seventy-eight pesticide-exposed farmers enrolled in the study. Polymorphism of PON Q192R was determined using PCR-RFLP and variation of GSTM1 was examined using conventional PCR. The methylation of the p16 gene promoter was determined using methylation-specific PCR. The result revealed 94.9% polymorphism of PON1 Q192R, which was higher in the R/R (Arg/Arg) genotypes than Q/R (Gln/Arg) and lowest in Q/Q (Gln/Gln) genotypes. We also found 82.1% GSTM1 null genotype among the farmers enrolled in the study. As many as 26.9% methylations of p16 gene promoter were found among farmers. Genetic variation of PON1 Q192R and GSTM1 were not found to be correlated to the methylation status of p16 gene promoter in the Javanese population.
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Affiliation(s)
- Maya G Ratna
- Master of Biomedical Science Program, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi A A Nugrahaningsih
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
| | - Eti N Sholikhah
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ery K Dwianingsih
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
| | - Rusdy G Malueka
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
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14
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González-Pérez LV, Isaza-Guzmán DM, Arango-Pérez EA, Tobón-Arroyave SI. Analysis of salivary detection of P16INK4A and RASSF1A promoter gene methylation and its association with oral squamous cell carcinoma in a Colombian population. J Clin Exp Dent 2020; 12:e452-e460. [PMID: 32509227 PMCID: PMC7263777 DOI: 10.4317/jced.56647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/24/2020] [Indexed: 01/19/2023] Open
Abstract
Background Epigenetic factors play a fundamental role in the etiopathogenesis of oral squamous cell carcinoma (OSCC). This study evaluated if salivary detection of P16INK4A/RASSF1A gene promoter methylation might be linked to the clinical/histological features of OSCC in a Colombian population.
Material and Methods Methylation-specific polymerase chain reaction (MSP-PCR) was used to detect the methylation frequency of P16INK4A/RASSF1A genes in DNA obtained from whole saliva collected of 40 healthy controls (HC) and 43 OSCC patients. Determination of the clinical performance of MSP-PCR assay was based on standard algorithms derived from two-way contingency table analysis. The association of methylation status of targeted genes with OSCC was analyzed in a multivariate binary logistic regression model.
Results There were significantly higher proportions of promoter methylation of these target genes in OSCC patients when compared with HC. The analysis of single methylated genes showed high specificity, good positive and negative predictive values, but was accompanied by a low sensitivity. OSCC cases with clinical stage III/IV, poorly differentiated, and severe cellular atypia showed a significantly greater proportion of methylated than that of unmethylated targeted genes in saliva samples. Logistic regression analysis indicated an independent association of P16INK4A and RASSF1A promoter methylation with OSCC diagnosis. A significant interaction effect between ageing and P16INK4A promoter methylation was also detected.
Conclusions Salivary detection of P16INK4A and RASSF1A promoter methylation appears to be independently associated with OSCC and may be linked to the tumor activity in the present population. Consequently, the targeting of these genes in saliva samples might constitute an important tool for diagnosis and prognosis purposes. Key words:Gene methylation, oral squamous cell carcinoma, P16INK4A, RASSF1A, saliva.
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Affiliation(s)
| | - Diana-María Isaza-Guzmán
- Titular Professor. Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Eduin-Alonso Arango-Pérez
- Oral and Maxillofacial Surgeon Resident. Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Antioquia. Medellín, Colombia
| | - Sergio-Iván Tobón-Arroyave
- Titular Professor. Laboratory of Immunodetection and Bioanalysis, Faculty of Dentistry, University of Antioquia. Medellín, Colombia.,Stomatologist and Oral Surgeon. Stomatology and Maxillofacial Surgery Unit, San Vicente Foundation University Hospital, Medellín, Colombia
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15
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Matsuda S, Mafune A, Kohda N, Hama T, Urashima M. Associations among smoking, MGMT hypermethylation, TP53-mutations, and relapse in head and neck squamous cell carcinoma. PLoS One 2020; 15:e0231932. [PMID: 32324779 PMCID: PMC7179834 DOI: 10.1371/journal.pone.0231932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/02/2020] [Indexed: 01/04/2023] Open
Abstract
Background Epigenetic silencing of the O6-methylguanine-DNA methyltransferase (MGMT) DNA repair enzyme via promoter hypermethylation (hmMGMT) may increase mutations in the TP53 oncosuppressor gene and contribute to carcinogenesis. The effects of smoking, which is a risk factor for head and neck squamous cell carcinoma (HNSCC), were investigated to determine whether they up- or down-regulate hmMGMT. Additionally, the impact of hmMGMT and disruptive TP53-mutations on relapse was investigated in patients with HNSCC. Methods This study included 164 patients with HNSCC who were negative for both p16 protein expression and human papilloma virus infection. The association of smoking and hmMGMT was investigated using multiple logistic regression analysis. Competing risk regression was used to evaluate the effects of hmMGMT and TP53-mutations in exon 2 to 11 on relapse of HNSCC. Results hmMGMT was observed in 84% of the 164 patients. TP53-mutations, specifically, G:C>A:T transition, were more frequent in patients with hmMGMT (32%) than in those without hmMGMT (8%). The frequency of disruptive TP53-mutations was not significantly different between groups. Compared with nonsmoking, heavy smoking of 20 pack-years or more was significantly associated with decreased hmMGMT (adjusted odds ratio, 0.08; 95% CI, 0.01 to 0.56; P = 0.01). Patients who had both hmMGMT and disruptive TP53-mutations showed a significantly higher relapse rate than all other patients (subdistribution hazard ratio, 1.77; 95% CI, 1.07 to 2.92; P = 0.026). Conclusions It was found that hmMGMT was suppressed by heavy smoking, and hmMGMT combined with disruptive TP53-mutations may indicate a poor prognosis in patients with HNSCC.
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Affiliation(s)
- Shinichi Matsuda
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Real World Data Science Department, Chugai Pharmaceutical Co. Ltd., Tokyo, Japan
| | - Aki Mafune
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Division of Kidney and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Nagisa Kohda
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
| | - Takanori Hama
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Department of Oto-Rhino-laryngology, The Jikei University School of Medicine, Tokyo, Japan
| | - Mitsuyoshi Urashima
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- * E-mail:
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16
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Dong YM, Qin LD, Tong YF, He QE, Wang L, Song K. Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns. PeerJ 2020; 8:e8349. [PMID: 32030321 PMCID: PMC6995662 DOI: 10.7717/peerj.8349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
Background When considering therapies for lung adenocarcinoma (LUAD) patients, the carcinogenic mechanisms of smokers are believed to differ from those who have never smoked. The rising trend in the proportion of nonsmokers in LUAD urgently requires the understanding of such differences at a molecular level for the development of precision medicine. Methods Three independent LUAD tumor sample sets—TCGA, SPORE and EDRN—were used. Genome patterns of expression (GE), copy number variation (CNV) and methylation (ME) were reviewed to discover the differences between them for both smokers and nonsmokers. Tobacco-related signature genes distinguishing these two groups of LUAD were identified using the GE, ME and CNV values of the whole genome. To do this, a novel iterative multi-step selection method based on the partial least squares (PLS) algorithm was proposed to overcome the high variable dimension and high noise inherent in the data. This method can thoroughly evaluate the importance of genes according to their statistical differences, biological functions and contributions to the tobacco exposure classification model. The kernel partial least squares (KPLS) method was used to further optimize the accuracies of the classification models. Results Forty-three, forty-eight and seventy-five genes were identified as GE, ME and CNV signatures, respectively, to distinguish smokers from nonsmokers. Using only the gene expression values of these 43 GE signature genes, ME values of the 48 ME signature genes or copy numbers of the 75 CNV signature genes, the accuracies of TCGA training and SPORE/EDRN independent validation datasets all exceed 76%. More importantly, the focal amplicon in Telomerase Reverse Transcriptase in nonsmokers, the broad deletion in ChrY in male nonsmokers and the greater amplification of MDM2 in female nonsmokers may explain why nonsmokers of both genders tend to suffer LUAD. These pattern analysis results may have clear biological interpretation in the molecular mechanism of tumorigenesis. Meanwhile, the identified signature genes may serve as potential drug targets for the precision medicine of LUAD.
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Affiliation(s)
- Yan-mei Dong
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Li-da Qin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yi-fan Tong
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qi-en He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ling Wang
- The First Affiliated Hospital Oncology, Dalian Medical University, Dalian, Liaoning, China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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17
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Impact of catechol-O-methyltransferase gene variants on methylation status of P16 and MGMT genes and their downregulation in colorectal cancer. Eur J Cancer Prev 2019; 28:68-75. [PMID: 30379684 DOI: 10.1097/cej.0000000000000485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Globally, colorectal cancer (CRC) is the third most commonly diagnosed cancer in males and the second most commonly diagnosed cancer in females, with 1.4 million new cases and almost 694 000 deaths estimated to have occurred in 2012. The development and progression of CRC is dictated by a series of alterations in diverse genes mostly proto-oncogenes and tumor suppressor genes. In this dreadful disease disturbances different from mutations called as epigenetic regulations are also taken into consideration and are thoroughly investigated. The present study was designed to analyze the promoter hypermethylation of CpG (cytosine, followed by guanine nucleotide) islands of cyclin-dependent kinase inhibitor 2A (P16) and O-methylguanine-DNA methyltransferase (MGMT) genes and its subsequent effect on the protein expression in CRC. The impact of the common functional polymorphism of the catechol-O-methyltransferase (COMT) gene, Val158Met, on promoter hypermethylation of P16 and MGMT genes in CRC was also investigated. The study included 200 CRC cases and equal numbers of normal samples. DNA was extracted using the kit method and methylation specific-PCR was performed for analysis of the promoter hypermethylation status. Total protein was isolated form all CRC cases and western blotting was performed for P16 and MGMT proteins. The COMT Val158Met polymorphism was analyzed by a PCR-restriction fragment length polymorphism assay. Epigenetic analysis showed that unlike other high-risk regions, the Kashmiri population has a different promoter hypermethylation profile of both P16 and MGMT genes, with frequent and significant promoter hypermethylation of both in CRC. The frequency of promoter hypermethylation of both genes was significantly higher in males and was insignificantly found to be higher in stage III/IV. The degree of P16 and MGMT promoter hypermethylation increased significantly with increasing severity of the lesion. We also found a significant correlation between P16 and MGMT promoter hypermethylation and loss of protein expression in CRC. A significant association was found between COMT polymorphism (homozygous variant) and P16 methylation status. Similar results were also found for MGMT hypermethylated cases.
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18
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Zhang Y, Li Y, Luo L, He Q, Gao Y, Feng H, Zhao L, Wei W, Fu S, Sun D. Factors Affecting Differential Methylation of DNA Promoters in Arsenic-Exposed Populations. Biol Trace Elem Res 2019; 189:437-446. [PMID: 30220071 DOI: 10.1007/s12011-018-1504-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/30/2018] [Indexed: 01/15/2023]
Abstract
The exposure/biotransformation of inorganic arsenic (iAs) may perturb DNA methylation patterns and subsequently influence disease risk by altering the expression of key genes. Interindividual variation in patterns of DNA methylation can be explained by the influence of environmental, genetic, and stochastic factors. Here, we examined promoter DNA methylation levels with urinary arsenical concentrations and investigated the genetic and nongenetic determinants of DNA methylation in 105 samples collected from populations in Shanxi Province, China, with high levels of arsenic in drinking water. Arsenic concentrations in water were determined by atomic absorption spectrophotometry (AA-6800, Shimadzu Co., Kyoto, Japan). Urine samples were measured using an atomic absorption spectrophotometer with an arsenic speciation pretreatment system (ASA-2sp, Shimadzu Co. Kyoto, Japan) for detection. Gene-specific (CDH1, EREG, ERCC2, GSTP1, and MGMT) DNA methylation was quantified by targeted bisulfite sequencing. Single-nucleotide polymorphism (SNP) genotyping was performed using a custom-by-design 2 × 48-Plex SNPscan™ Kit. These results revealed CDH1 with promoter DNA methylation levels associated with iAs. After the exclusion of confounding factors, age was correlated with increased methylation of the CDH1 gene. The susceptibility of the CDH1 and GSTP1 gene promoters to methylation was increased in individuals carrying the DNMT3B (SNP rs2424932) GA genotype, and the susceptibility of the CDH1 gene promoters to methylation was increased in individuals carrying the DNMT3B (SNP rs6087990) TC genotype. Although the above results must still be replicated in larger samples, the findings improve our understanding of the pathogenesis of arsenic and may highlight certain DNA methylation markers as attractive surrogate markers for prevention research.
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Affiliation(s)
- Yanting Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Yuanyuan Li
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Lanrong Luo
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Qian He
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Yanhui Gao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Hongqi Feng
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Lijun Zhao
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Wei Wei
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China
| | - Songbo Fu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China.
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China.
| | - Dianjun Sun
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, China.
- Key Lab of Etiology and Epidemiology, Education Bureau of Hei Long Jiang Province & Ministry of Health, Harbin, 150081, China.
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19
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Paydar P, Asadikaram G, Nejad HZ, Akbari H, Abolhassani M, Moazed V, Nematollahi MH, Ebrahimi G, Fallah H. Epigenetic modulation of BRCA-1 and MGMT genes, and histones H4 and H3 are associated with breast tumors. J Cell Biochem 2019; 120:13726-13736. [PMID: 30938887 DOI: 10.1002/jcb.28645] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Aberrant patterns in promoter methylation of tumor-suppressor genes and posttranslational modifications of histone proteins are considered as major features of malignancy. In this study, we aimed to investigate promoter methylation of three tumor-suppressor genes (BRCA-1, MGMT, and P16) and three histone marks (H3K9ac, H3K18ac, and H4K20me3) in patients with breast tumors. This case-control study included 27 patients with malignant breast tumors (MBT) and 31 patients with benign breast tumors (BBT). The methylation-specific PCR was used for determining promoter methylation of BRCA-1, MGMT, and P16 genes. Western blot analysis was performed to detect histone lysine acetylation (H3K9ac and H3K18ac) and lysine methylation (H4K20me3). BRCA-1 promoter methylation was detected in 44.4% of the MBT whereas this alteration was found in 9.7% of BBT (P = 0.005). The Kaplan-Meier analysis indicated that hypermethylation in BRCA-1 promoter was significantly associated with poor overall survival of patients with breast cancer (P = 0.039). MGMT promoter methylation was identified in 18.5% of MBT and 0.0% of the BBT (P = 0.01). The frequency of P16 promoter methylation was 25.8% in BBT and 11.1% in MBT (P = 0.12). As compared with BBT, MBT samples displayed the aberrant patterns of histones marks with hypomethylation of H4K20 and hypoacetylation of H3K18 (P = 0.03 and P = 0.04, respectively). There was a negative significant correlation between H3K9ac levels and tumor size in MBT group (r = -0.672; P = 0.008). The present findings suggest that promoter hypermethylation of MGMT and BRCA-1 genes along with alterations in H3K18ac and H4K20me3 levels may have prognostic values in patients with breast cancer. Moreover, the detection of these epigenetic modifications in breast tumors could be helpful in finding new methods for breast cancer therapy.
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Affiliation(s)
- Parisa Paydar
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman, Iran.,Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Asadikaram
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Neuroscience Research Center, Institute of Neuropharmacology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Zeynali Nejad
- Department of Surgery, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamed Akbari
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Moslem Abolhassani
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Vahid Moazed
- Department of Hematology and Oncology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Ghasem Ebrahimi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Fallah
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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20
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[Bioinformatics Analysis of DNA Methylation in the Promoters of LincRNA
in Lung Adenocarcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2018; 21:470-475. [PMID: 29945706 PMCID: PMC6022035 DOI: 10.3779/j.issn.1009-3419.2018.06.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Previous studies have found the lincRNAs play important roles in the occurrence and development of lung adenocarcinoma, but their regulated mechanims are still unclear. The aim of this study is to evaluate the relationship between DNA methylation and lincRNA expression, and the effect of prognosis in lung adenocarcinoma. METHODS The whole genome Illumina Methylation 450 DNA methylatiuon data and RNAseq for lung adenocarcinoma were download from TCGA. DNA methylation around lincRNA and their relationship to gene expression were analyzed. Their contribution to lung adenocarcinoma were further analyzed by comparing DNA methylation and lincRNA expression in tumor and adjacent tissues. RESULTS The methylation level in promoter region was lower than other positions in lincRNA, and was negatively correlated with gene expression. There were 427 lincRNA genes showed differential DNA methylation in their promoter regions in tumor and adjacent tissues. Among these, 15 lincRNA genes showed differential gene expression and negatively correlated with DNA methylation, including FENDRR (a tumor progression and metastasis gene) whose high methylation in its promoter showed poor survival in lung adenocarcinoma. CONCLUSIONS The expression of lincRNA can be regulated by DNA methylation in their promoter regions, and the level of DNA methylation is related to patient prognosis in lung adenocarcinoma.
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21
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Zhou N, Gu Q. Prognostic and clinicopathological value of p16 protein aberrant expression in colorectal cancer: A PRISMA-compliant Meta-analysis. Medicine (Baltimore) 2018; 97:e0195. [PMID: 29561443 PMCID: PMC5895319 DOI: 10.1097/md.0000000000010195] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Several studies have examined the potential role of p16 protein expression as a diagnostic and prognostic biomarker in various cancers. However, it remains unclear whether p16 protein expression is a prognostic and diagnostic factor for colorectal cancer. Therefore, this meta-analysis is conducted to evaluate the associations of p16 protein expression with overall survival (OS) and clinicopathological characteristics of colorectal cancer. METHODS According to PRISMA guideline, relevant literatures were identified by searching Medicine, Web of Science, WanFang, and CNKI databases. The pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were extracted from included studies to assess the association between p16 protein expression and OS of patients with colorectal cancer. Other relevant data were extracted to evaluate the correlations of p16 protein expression with risk and clinicopathological characteristics of colorectal cancer. Stata 12.0 software was applied to calculate the strength of association between p16 protein expression and colorectal cancer. RESULTS Forty-one studies were included to evaluate the association between p16 protein expression and colorectal cancer. Nine studies involving 1731 patients with colorectal cancer found that there was no association between p16 protein expression and OS of colorectal cancer in the overall analysis (HR = 0.78, 95% CI: 0.55-1.10). However, p16 protein overexpression was significantly associated with a better prognosis in patients with colorectal cancer when cut-off value of p16 protein expression was <10% (HR = 0.23, 95% CI: 0.08-0.66). The results of subgroup analysis based on ethnicity indicated that p16 protein overexpression was a risk factor for the occurrence of colorectal cancer in Caucasians (odds ratio = 28.95, 95% CI: 6.08-137.89), but not in Asians. Furthermore, p16 protein overexpression was significantly associated with the Dukes stage, lymph node metastasis, tumor location, and Tumor Lymph Node Metastasis-stage of colorectal cancer. CONCLUSIONS p16 protein overexpression might be a useful biomarker to predict the clinicopathological progress and prognosis of colorectal cancer.
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22
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Chen L, Wang Y, Liu F, Xu L, Peng F, Zhao N, Fu B, Zhu Z, Shi Y, Liu J, Wu R, Wang C, Yao S, Li Y. A systematic review and meta-analysis: Association between MGMT hypermethylation and the clinicopathological characteristics of non-small-cell lung carcinoma. Sci Rep 2018; 8:1439. [PMID: 29362385 PMCID: PMC5780517 DOI: 10.1038/s41598-018-19949-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 01/10/2018] [Indexed: 12/21/2022] Open
Abstract
The relationship between O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation and clinicopathological characteristics of non-small-cell lung carcinoma (NSCLC) has remained controversial and unclear. Therefore, in this study we have undertaken a systematic review and meta-analysis of relevant studies to quantitatively investigate this association. We identified 30 eligible studies investigating 2714 NSCLC patients. The relationship between MGMT hypermethylation and NSCLC was identified based on 20 studies, including 1539 NSCLC patient tissue and 1052 normal and adjacent tissue samples (OR = 4.60, 95% CI = 3.46~6.11, p < 0.00001). MGMT methylation varied with ethnicity (caucasian: OR = 4.56, 95% CI = 2.63~7.92, p < 0.00001; asian: OR = 5.18, 95% CI = 2.03~13.22, p = 0.0006) and control style (autologous: OR = 4.44, 95% CI = 3.32~5.92, p < 0.00001; heterogeneous: OR = 9.05, 95% CI = 1.79~45.71, p = 0.008). In addition, MGMT methylation was observed to be specifically associated with NSCLC clinical stage, and not with age, sex, smoking, pathological types, and differentiation status. Also MGMT methylation did not impact NSCLC patients survival (HR = 1.32, 95% CI = 0.77~2.28, p = 0.31). Our study provided clear evidence about the association of MGMT hypermethylation with increased risk of NSCLC.
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Affiliation(s)
- Lin Chen
- Department of Internal Neurology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Yong Wang
- Department of Medical Oncology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Fen Liu
- Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Liyao Xu
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Feifei Peng
- Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Ning Zhao
- Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Biqi Fu
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Zijie Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Yu Shi
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China
| | - Jiansheng Liu
- Department of Medical Oncology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Renrui Wu
- Department of Internal Neurology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Chen Wang
- Department of Internal Neurology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Shengmin Yao
- Department of Internal Neurology, The Affiliated Ganzhou Hospital of Nanchang University (Ganzhou People's Hospital), Ganzhou, Jiangxi, 341000, China
| | - Yong Li
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchan, Jiangxi, 330000, China.
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Abstract
Lung cancer is the leading cause of cancer-related deaths in the world. Despite significant advances in the early detection and treatment of the disease, the prognosis remains poor, with an overall 5-year survival rate ranging from 15% to 20%. This poor prognosis results largely from early micrometastatic spread of cancer cells to nearby lymph nodes or tissues and partially from early recurrence after curative surgical resection. Recently, precision medicines that target potential oncogenic driver mutations have been approved to treat lung cancer. However, some lung cancer patients do not have targetable mutations, and many patients develop resistance to targeted therapy. Tumor heterogeneity and mutational density are also challenges in treating lung cancer, which underscores the need for developing alternative therapeutic strategies for treating lung cancer. Epigenetic therapy may circumvent the problems of tumor heterogeneity and drug resistance by affecting the expression of several hundred target genes. This review highlights precision medicine using an innovative approach of epigenetic priming prior to conventional standard therapy or targeted cancer therapy in lung cancer.
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Affiliation(s)
- Dongho Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea. .,Samsung Medical Center, Research Institute for Future Medicine, Seoul, South Korea.
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24
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Development of diagnostic model of lung cancer based on multiple tumor markers and data mining. Oncotarget 2017; 8:94793-94804. [PMID: 29212267 PMCID: PMC5706913 DOI: 10.18632/oncotarget.21935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/26/2017] [Indexed: 01/14/2023] Open
Abstract
Objective To develop early intelligent discriminative model of lung cancer and evaluate the efficiency of diagnosis value. Methods Based on the genetic polymorphism profile of CYP1A1-rs1048943, GSTM1, mEH-rs1051740, XRCC1-rs1799782 and XRCC1-rs25489 and the methylations of p16 and RASSF1A gene, and the length of telomere in the peripheral blood from 200 lung cancer patients and 200 health persons, the discriminative model was established through decision tree and ANN technique. Results ACU of the discriminative model based on multiple tumour markers increased by about 10%; The accuracy rate of decision tree model and ANN model for testing set were 93.00% and 89.62% respectively. The ROC analysis showed the decision tree model’s AUC is 0.929 (0.894∼0.964), the ANN model’s AUC is 0.894 (0.853∼0.935). However, the classify accuracy rate and AUC of Fisher discriminatory analysis model are all about 0.7. Conclusion The early intelligent discriminative model of lung cancer based on multiple tumor markers and data mining techniques has a higher accuracy rate and might be useful for early diagnosis of lung cancer.
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25
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Christmann M, Kaina B. Epigenetic regulation of DNA repair genes and implications for tumor therapy. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:15-28. [PMID: 31395346 DOI: 10.1016/j.mrrev.2017.10.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/31/2022]
Abstract
DNA repair represents the first barrier against genotoxic stress causing metabolic changes, inflammation and cancer. Besides its role in preventing cancer, DNA repair needs also to be considered during cancer treatment with radiation and DNA damaging drugs as it impacts therapy outcome. The DNA repair capacity is mainly governed by the expression level of repair genes. Alterations in the expression of repair genes can occur due to mutations in their coding or promoter region, changes in the expression of transcription factors activating or repressing these genes, and/or epigenetic factors changing histone modifications and CpG promoter methylation or demethylation levels. In this review we provide an overview on the epigenetic regulation of DNA repair genes. We summarize the mechanisms underlying CpG methylation and demethylation, with de novo methyltransferases and DNA repair involved in gain and loss of CpG methylation, respectively. We discuss the role of components of the DNA damage response, p53, PARP-1 and GADD45a on the regulation of the DNA (cytosine-5)-methyltransferase DNMT1, the key enzyme responsible for gene silencing. We stress the relevance of epigenetic silencing of DNA repair genes for tumor formation and tumor therapy. A paradigmatic example is provided by the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT), which is silenced in up to 40% of various cancers through CpG promoter methylation. The CpG methylation status of the MGMT promoter strongly correlates with clinical outcome and, therefore, is used as prognostic marker during glioblastoma therapy. Mismatch repair genes are also subject of epigenetic silencing, which was shown to correlate with colorectal cancer formation. For many other repair genes shown to be epigenetically regulated the clinical outcome is not yet clear. We also address the question of whether genotoxic stress itself can lead to epigenetic alterations of genes encoding proteins involved in the defense against genotoxic stress.
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Affiliation(s)
- Markus Christmann
- Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
| | - Bernd Kaina
- Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany.
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26
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Sobieszkoda D, Czech J, Gablo N, Kopanska M, Tabarkiewicz J, Kolacinska A, Robak T, Zawlik I. MGMT promoter methylation as a potential prognostic marker for acute leukemia. Arch Med Sci 2017; 13:1433-1441. [PMID: 29181075 PMCID: PMC5701700 DOI: 10.5114/aoms.2017.71067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023] Open
Abstract
INTRODUCTION It has been proved that genetic and epigenetic changes play a significant role in the development and progression of acute leukemia. The aim of our study was to evaluate the frequency and prognostic implications of genetic and epigenetic alterations in p15, MGMT, DNMT3A and TP53 genes in acute leukemias. MATERIAL AND METHODS We included in the study 59 patients with acute leukemia. Evaluation of TP53 and DNMT3A mutations was performed using sequencing analysis and PCR-RFLP, respectively. Methylation status of MGMT and p15 genes was evaluated using MSP and COBRA, respectively. For assessment of global DNA methylation ELISA-based kit was used. RESULTS We found that overall survival was higher for ALL patients. MGMT promoter methylation was significantly associated with patients age at the time of diagnosis (p = 0.03). TP53 and DNMT3A mutations were observed only in AML patients (16.67% and 8.8%, respectively). Patients with acute leukemia and p15 promoter methylation had significantly more frequently mutated TP53 gene (p = 0.04) and AML patients with p15 promoter methylation had significantly more frequently detected global hypomethylation of DNA (p = 0.009). In the group of ALL patients we noted an opposite trend: only patients negative for p15 promoter methylation were characterized by global DNA hypomethylation. CONCLUSIONS Our findings demonstrate that MGMT promoter methylation can have a considerable impact on the development of acute leukemia in older patients. DNMT3A and TP53 mutations may play a significant role in AML development. However, further studies conducted in a larger cohort of patients are needed to determine its clinical utility.
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Affiliation(s)
- Dominika Sobieszkoda
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Joanna Czech
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Natalia Gablo
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Marta Kopanska
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Jacek Tabarkiewicz
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Immunology, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Agnieszka Kolacinska
- Department of Head and Neck Cancer Surgery, Medical University of Lodz, Lodz, Poland
- Department of Surgical Oncology, Cancer Center, Copernicus Memorial Hospital, Lodz, Poland
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Copernicus Memorial Hospital, Lodz, Poland
| | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
- Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
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27
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Barrow TM, Klett H, Toth R, Böhm J, Gigic B, Habermann N, Scherer D, Schrotz-King P, Skender S, Abbenhardt-Martin C, Zielske L, Schneider M, Ulrich A, Schirmacher P, Herpel E, Brenner H, Busch H, Boerries M, Ulrich CM, Michels KB. Smoking is associated with hypermethylation of the APC 1A promoter in colorectal cancer: the ColoCare Study. J Pathol 2017; 243:366-375. [PMID: 28791728 DOI: 10.1002/path.4955] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 07/02/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022]
Abstract
Smoking tobacco is a known risk factor for the development of colorectal cancer and for mortality associated with the disease. Smoking has been reported to be associated with changes in DNA methylation in blood and in lung tumour tissues, although there has been scant investigation of how epigenetic factors may be implicated in the increased risk of developing colorectal cancer. To identify epigenetic changes associated with smoking behaviours, we performed epigenome-wide analysis of DNA methylation in colorectal tumours from 36 never-smokers, 47 former smokers, and 13 active smokers, and in adjacent mucosa from 49 never-smokers, 64 former smokers, and 18 active smokers. Our analyses identified 15 CpG sites within the APC 1A promoter that were significantly hypermethylated and 14 CpG loci within the NFATC1 gene body that were significantly hypomethylated (pLIS < 1 × 10-5 ) in the tumours of active smokers. The APC 1A promoter was hypermethylated in 7 of 36 tumours from never-smokers (19%), 12 of 47 tumours from former smokers (26%), and 8 of 13 tumours from active smokers (62%). Promoter hypermethylation was positively associated with duration of smoking (Spearman rank correlation, ρ = 0.26, p = 0.03) and was confined to tumours, with hypermethylation never being observed in adjacent mucosa. Further analysis of adjacent mucosa revealed significant hypomethylation of four loci associated with the TNXB gene in tissue from active smokers. Our findings provide exploratory evidence for hypermethylation of the key tumour suppressor gene APC being implicated in smoking-associated colorectal carcinogenesis. Further work is required to establish the validity of our observations in independent cohorts. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Timothy M Barrow
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hagen Klett
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Reka Toth
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Böhm
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Biljana Gigic
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Surgical Oncology, University Clinic Heidelberg, Heidelberg, Germany
| | - Nina Habermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Skender
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clare Abbenhardt-Martin
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lin Zielske
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Department of Surgical Oncology, University Clinic Heidelberg, Heidelberg, Germany
| | - Alexis Ulrich
- Department of Surgical Oncology, University Clinic Heidelberg, Heidelberg, Germany
| | - Peter Schirmacher
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of General Pathology, University Clinic Heidelberg, Heidelberg, Germany
| | - Esther Herpel
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of General Pathology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.,Lübeck Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Cornelia M Ulrich
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Population Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Karin B Michels
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.,Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, California, USA
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28
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张 少, 薛 志. [Progress of Epigenetic Methylation in Lung Cancer Research]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2017; 20:635-640. [PMID: 28935018 PMCID: PMC5973367 DOI: 10.3779/j.issn.1009-3419.2017.09.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/20/2017] [Accepted: 05/12/2017] [Indexed: 11/28/2022]
Abstract
Lung cancer is becoming an increasing threat to Chinese residents and its incidence continues to rise while the treatment effect is far from satisfactory. Hence, it is essential to improve the level of early diagnosis, treatment, prognosis in lung cancer. An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence. The epigenetic studies, such as DNA methylation and histone methylation, are progressing rapidly in oncology research. A comprehensive understanding of its development status and existing problems is of great significance for the future research and the implementation of precision medicine. Herein, we aim to outline the progress of DNA methylation and histone methylation modification in lung cancer and make a prospect for the future research.
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Affiliation(s)
- 少伟 张
- />100853 北京,中国人民解放军总医院胸外科一病区Department of Toracic Surgery, PLA General Hospital, Beijing 100853, China
| | - 志强 薛
- />100853 北京,中国人民解放军总医院胸外科一病区Department of Toracic Surgery, PLA General Hospital, Beijing 100853, China
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29
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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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30
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Gaballah IF, Helal SF, Mourad BH. Early detection of lung cancer potential among Egyptian wood workers. INTERNATIONAL JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH 2017; 23:120-127. [PMID: 29359635 PMCID: PMC6060858 DOI: 10.1080/10773525.2018.1428265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023]
Abstract
Wood dust is known to be a human carcinogen, with a considerable risk of lung cancer. The increased cancer risk is likely induced through its genotoxic effects resulting from oxidative DNA damage. This study aimed at assessing the genotoxicity of wood dust and demonstrating the role of sputum PCR as a screening tool for early prediction of lung cancer among wood workers. The study was carried out in the carpentry section of a modernized factory involved with the manufacture of wooden furniture in Greater Cairo, Egypt. Environmental assessment of respirable wood dust concentrations was done. Frequency of chromosomal aberrations (CA%) and sister chromatid exchanges (SCE%) in peripheral blood lymphocytes (PBL) was assessed and comet assays were performed in samples from among the study population (n = 86). Levels of superoxide dismutase (SOD) and glutathione peroxidase (GPx) enzymes were measured. The polymerase chain reaction (PCR) was used to study hypermethylation of p16 and ̸or O6-methylguanine-DNA methyltransferase (MGMT) gene promoters in sputum DNA. The concentrations of respirable wood dust exceeded the Egyptian and international permissible limits with highest levels generated by sawing operations. Laboratory investigations revealed statistically significantly higher frequencies of CA and SCE as well as increased comet tail length associated with significant decrement in the levels of SOD and GPx among exposed group. A statistically significant elevation in the extent of hypermethylation was detected for the p16 and MGMT gene promoters in the sputum DNA of studied wood workers. The study results support the conclusion that prolonged unprotected occupational exposure to wood dust is associated with possible genotoxicity and oxidative stress that might raise the risk for carcinogenesis including lung cancer.
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31
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Molecular Genetic and Epigenetic Basis of Multiple Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 958:65-90. [DOI: 10.1007/978-3-319-47861-6_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Alkuhlani A, Nassef M, Farag I. Multistage feature selection approach for high-dimensional cancer data. Soft comput 2016. [DOI: 10.1007/s00500-016-2439-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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33
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Regulatory roles of epigenetic modulators, modifiers and mediators in lung cancer. Semin Cancer Biol 2016; 42:4-12. [PMID: 27840279 DOI: 10.1016/j.semcancer.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 12/19/2022]
Abstract
Lung cancer as the leading cause of cancer-related deaths can be initiated and progressed by the interaction between dynamically genetic and epigenetic elements, although mechanisms mediating lung cancer development and progression remain unclear. Tumor progenitor genes may contribute to lung carcinogenesis and cancer progression, are epigenetically disrupted at the early stages of malignancies even before mutations, and alter cell differentiation throughout tumor evolution. The present review explores potential roles and mechanisms of epigenetic modulators, modifiers and mediators in the development of lung cancer. We also overviewed potential mechanisms by which epigenetic modulators, modifiers and mediators control and regulate 3D nuclear architectures, and discussed translational efforts to epigenetic modifications for treatment of lung cancer. Deep understanding of epigenetic modulators, modifiers and mediators will benefit the discovery and development of new diagnostics and therapies for lung cancer.
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34
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Methylation of MGMT Is Associated with Poor Prognosis in Patients with Stage III Duodenal Adenocarcinoma. PLoS One 2016; 11:e0162929. [PMID: 27643594 PMCID: PMC5028050 DOI: 10.1371/journal.pone.0162929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/30/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND O6-methylguanine-DNA methyltransferase (MGMT) methylation status has not been extensively investigated in duodenal adenocarcinoma (DA). The aim of this study was to evaluate the MGMT methylation status and examine its possible prognostic value in patients with stage III DA. METHODS Demographics, tumor characteristics and survival were available for 64 patients with stage III DA. MGMT methylation was detected by using MethyLight. A Cox proportional hazard model was built to predict survival, adjusted for clinicopathological characteristics and tumor molecular features, including the CpG island methylator phenotype (CIMP), microsatellite instability (MSI), and KRAS mutations. RESULTS MGMT methylation was detected in 17 of 64 (26.6%) patients, and was not correlated with sex, age, tumor differentiation, CIMP, MSI, or KRAS mutations. MGMT methylation was the only one factor associated with both overall survival (OS) and disease-free survival (DFS) on both univariate and multivariate analyses. In patients treated with surgery alone, MGMT-methylated group had worse OS and DFS when compared with MGMT-unmethylated group. However, in patients treated with chemotherapy/radiotherapy, outcomes became comparable between the two groups. CONCLUSIONS Our results demonstrate MGMT methylation is a reliable and independent prognostic factor in DAs. Methylation of MGMT is associated with poor prognosis in patients with stage III DAs.
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35
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Shen Z, Zhou C, Li J, Ye D, Li Q, Wang J, Cui X, Chen X, Bao T, Duan S. Promoter hypermethylation of miR-34a contributes to the risk, progression, metastasis and poor survival of laryngeal squamous cell carcinoma. Gene 2016; 593:272-6. [PMID: 27450916 DOI: 10.1016/j.gene.2016.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 12/12/2022]
Abstract
MiR-34a is a direct transcriptional target of p53, which induces cell cycle arrest, senescence, and apoptosis. Recently, we and others identified abnormal expression of miR-34a in laryngeal squamous cell carcinoma (LSCC). The aim of our present study was to investigate the contribution of miR-34a promoter methylation to LSCC. Bisulfite pyrosequencing technology was applied to measure DNA methylation levels of six CpG sites in the miR-34a promoter from 104 LSCC tumor tissues and their corresponding adjacent tissues. Our results showed that the methylation levels of the miR-34a promoter were significantly higher in cancer tissues compared with the adjacent tissues (adjusted P=5.05E-10). A breakdown analysis for cigarette smoking behavior indicated a significantly elevated tendency of miR-34a methylation level in LSCC patients with smoking behavior but not in LSCC patients without smoking behavior (Smoking: Tumor vs Normal, adjusted P=3.12E-9; Non-smoking: Tumor vs Normal, adjusted P=0.073). In addition, miR-34a promoter methylation frequency remarkably increased in the advanced stage patients (adjusted P=0.003) and advanced T classified tumors (adjusted P=0.015). Moreover, significant association of miR-34a promoter hypermethylation with LSCC lymph metastasis was observed (adjusted P=0.002). Meanwhile, Kaplan-Meier survival curves results showed that high methylation of miR-34a promoter were associated with poor overall survival (log-rank test, P=0.023). Our study revealed that miR-34a promoter hypermethylation was a risk factor for LSCC, played a critical role in the disease progression and metastasis, and could serve as a poor prognostic factor for LSCC.
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Affiliation(s)
- Zhisen Shen
- Lihuili Hospital of Ningbo University, Ningbo 315040, China.
| | - Chongchang Zhou
- Lihuili Hospital of Ningbo University, Ningbo 315040, China; The Medical School of Ningbo University, Ningbo 315211, China
| | - Jinyun Li
- The Medical School of Ningbo University, Ningbo 315211, China
| | - Dong Ye
- Lihuili Hospital of Ningbo University, Ningbo 315040, China
| | - Qun Li
- Lihuili Hospital of Ningbo University, Ningbo 315040, China
| | - Jian Wang
- Lihuili Hospital of Ningbo University, Ningbo 315040, China; The Medical School of Ningbo University, Ningbo 315211, China
| | - Xiang Cui
- Lihuili Hospital of Ningbo University, Ningbo 315040, China; The Medical School of Ningbo University, Ningbo 315211, China
| | - Xiaoying Chen
- The Medical School of Ningbo University, Ningbo 315211, China
| | - Tianlian Bao
- The Medical School of Ningbo University, Ningbo 315211, China
| | - Shiwei Duan
- The Medical School of Ningbo University, Ningbo 315211, China.
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The Impact of External Factors on the Epigenome: In Utero and over Lifetime. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2568635. [PMID: 27294112 PMCID: PMC4887632 DOI: 10.1155/2016/2568635] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 01/07/2023]
Abstract
Epigenetic marks change during fetal development, adult life, and aging. Some changes play an important role in the establishment and regulation of gene programs, but others seem to occur without any apparent physiological role. An important future challenge in the field of epigenetics will be to describe how the environment affects both of these types of epigenetic change and to learn if interaction between them can determine healthy and disease phenotypes during lifetime. Here we discuss how chemical and physical environmental stressors, diet, life habits, and pharmacological treatments can affect the epigenome during lifetime and the possible impact of these epigenetic changes on pathophysiological processes.
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37
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Ansari J, Shackelford RE, El-Osta H. Epigenetics in non-small cell lung cancer: from basics to therapeutics. Transl Lung Cancer Res 2016; 5:155-71. [PMID: 27186511 DOI: 10.21037/tlcr.2016.02.02] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer remains the number one cause of cancer-related deaths worldwide with 221,200 estimated new cases and 158,040 estimated deaths in 2015. Approximately 80% of cases are non-small cell lung cancer (NSCLC). The diagnosis is usually made at an advanced stage where the prognosis is poor and therapeutic options are limited. The evolution of lung cancer is a multistep process involving genetic, epigenetic, and environmental factor interactions that result in the dysregulation of key oncogenes and tumor suppressor genes, culminating in activation of cancer-related signaling pathways. The past decade has witnessed the discovery of multiple molecular aberrations that drive lung cancer growth, among which are epidermal growth factor receptor (EGFR) mutations and translocations involving the anaplastic lymphoma kinase (ALK) gene. This has translated into therapeutic agent developments that target these molecular alterations. The absence of targetable mutations in 50% of NSCLC cases and targeted therapy resistance development underscores the importance for developing alternative therapeutic strategies for treating lung cancer. Among these strategies, pharmacologic modulation of the epigenome has been used to treat lung cancer. Epigenetics approaches may circumvent the problem of tumor heterogeneity by affecting the expression of multiple tumor suppression genes (TSGs), halting tumor growth and survival. Moreover, it may be effective for tumors that are not driven by currently recognized druggable mutations. This review summarizes the molecular pathology of lung cancer epigenetic aberrations and discusses current efforts to target the epigenome with different pharmacological approaches. Our main focus will be on hypomethylating agents, histone deacetylase (HDAC) inhibitors, microRNA modulations, and the role of novel epigenetic biomarkers. Last, we will address the challenges that face this old-new strategy in treating lung cancer.
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Affiliation(s)
- Junaid Ansari
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Rodney E Shackelford
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Hazem El-Osta
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
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Jin Y, Xu P, Liu X, Zhang C, Tan C, Chen C, Sun X, Xu Y. Cigarette Smoking, BPDE-DNA Adducts, and Aberrant Promoter Methylations of Tumor Suppressor Genes (TSGs) in NSCLC from Chinese Population. Cancer Invest 2016; 34:173-80. [PMID: 27042875 DOI: 10.3109/07357907.2016.1156689] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Non-small cell lung cancer (NSCLC) is related to the genetic and epigenetic factors. The goal of this study was to determine association of cigarette smoking and BPDE-DNA adducts with promoter methylations of several genes in NSCLC. Methylation of the promoters of p16, RARβ, DAPK, MGMT, and TIMP-3 genes of tumor tissues from 199 lung cancer patients was analyzed with methylation-specific PCR (MSP), and BPDE-DNA adduct level in lung cancer tissue was obtained by ELISA. Level of BPDE-DNA adduct increased significantly in males, aged people (over 60 years), and smokers; however, no significant difference was found while comparing the BPDE-DNA adduct levels among different tumor types, locations, and stages. Cigarette smoking was also associated with increased BPDE-DNA adducts level (OR = 2.43, p > .05) and increased methylation level in at least 1 gene (OR = 5.22, p < .01), both in dose-response manner. Similarly, cigarette smoking also significantly increase the risk of p16 or DAPK methylation (OR = 3.02, p < .05 for p16, and 3.66, p < .05 for DAPK). The highest risk of BPDE-DNA adducts was detected among individuals with cigarette smoking for more than 40 pack-years (OR = 4.21, p < .01). Furthermore, the present study did not show that BPDE-DNA adducts are significantly associated with abnormal TSGs methylations in NSCLC, including SCC and AdO, respectively. Conclusively, cigarette smoking is significantly associated with the increase of BPDE-DNA adduct level, promoter hypermethylation of p16 and DAPK genes, while BPDE-DNA adduct was not significantly related to abnormal promoter hypermethylation in TSGs, suggesting that BPDE-DNA adducts and TSGs methylations play independent roles in NSCLC.
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Affiliation(s)
- Yongtang Jin
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Peiwei Xu
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Xinneng Liu
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Chunye Zhang
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Cong Tan
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Chunmei Chen
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Xiaoyu Sun
- a Department of Environmental Medicine, Zhejiang University School of Medicine, Zhejiang University , Hangzhou , China
| | - Yingchun Xu
- b Institute of Pharmacology, Zhejiang University School of Pharmacology, Zhejiang University , Hangzhou , China
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Xiao FH, Kong QP, Perry B, He YH. Progress on the role of DNA methylation in aging and longevity. Brief Funct Genomics 2016; 15:454-459. [PMID: 27032421 DOI: 10.1093/bfgp/elw009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aging is a major risk factor for individuals' health problems. Moreover, environmental signals have a widespread influence on the aging process. Epigenetic modification, e.g. DNA methylation, represents a link between genetic and environmental signals via the regulation of gene transcription. An abundance of literature indicates that aberrant epigenetic change occurs throughout the aging process at both the cellular and the organismal level. In particular, DNA methylation presents globally decreasing and site-specific increasing in aging. In this review, we focus on the crucial roles of DNA methylation in aging and age-related disease and highlight the great potential of DNA methylation as a therapeutic target in preventing age-related diseases and promoting healthy longevity.
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Abstract
Tobacco smoking is the most common cause of lung cancer, but approximately 10–25% of patients with lung cancer are life-long never smokers. The cause of lung cancer in never smokers is unknown, although tobacco-smoke exposure may play a role in some of these patients. Lung cancer that develops in the absence of significant tobacco-smoke exposure appears to be a unique disease entity with novel genomic and epigenomic alterations and activation of molecular pathways that are not generally seen in tobacco-smoke-induced lung cancer. These molecular alterations are very likely responsible for the unique clinico-pathological features of lung cancer in never smokers (LCINS), and some of these molecular alterations – such as the activating EGFR TK mutations and EML4–ALK fusion – significantly influence therapeutic choices and treatment outcomes. In the last few years there has been a number of studies exploring the molecular characteristics of LCINS, and some of them have reported new and significant findings. Here we review the key findings from these studies and discuss their potential therapeutic implications.
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Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Viñuela A, Grundberg E, Nelson CP, Meduri E, Buil A, Cambien F, Hengstenberg C, Erdmann J, Schunkert H, Goodall AH, Ouwehand WH, Dermitzakis E, Spector TD, Samani NJ, Deloukas P. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2015; 9:1382-96. [PMID: 25424692 DOI: 10.4161/15592294.2014.969637] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Smoking is a major risk factor in many diseases. Genome wide association studies have linked genes for nicotine dependence and smoking behavior to increased risk of cardiovascular, pulmonary, and malignant diseases. We conducted an epigenome wide association study in peripheral-blood DNA in 464 individuals (22 current smokers and 263 ex-smokers), using the Human Methylation 450 K array. Upon replication in an independent sample of 356 twins (41 current and 104 ex-smokers), we identified 30 probes in 15 distinct loci, all of which reached genome-wide significance in the combined analysis P < 5 × 10(-8). All but one probe (cg17024919) remained significant after adjusting for blood cell counts. We replicated all 9 known loci and found an independent signal at CPOX near GPR15. In addition, we found 6 new loci at PRSS23, AVPR1B, PSEN2, LINC00299, RPS6KA2, and KIAA0087. Most of the lead probes (13 out of 15) associated with cigarette smoking, overlapped regions of open chromatin (FAIRE and DNaseI hypersensitive sites) or/and H3K27Ac peaks (ENCODE data set), which mark regulatory elements. The effect of smoking on DNA methylation was partially reversible upon smoking cessation for longer than 3 months. We report the first statistically significant interaction between a SNP (rs2697768) and cigarette smoking on DNA methylation (cg03329539). We provide evidence that the metSNP for cg03329539 regulates expression of the CHRND gene located circa 95 Kb downstream of the methylation site. Our findings suggest the existence of dynamic, reversible site-specific methylation changes in response to cigarette smoking , which may contribute to the extended health risks associated with cigarette smoking.
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Key Words
- AHRR, aryl-hydrocarbon receptor repressor
- ALPP, alkaline phosphatase, placental
- AVPR1B, arginine vasopressin
- CHRND
- CHRND, cholinergic nicotinic receptor
- COPD, chronic obstructive pulmonary disease
- CPOX
- CPOX, coproporphyrinogen oxidase
- DNA methylation
- DNMT, DNA methyltransferase
- EWAS, epigenome wide association study
- FDR, false discovery rate
- GWAS, genome-wide association studies
- PRSS23, serine protease 23
- PSEN2, presenilin-2 gene
- RPS6KA2, ribosomal protein S6 kinase
- epigenome-wide screen
- gene network
- metQTL, methylation quantitative trait loci
- metQTLs
- rs2697768
- smoking
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Zampieri M, Ciccarone F, Calabrese R, Franceschi C, Bürkle A, Caiafa P. Reconfiguration of DNA methylation in aging. Mech Ageing Dev 2015; 151:60-70. [PMID: 25708826 DOI: 10.1016/j.mad.2015.02.002] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 12/12/2022]
Abstract
A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.
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Affiliation(s)
- Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, Bologna 40126, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.
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Langevin SM, Kratzke RA, Kelsey KT. Epigenetics of lung cancer. Transl Res 2015; 165:74-90. [PMID: 24686037 PMCID: PMC4162853 DOI: 10.1016/j.trsl.2014.03.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/25/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality in the United States. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA expression, have been reported widely in the literature to play a major role in the genesis of lung cancer. The goal of this review is to summarize the common epigenetic changes associated with lung cancer to give some clarity to its etiology, and to provide an overview of the potential translational applications of these changes, including applications for early detection, diagnosis, prognostication, and therapeutics.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Robert A Kratzke
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minn
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI.
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MGMT gene silencing by promoter hypermethylation in gastric cancer in a high incidence area. Cell Oncol (Dordr) 2014; 37:245-52. [PMID: 25008999 DOI: 10.1007/s13402-014-0179-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Inactivation of tumor suppressor and DNA repair genes by promoter hypermethylation does commonly occur in human cancers. O(6)-methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that removes methyl groups as well as larger adducts at the O(6) position of guanine. In the absence of MGMT activity, O(6)-methylguanine mispairs with thymine during DNA replication, resulting in G:C to A:T transitions. Promoter hypermethylation of the MGMT gene has been observed in various cancers, including gastric cancer. Here, we aimed at assessing the promoter hypermethylation, mutation and expression status of the MGMT gene in patients from a geographic region with a high incidence of gastric cancer (Kashmir, North India) and to investigate their association with various clinicopathological characteristics. METHODS In this study 82 gastric cancer samples and adjacent normal tissues were included. Mutations in the MGMT gene were detected by single stranded conformational polymorphism (SSCP) analysis and direct sequencing. Methylation-specific polymerase chain reaction (MS-PCR) and Western blot analyses were performed to detect promoter hypermethylation and concomitant (loss of) expression of the MGMT gene. RESULTS Promoter hypermethylation of the MGMT gene was found in 52.44% (43 of 82) of the tumor samples and loss of MGMT protein expression was detected in 45.12% (37 of 82) of the tumor samples. Hypermethylation and loss of expression were significantly associated with higher tumor grades (moderately/poorly differentiated) (P < 0.05) and higher tumor stages (III/IV) (P < 0.05). In addition, MGMT hypermethylation and loss of expression were found to be significantly associated with high salt tea consumption (P < 0.05). CONCLUSIONS Our results indicate that MGMT promoter hypermethylation and concomitant loss of MGMT protein expression may play an important role in the development of gastric cancer in the Kashmiri population. High salt tea consumption may be a risk factor.
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Chen YZ, Liu D, Zhao YX, Wang HT, Gao Y, Chen Y. Relationships between p16 gene promoter methylation and clinicopathologic features of colorectal cancer: a meta-analysis of 27 cohort studies. DNA Cell Biol 2014; 33:729-38. [PMID: 24979649 DOI: 10.1089/dna.2013.2253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many existing studies have demonstrated that p16 promoter methylation might be correlated with the clinicopathologic features of colorectal cancer (CRC), but individually published results are inconclusive. This meta-analysis aimed to derive a more precise estimation of the relationships between p16 promoter methylation and the clinicopathologic features of CRC. We searched the CISCOM, CINAHL, Web of Science, PubMed, Google Scholar, EBSCO, Cochrane Library, and CBM databases from inception through August 1, 2013. Meta-analysis was performed using the STATA 12.0 software. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated under fixed- or random-effects models. Twenty-seven clinical cohort studies were included with a total of 3311 CRC patients. Our meta-analysis results revealed that p16 promoter methylation was associated with pathological characteristics of CRC (tumor, nodes, metastasis stage: OR=1.55, 95% CI: 1.14-2.13, p=0.006; lymph node metastasis: OR=2.40, 95% CI: 1.37-4.19, p=0.002; histologic grade: OR=2.72, 95% CI: 1.63-4.54, p<0.001; Dukes stage: OR=2.06, 95% CI: 1.57-2.71, p=0.002; tumor size: OR=1.99, 95% CI: 1.03-3.85, p=0.041; location: OR=2.49, 95% CI: 1.95-3.18, p<0.001, respectively). Subgroup analysis by ethnicity suggested that there were also significant correlations between p16 gene promoter methylation and pathological characteristics of CRC among both Caucasian and Asian populations (all p<0.05). Our meta-analysis suggests that promoter methylation of the p16 gene may be strongly correlated with the clinicopathologic features of CRC. Thus, p16 gene promoter methylation may be a potential biomarker for CRC.
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Affiliation(s)
- Yan-Zhi Chen
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University , Shenyang, People's Republic of China
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Shofer S, Beyea M, Li S, Bastian LA, Wahidi MM, Kelley M, Lipkus IM. Feasibility of using an epigenetic marker of risk for lung cancer, methylation of p16, to promote smoking cessation among US veterans. BMJ Open Respir Res 2014; 1:e000032. [PMID: 25478181 PMCID: PMC4212704 DOI: 10.1136/bmjresp-2014-000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/27/2014] [Accepted: 06/08/2014] [Indexed: 11/29/2022] Open
Abstract
Introduction Providing smokers feedback using epigenetic markers of lung cancer risk has yet to be tested as a strategy to motivate smoking cessation. Epigenetic modification of Rb-p16 (p16) due to tobacco exposure is associated with increased risk of developing lung cancer. This study examined the acceptance of testing for methylated p16 and the understanding of test results in smokers at risk for development of lung cancer. Methods Thirty-five current smokers with airways obstruction viewed an educational presentation regarding p16 function followed by testing for the presence of methylated p16 in sputum. Participants were offered smoking cessation assistance and asked to complete surveys at the time of enrolment regarding their understanding of the educational material, perception of risk associated with smoking and desire to quit. Participants were notified of their test result and follow-up surveys were administered 2 and 10 weeks after notification of their test result. Results Twenty per cent of participants had methylated p16. Participants showed high degree of understanding of educational materials regarding the function and risk associated with p16 methylation. Sixty-seven per cent and 57% of participants with low-risk and high-risk test results, respectively, reported that the information was more likely to motivate them to quit smoking. Smoking cessation rates were similar between methylated and non-methylated participants. Conclusions Testing for an epigenetic marker of lung cancer risk is accepted and understood by active smokers. A low-risk test result does not decrease motivation to stop smoking. Trial registration number NCT01038492.
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Affiliation(s)
- Scott Shofer
- Pulmonary Section , Durham Veteran Affairs Medical Center , Durham, North Carolina , USA ; Division of Pulmonary, Allergy, and Critical Care , Duke University Medical Center , Durham, North Carolina , USA
| | | | - Sufeng Li
- Division of Hematology/Oncology , Duke University Medical Center , Durham, North Carolina , USA
| | - Lori A Bastian
- Department of Internal Medicine , Veteran Administration Connecticut Healthcare System , West Haven, Connecticut , USA ; Department of Internal Medicine , University of Connecticut Health Center , Farmington, Connecticut , USA
| | - Momen M Wahidi
- Division of Pulmonary, Allergy, and Critical Care , Duke University Medical Center , Durham, North Carolina , USA
| | - Michael Kelley
- Division of Hematology/Oncology , Duke University Medical Center , Durham, North Carolina , USA ; Hematology and Oncology Section, Durham Veterans Affairs Medical Center, Durham, North Carolina , USA
| | - Isaac M Lipkus
- Duke University School of Nursing , Durham, North Carolina , USA
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Vogelsang M, Paccez JD, Schäfer G, Dzobo K, Zerbini LF, Parker MI. Aberrant methylation of the MSH3 promoter and distal enhancer in esophageal cancer patients exposed to first-hand tobacco smoke. J Cancer Res Clin Oncol 2014; 140:1825-33. [PMID: 24934723 DOI: 10.1007/s00432-014-1736-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/04/2014] [Indexed: 12/15/2022]
Abstract
PURPOSE Polymorphisms in MSH3 gene confer risk of esophageal cancer when in combination with tobacco smoke exposure. The purpose of this study was to investigate the methylation status of MSH3 gene in esophageal cancer patients in order to further elucidate possible role of MSH3 in esophageal tumorigenesis. METHODS We applied nested methylation-specific polymerase chain reaction to investigate the methylation status of the MSH3 promoter in tumors and matching adjacent normal-looking tissues of 84 esophageal cancer patients from a high-risk South African population. The Cancer Genome Atlas data were used to examine DNA methylation profiles at 17 CpG sites located in the MSH3 locus. RESULTS Overall, promoter methylation was detected in 91.9 % of tumors, which was significantly higher compared to 76.0 % in adjacent normal-looking esophageal tissues (P = 0.008). When samples were grouped according to different demographics (including age, gender and ethnicity) and smoking status of patients, methylation frequencies were found to be significantly higher in tumor tissues of Black subjects (P = 0.024), patients of 55-65 years of age (P = 0.032), males (P = 0.037) and tobacco smokers (P = 0.015). Furthermore, methylation of the MSH3 promoter was significantly more frequent in tumor samples from smokers compared to tumor samples from non-smokers [odds ratio (OR) = 31.9, P = 0.031]. The TCGA data confirmed significantly higher DNA methylation level at the MSH3 promoter region in tumors (P = 0.0024). In addition, we found evidence of an aberrantly methylated putative MSH3-associated distal enhancer element. CONCLUSION Our results suggest that methylation of MSH3 together with exposure to tobacco smoke is involved in esophageal carcinogenesis. Due to the active role of the MSH3 protein in modulating chemosensitivity of cells, methylation of MSH3 should further be examined in association with the outcome of esophageal cancer treatment using anticancer drugs.
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Affiliation(s)
- Matjaz Vogelsang
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, UCT Medical Campus, Anzio Road, Observatory, Cape Town, 7925, South Africa
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Promoter region hypermethylation and mRNA expression of MGMT and p16 genes in tissue and blood samples of human premalignant oral lesions and oral squamous cell carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:248419. [PMID: 24991542 PMCID: PMC4058681 DOI: 10.1155/2014/248419] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/23/2014] [Accepted: 05/13/2014] [Indexed: 01/09/2023]
Abstract
Promoter methylation and relative gene expression of O(6)-methyguanine-DNA-methyltransferase (MGMT) and p16 genes were examined in tissue and blood samples of patients with premalignant oral lesions (PMOLs) and oral squamous cell carcinoma (OSCC). Methylation-specific PCR and reverse transcriptase PCR were performed in 146 tissue and blood samples from controls and patients with PMOLs and OSCC. In PMOL group, significant promoter methylation of MGMT and p16 genes was observed in 59% (P = 0.0010) and 57% (P = 0.0016) of tissue samples, respectively, and 39% (P = 0.0135) and 33% (P = 0.0074) of blood samples, respectively. Promoter methylation of both genes was more frequent in patients with OSCC, that is, 76% (P = 0.0001) and 82% (P = 0.0001) in tissue and 57% (P = 0.0002) and 70% (P = 0.0001) in blood, respectively. Significant downregulation of MGMT and p16 mRNA expression was observed in both tissue and blood samples from patients with PMOLs and OSCC. Hypermethylation-induced transcriptional silencing of MGMT and p16 genes in both precancer and cancer suggests important role of these changes in progression of premalignant state to malignancy. Results support use of blood as potential surrogate to tissue samples for screening or diagnosing PMOLs and early OSCC.
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CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. J Thorac Oncol 2014; 8:1378-88. [PMID: 24077454 DOI: 10.1097/jto.0b013e3182a46c0c] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION CDKN2A (p16) inactivation is common in lung cancer and occurs via homozygous deletions, methylation of promoter region, or point mutations. Although p16 promoter methylation has been linked to KRAS mutation and smoking, the associations between p16 inactivation mechanisms and other common genetic mutations and smoking status are still controversial or unknown. METHODS We determined all three p16 inactivation mechanisms with the use of multiple methodologies for genomic status, methylation, RNA, and protein expression, and correlated them with EGFR, KRAS, STK11 mutations and smoking status in 40 cell lines and 45 tumor samples of primary non-small-cell lung carcinoma. We also performed meta-analyses to investigate the impact of smoke exposure on p16 inactivation. RESULTS p16 inactivation was the major mechanism of RB pathway perturbation in non-small-cell lung carcinoma, with homozygous deletion being the most frequent method, followed by methylation and the rarer point mutations. Inactivating mechanisms were tightly correlated with loss of mRNA and protein expression. p16 inactivation occurred at comparable frequencies regardless of mutational status of EGFR, KRAS, and STK11, however, the major inactivation mechanism of p16 varied. p16 methylation was linked to KRAS mutation but was mutually exclusive with EGFR mutation. Cell lines and tumor samples demonstrated similar results. Our meta-analyses confirmed a modest positive association between p16 promoter methylation and smoking. CONCLUSION Our results confirm that all the inactivation mechanisms are truly associated with loss of gene product and identify specific associations between p16 inactivation mechanisms and other genetic changes and smoking status.
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A critical re-assessment of DNA repair gene promoter methylation in non-small cell lung carcinoma. Sci Rep 2014; 4:4186. [PMID: 24569633 PMCID: PMC3935198 DOI: 10.1038/srep04186] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/13/2014] [Indexed: 12/14/2022] Open
Abstract
DNA repair genes that have been inactivated by promoter methylation offer potential therapeutic targets either by targeting the specific repair deficiency, or by synthetic lethal approaches. This study evaluated promoter methylation status for eight selected DNA repair genes (ATM, BRCA1, ERCC1, MGMT, MLH1, NEIL1, RAD23B and XPC) in 56 non-small cell lung cancer (NSCLC) tumours and 11 lung cell lines using the methylation-sensitive high resolution melting (MS-HRM) methodology. Frequent methylation in NEIL1 (42%) and infrequent methylation in ERCC1 (2%) and RAD23B (2%) are reported for the first time in NSCLC. MGMT methylation was detected in 13% of the NSCLCs. Contrary to previous studies, methylation was not detected in ATM, BRCA1, MLH1 and XPC. Data from The Cancer Genome Atlas (TCGA) was consistent with these findings. The study emphasises the importance of using appropriate methodology for accurate assessment of promoter methylation.
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