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Matulevičius A, Žukauskaitė K, Gineikaitė R, Dasevičius D, Trakymas M, Naruševičiūtė I, Ušinskienė J, Ulys A, Jankevičius F, Jarmalaitė S. Combination of DNA methylation biomarkers with multiparametric magnetic resonance and ultrasound imaging fusion biopsy to detect the local spread of prostate cancer. Prostate 2023; 83:1572-1583. [PMID: 37614027 DOI: 10.1002/pros.24615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/04/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND This study aimed to investigate the extent of field cancerization adjacent to index lesions in prostate cancer (PCa) by measuring DNA methylation of selected tumor suppressor genes in the perifocal tissue of PCa not visible on multiparametric magnetic resonanse imaging (mpMRI) for the safe zone of focal therapy identification. METHODS A total of 272 patients were enrolled in this study, 44 patients' tissue biosamples were included in the field cancerization research, and 272 urine samples were included in the urine-based test development. Targeted biopsies were performed using the mpMRI/ultrasoundimage fusion system. RESULTS Quantitative analysis revealed significantly higher DNA methylation levels of RARB, RASSF1, GSTP1 & APC genes in the index lesion compared with perifocal tissue samples 10 mm away from it (p < 0.0001). Notably, the RARB, GSTP1 & APC and RARB, RASSF1, GSTP1 & APC biomarker combinations exhibited the highest sensitivity and specificity comparing the extent of DNA methylation in index lesions and noncancerous prostate tissues 20 mm away (both area under the curve [AUC] = 0.98; p < 0.0001). The analysis of the potential urinary biomarkers showed that the combination of all four DNA methylation biomarkers with prostate-specific antigen (PSA) or PSA density (PSAD) in the blood significantly improves the detection of clinically significant PCa (csPCa). The combination of the four-biomarker test with PSAD allowed the identification of csPCa with ≥90% sensitivity and specificity. CONCLUSION Thus, this study suggests that for focal therapy by region target hemi-ablation, the safe distance from the index lesion is no less than 10 mm. Noninvasive urine DNA methylation tests in combination with PSAD could be used for further follow-up of the patients, but larger prospective studies with external validation are needed.
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Affiliation(s)
- Augustinas Matulevičius
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Kristina Žukauskaitė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
| | | | - Darius Dasevičius
- National Centre of Pathology, Affiliate of Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | | | | | | | | | - Feliksas Jankevičius
- Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaitė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
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Qiao R, Zhu Q, Di F, Liu C, Song Y, Zhang J, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Hypomethylation of DYRK4 in peripheral blood is associated with increased lung cancer risk. Mol Carcinog 2023; 62:1745-1754. [PMID: 37530470 DOI: 10.1002/mc.23612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. It is urgent to identify new biomarkers for the early detection of LC. DNA methylation in peripheral blood has been reported to be associated with cancers. We conducted two independent case-control studies and a nested case-control study (168 LC cases and 167 controls in study Ⅰ, 677 LC cases and 833 controls in study Ⅱ, 147 precancers and 21 controls in the nested case-control study). The methylation levels of DYRK4 CpG sites were measured using mass spectrometry and their correlations with LC were analyzed by logistic regression and nonparametric tests. Bonferroni correction was used for the multiple comparisons. LC-related decreased DYRK4 methylation was discovered in Study I and validated in Study II (the odds ratios [ORs] for the lowest vs. highest quartile of all three DYRK4 CpG sites ranged from 1.64 to 2.09, all p < 0.001). Combining the two studies, hypomethylation of DYRK4 was observed in stage I cases (ORs per -10% methylation ranged from 1.16 to 1.38, all p < 5.9E-04), and could be enhanced by male gender (ORs ranged from 1.77 to 4.17 via interquartile analyses, all p < 0.017). Hypomethylation of DYRK4_A_CpG_2 was significantly correlated with tumor size, length, and stage (p = 0.034, 0.002, and 0.002, respectively) in LC cases. Our study disclosed the association between DYRK4 hypomethylation in peripheral blood and LC, suggesting the feasibility of blood-based DNA methylation as new biomarker for LC detection.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Jin Zhang
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
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Saffron, Its Active Components, and Their Association with DNA and Histone Modification: A Narrative Review of Current Knowledge. Nutrients 2022; 14:nu14163317. [PMID: 36014823 PMCID: PMC9414768 DOI: 10.3390/nu14163317] [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: 06/16/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Intensive screening for better and safer medications to treat diseases such as cancer and inflammatory diseases continue, and some phytochemicals have been discovered to have anti-cancer and many therapeutical activities. Among the traditionally used spices, Crocus sativus (saffron) and its principal bioactive constituents have anti-inflammatory, antioxidant, and chemopreventive properties against multiple malignancies. Early reports have shown that the epigenetic profiles of healthy and tumor cells vary significantly in the context of different epigenetic factors. Multiple components, such as carotenoids as bioactive dietary phytochemicals, can directly or indirectly regulate epigenetic factors and alter gene expression profiles. Previous reports have shown the interaction between active saffron compounds with linker histone H1. Other reports have shown that high concentrations of saffron bind to the minor groove of calf thymus DNA, resulting in specific structural changes from B- to C-form of DNA. Moreover, the interaction of crocin G-quadruplex was reported. A recent in silico study has shown that residues of SIRT1 interact with saffron bio-active compounds and might enhance SIRT1 activation. Other reports have shown that the treatment of Saffron bio-active compounds increases γH2AX, decreases HDAC1 and phosphorylated histone H3 (p-H3). However, the question that still remains to be addressed how saffron triggers various epigenetic changes? Therefore, this review discusses the literature published till 2022 regarding saffron as dietary components and its impact on epigenetic mechanisms. Novel bioactive compounds such as saffron components that lead to epigenetic alterations might be a valuable strategy as an adjuvant therapeutic drug.
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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Li R, Shui L, Jia J, Wu C. Construction and Validation of Novel Diagnostic and Prognostic DNA Methylation Signatures for Hepatocellular Carcinoma. Front Genet 2020; 11:906. [PMID: 32922438 PMCID: PMC7456968 DOI: 10.3389/fgene.2020.00906] [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: 01/11/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent life-threatening human cancers and the leading cause of cancer-related mortality, with increased global incidence within the last decade. Identification of effective diagnostic and prognostic biomarkers would enable reliable risk stratification and efficient screening of high-risk patients, thereby facilitating clinical decision-making. Herein, we performed a comprehensive, robust DNA methylation analysis based on genome-wide DNA methylation profiling. We constructed a diagnostic signature with five DNA methylation markers, which precisely distinguished HCC patients from normal controls. Cox regression and LASSO analysis were applied to construct a prognostic signature with four DNA methylation markers. A one-to-one correlation analysis was carried out between genes of the whole genome and our prognostic signature. Exploration of the biological function and the role of the underlying significantly correlated genes was conducted. A mixed dataset of 463 HCC patients and 253 normal controls, derived from six independent datasets, was used to valid the diagnostic signature. Results showed a specificity of 96.84% and sensitivity of 96.77%. Class scores for the diagnostic signature were significantly different between normal controls, individuals with liver diseases, and HCC patients. The present signature has the potential to serve as a biomarker to monitor health in normal controls. Additionally, HCC patients were successfully separated into low-risk and high-risk groups by the prognostic signature, with a better prognosis for patients in the low-risk group. Kaplan-Meier and ROC analysis confirmed that the prognostic signature performed well. We found eight of the top ten genes to positively correlate with risk scores of the prognostic signature, and to be involved in cell cycle regulation. This eight-gene panel also served as a prognostic signature. The robust evidence presented in this study therefore demonstrates the effectiveness of the prognostic signature. In summary, we constructed diagnostic and prognostic signatures, which have potential for use in diagnosis, surveillance, and prognostic prediction for HCC patients. Eight genes that were significantly and positively correlated with the prognostic signature were strongly associated with cell cycle processes. Therefore, the prognostic signature can be used as a guide by which to measure responsiveness to cell-cycle-targeting agents.
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Affiliation(s)
- Ran Li
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Liyan Shui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junling Jia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for Precision Medicine, Zhongtong-Lanbo Diagnostic Ltd, Beijing, China
| | - Chao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Metere A, Graves CE. Factors Influencing Epigenetic Mechanisms: Is There A Role for Bariatric Surgery? High Throughput 2020; 9:ht9010006. [PMID: 32244851 PMCID: PMC7151212 DOI: 10.3390/ht9010006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is the interaction between the genome and environmental stimuli capable of influencing gene expression during development and aging. A large number of studies have shown that metabolic diseases are highly associated with epigenetic alterations, suggesting that epigenetic factors may play a central role in obesity. To investigate these relationships, we focus our attention on the most common epigenetic modifications that occur in obesity, including DNA methylation and post-translational modifications of histones. We also consider bariatric surgery as an epigenetic factor, evaluating how the anatomic and physiologic modifications induced by these surgical techniques can change gene expression. Here we discuss the importance of epigenetic mechanisms in chronic disease and cancer, and the role of epigenetic disturbances in obesity, with a focus on the role of bariatric surgery.
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Affiliation(s)
- Alessio Metere
- Surgical Sciences Department, “Sapienza” University of Rome, Viale Regina Elena 261, 00161 Rome, Italy
- Correspondence:
| | - Claire E. Graves
- Department of Surgery, University of California, San Francisco, 1600 Divisadero St., San Francisco, CA 94115, USA;
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Donovan MG, Wren SN, Cenker M, Selmin OI, Romagnolo DF. Dietary fat and obesity as modulators of breast cancer risk: Focus on DNA methylation. Br J Pharmacol 2020; 177:1331-1350. [PMID: 31691272 DOI: 10.1111/bph.14891] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) is the most common cancer and second leading cause of cancer mortality in women worldwide. Validated biomarkers enhance efforts for early detection and treatment, which reduce the risk of mortality. Epigenetic signatures have been suggested as good biomarkers for early detection, prognosis and targeted therapy of BC. Here, we highlight studies documenting the modifying effects of dietary fatty acids and obesity on BC biomarkers associated with DNA methylation. We focus our analysis on changes elicited in writers of DNA methylation (i.e., DNA methyltransferases), global DNA methylation and gene-specific DNA methylation. To provide context, we precede this discussion with a review of the available evidence for an association between BC incidence and both dietary fat consumption and obesity. We also include a review of well-vetted BC biomarkers related to cytosine-guanine dinucleotides methylation and how they influence BC risk, prognosis, tumour characteristics and response to treatment. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.
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Affiliation(s)
- Micah G Donovan
- Interdisciplinary Cancer Biology Graduate Program, University of Arizona, Tucson, Arizona
| | - Spencer N Wren
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Mikia Cenker
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Ornella I Selmin
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
| | - Donato F Romagnolo
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona.,The University of Arizona Cancer Center, Tucson, Arizona
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Dzobo K, Senthebane DA, Thomford NE, Rowe A, Dandara C, Parker MI. Not Everyone Fits the Mold: Intratumor and Intertumor Heterogeneity and Innovative Cancer Drug Design and Development. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:17-34. [PMID: 29356626 DOI: 10.1089/omi.2017.0174] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disruptive innovations in medicine are game-changing in nature and bring about radical shifts in the way we understand human diseases, their treatment, and/or prevention. Yet, disruptive innovations in cancer drug design and development are still limited. Therapies that cure all cancer patients are in short supply or do not exist at all. Chief among the causes of this predicament is drug resistance, a mechanism that is much more dynamic than previously understood. Drug resistance has limited the initial success experienced with biomarker-guided targeted therapies as well. A major contributor to drug resistance is intratumor heterogeneity. For example, within solid tumors, there are distinct subclones of cancer cells, presenting profound complexity to cancer treatment. Well-known contributors to intratumor heterogeneity are genomic instability, the microenvironment, cellular genotype, cell plasticity, and stochastic processes. This expert review explains that for oncology drug design and development to be more innovative, we need to take into account intratumor heterogeneity. Initially thought to be the preserve of cancer cells, recent evidence points to the highly heterogeneous nature and diverse locations of stromal cells, such as cancer-associated fibroblasts (CAFs) and cancer-associated macrophages (CAMs). Distinct subpopulations of CAFs and CAMs are now known to be located immediately adjacent and distant from cancer cells, with different subpopulations exerting different effects on cancer cells. Disruptive innovation and precision medicine in clinical oncology do not have to be a distant reality, but can potentially be achieved by targeting these spatially separated and exclusive cancer cell subclones and CAF subtypes. Finally, we emphasize that disruptive innovations in drug discovery and development will likely come from drugs whose effect is not necessarily tumor shrinkage.
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Affiliation(s)
- Kevin Dzobo
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa .,2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Dimakatso Alice Senthebane
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa .,2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Nicholas Ekow Thomford
- 3 Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Arielle Rowe
- 1 International Centre for Genetic Engineering and Biotechnology (ICGEB) , Cape Town, South Africa
| | - Collet Dandara
- 3 Pharmacogenetics Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - M Iqbal Parker
- 2 Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
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Hentze JL, Høgdall CK, Høgdall EV. Methylation and ovarian cancer: Can DNA methylation be of diagnostic use? Mol Clin Oncol 2019; 10:323-330. [PMID: 30847169 DOI: 10.3892/mco.2019.1800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer is a silent killer and, due to late diagnosis and frequent chemo resistance in patients, the primary cause of fatality amongst the various types of gynecological cancer. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, thereby saving lives. Biomarkers could also improve treatment, by predicting which patients will benefit from specific treatment strategies. DNA methylation is an epigenetic mechanism, and 'methylation imbalance' is characteristic of cancer. Previous research suggests that changes in DNA methylation can be used diagnostically, and that they may predict resistance to treatment. This paper gives an up-to-date overview of research investigating the potential of DNA methylation-based markers for diagnostics, prognostics, screening and prediction of drug resistance for ovarian cancer patients. DNA methylation cancer-biomarkers may be useful for cancer treatment, particularly since they are chemically stable and since cancer-associated changes in methylation typically precedes tumor growth. DNA methylation markers could improve diagnosis and treatment and might even be used for screening in the future. Furthermore, DNA methylation biomarkers could facilitate the development of precision medicine. However, at this point no biomarkers for ovarian cancer have a sufficient combination of sensitivity and specificity in a clinical setting. A reason for this is that most studies have focused on a single or a few methylation sites. More large screenings and genome-wide studies must be performed to increase the chance of identifying a DNA methylation marker which can identify ovarian cancer.
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Affiliation(s)
- Julie L Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Claus K Høgdall
- Department of Gynecology, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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Strzelczyk JK, Krakowczyk Ł, Owczarek AJ. Methylation status of SFRP1, SFRP2, RASSF1A, RARβ and DAPK1 genes in patients with oral squamous cell carcinoma. Arch Oral Biol 2018; 98:265-272. [PMID: 30576962 DOI: 10.1016/j.archoralbio.2018.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/20/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
Our study assessed the methylation status of the SFRP1, SFRP2, RASSF1A, RARβ and DAPK1 genes, which are associated with epigenetic silencing in cancers. In a group of 75 patients with oral squamous cell carcinoma, aberrant methylation was detected using methylation-specific PCR in tumours and matched margins. Our results showed significantly higher methylation frequency in tumours than in surgical margin of SFRP2 (26.6% vs 11.9%, p < 0.05) and DAPK1 (65.3% vs 41.3%, p < 0.01) genes. Moreover, methylation of the SFRP1 and DAPK1 genes was associated with older age. Advanced tumour stages were associated with lower rates of SFRP1 gene methylation. Decreased methylation levels of the SFRP2 and RASSF1A genes were associated with positive N stage. On the contrary, lymph node metastasis were associated with higher methylation rates of RARβ and DAPK1 genes. Patients with a familial history of cancer were associated with more frequently methylated SFRP1, SFRP2 and DAPK1 genes. Hypermethylation of DAPK1 was associated with decreased risk of death in patients. Our results are suggestive, although not conclusive, that some epigenetic changes, especially frequent hypermethylation of SFRP2 and DAPK1 genes, can be useful as potential diagnostic biomarkers of oral cavity cancer. Moreover, estimating the methylation status in surgical margins could become an additional strategy for more accurate treatment methods. Further efforts are needed to identify and validate this finding on a larger patient group and using new advanced methylation testing methods.
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Affiliation(s)
- Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Jordana 19 Str., 41-808 Zabrze, Medical University of Silesia in Katowice, Poland.
| | - Łukasz Krakowczyk
- Clinic of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-101 Gliwice, Poland.
| | - Aleksander Jerzy Owczarek
- Department of Statistics, Department of Instrumental Analysis, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Ostrogórska 30 Str., 41-200 Sosnowiec, Medical University of Silesia in Katowice, Poland.
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Strzelczyk JK, Krakowczyk Ł, Owczarek AJ. Aberrant DNA methylation of the p16, APC, MGMT, TIMP3 and CDH1 gene promoters in tumours and the surgical margins of patients with oral cavity cancer. J Cancer 2018; 9:1896-1904. [PMID: 29896273 PMCID: PMC5995944 DOI: 10.7150/jca.24477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/10/2018] [Indexed: 12/15/2022] Open
Abstract
Oral cavity cancer is a type of head and neck squamous cell carcinoma (HNSCC) and contributes to significant morbidity and mortality each year. An epigenetic pathway of transcriptional inactivation for many genes has been described in various cancers, including HNSCC. For our study, we selected genes for which silencing caused by hypermethylation can promote cancer development. In 75 primary HNSCC tumours and paired surgical margins, we investigated the methylation status of the p16, APC, MGMT, TIMP3 and CDH1 gene promoters by methylation-specific PCR after bisulphite treatment. The promoter methylation rates of p16, APC, MGMT, TIMP3 and CDH1 in tumours were 58.67%, 49.33%, 58.67%, 50.67%, and 57.33% and 50.67%, 41.33%, 37.33%, 42.67%, and 25.33% in the surgical margin, respectively. Our observations confirm the presence of epigenetic changes not only in the cancer cells, but also in the surrounding mucosa and represent a basis for further analysis to unravel these complicated issues. Appropriate cancer risk assessment based on epigenetic alterations in surgical margins may influence a patient's diagnosis and cure.
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Affiliation(s)
- Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Jordana 19 Str., 41-808 Zabrze, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Łukasz Krakowczyk
- Clinic of Oncological and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-101 Gliwice, Poland
| | - Aleksander Jerzy Owczarek
- Department of Statistics, Department of Instrumental Analysis, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Ostrogórska 30 Str., 41-200 Sosnowiec, Medical University of Silesia in Katowice, Sosnowiec, Poland
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Belmar-Lopez C, Castaneda CA, Castillo M, García-Corrochano P, Orrego E, Meléndez B, Casavilca S, Flores C, Orrego E. MGMT promoter methylation in Peruvian patients with glioblastoma. Ecancermedicalscience 2018. [PMID: 29515653 PMCID: PMC5834313 DOI: 10.3332/ecancer.2018.812] [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: 11/16/2022] Open
Abstract
Purpose O6-methylguanine–DNA methyltransferase (MGMT) promoter methylation predicts the outcome and response to alkylating chemotherapy in glioblastoma. The aim of this study is to evaluate the prevalence of MGMT methylation in Peruvian glioblastoma cases. Patients and methods We evaluated retrospectively 50 cases of resected glioblastoma during the period 2008–2013 at Instituto Nacional de Enfermedades Neoplasicas in Peru. Samples consisted of paraffin embedded and frozen tumour tissue. MGMT-promoter methylation status and the expression level of MGMT gene were evaluated by methylation-specific PCR and real-time PCR, respectively. Results Unmethylated, methylated and partially methylated statuses were found in 54%, 20% and 26% of paraffin-embedded samples, respectively. Methylation status was confirmed in the Virgen de la Salud Hospital and frozen samples. There was an association between the status of MGMT-promoter methylation and the level of gene expression (p = 0.001). Methylation was associated with increased progression-free survival (p = 0.002) and overall survival (OS) (p < 0.001). Conclusion MGMT-promoter methylation frequency in Peruvian glioblastoma is similar to that reported in other populations and the detection test has been standardised.
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Affiliation(s)
- Carolina Belmar-Lopez
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas. Av Angamos Este 2520, Surquillo, Lima 15038, Peru
| | - Carlos A Castaneda
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas. Av Angamos Este 2520, Surquillo, Lima 15038, Peru.,Faculty of Medicine, Universidad Peruana San Juan Bautista. Av Jose Antonio Lavalle s/n, Chorrillos, Lima 15067, Peru
| | - Miluska Castillo
- Department of Research, Instituto Nacional de Enfermedades Neoplasicas. Av Angamos Este 2520, Surquillo, Lima 15038, Peru
| | | | - Enrique Orrego
- Department of Neurosurgery, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru
| | - Barbara Meléndez
- Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital. Av De Barber s/n, Toledo 45005, Spain
| | - Sandro Casavilca
- Department of Pathology, Instituto Nacional de Enfermedades Neoplasicas. Av Angamos Este 2520, Surquillo, Lima 15038, Peru
| | - Claudio Flores
- Department of Research, Oncosalud. Av Guardia Civil 571, San Borja, Lima 15036, Peru
| | - Enrique Orrego
- Department of Neurosurgery, Instituto Nacional de Enfermedades Neoplasicas, Lima 15038, Peru
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Health protective behavior scale: Development and psychometric evaluation. PLoS One 2018; 13:e0190390. [PMID: 29309423 PMCID: PMC5757924 DOI: 10.1371/journal.pone.0190390] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
Objective A healthy lifestyle includes health protective and health promoting behaviors. Health promoting lifestyle profiles have been developed, but measures of health protective behavior are still lacking. This study sought to develop a health protecting behavior scale. Methods An initial item pool for the Health Protective Behavior Scale (HPBS) was generated based on read and referred literature and a single-item open-ended survey. An expert group screened this initial item pool using an item-level content validity index. Pilot testing was conducted. The degree of variation, the response rate, the item-total correlation coefficient, and the factor loading in factor analysis and item analysis were used to screen items using data of pilot testing. 454 subjects were recruited evaluate the psychometric properties of the HPBS. Analyses included internal consistency, test-retest reliability, factor analysis, parallel analysis, correlation analysis and criterion validity analysis. Results The final iteration of the HPBS was developed with 32 items and five dimensions: interpersonal support, general behavior, self-knowledge, nutrition behavior and health care. Cronbach’s alpha coefficient, and test-retest reliability were 0.89 and 0.89 respectively. Correlation coefficients of the five dimensions ranged from 0.28 to 0.55. The Spearman correlation coefficient between the total scores on the WHOQOL-BREF and on the HPBS was 0.34. Conclusions HPBS has sufficient validity and reliability to measure health protective behaviors in adults.
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14
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Metabolic Phase I (CYPs) and Phase II (GSTs) Gene Polymorphisms and Their Interaction with Environmental Factors in Nasopharyngeal Cancer from the Ethnic Population of Northeast India. Pathol Oncol Res 2017; 25:33-44. [PMID: 28952035 DOI: 10.1007/s12253-017-0309-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 09/13/2017] [Indexed: 01/06/2023]
Abstract
Multiple genetic and environmental factors and their interaction are believed to contribute in the pathogenesis of Nasopharyngeal Cancer (NPC). We investigate the role of Metabolic Phase I (CYPs) and Phase II (GSTs) gene polymorphisms, gene-gene and gene-environmental interaction in modulating the susceptibility to NPC in Northeast India. To determine the association of metabolic gene polymorphisms and environmental habits, 123 cases and 189 controls blood/swab samples were used for PCR and confirmed by Sanger sequencing. Analysis for GSTM1 and GSTT1 gene polymorphism was done by multiplex PCR. The T3801C in the 3'- flanking region of CYP1A1 gene was detected by PCR-RFLP method. The Logistic regression analysis was used to estimate odds ratios (OR) and 95% confidence intervals (95% CI). The GSTM1 null genotype alone (OR = 2.76) was significantly associated with NPC risk (P < 0.0001). The combinations of GSTM1 null and GSTT1 null genotypes also higher, 3.77 fold (P < 0.0001), risk of NPC, while GSTM1 null genotype along with CYP1A1 T3801C TC + CC genotype had 3.22 (P = 0.001) fold risk. The most remarkable risk was seen among individual carrying GSTM1 null, GSTT1 null genotypes and CYP1A1 T3801C TC + CC genotypes (OR = 5.71, P = 0.001). Further; analyses demonstrate an enhanced risk of NPC in smoked meat (OR = 5.56, P < 0.0001) and fermented fish consumers (OR = 5.73, P < 0.0001) carrying GSTM1 null genotype. An elevated risk of NPC was noted in smokers (OR = 12.67, P < 0.0001) and chewers (OR = 5.68, P < 0.0001) with GSTM1 null genotype. However, smokers had the highest risk of NPC among individuals carrying GSTT1 null genotype (OR = 4.46, P = 0.001) or CYP1A1 T3801C TC + CC genotype (OR = 7.13, P < 0.0001). The association of null genotypes and mutations of metabolic neutralizing genes along with the environmental habits (tobacco smokers and chewers, smoke meat, fermented fishes) can be used as a possible biomarker for early detection and preventive measure of NPC.
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15
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Datta S, Nam HS, Hayashi M, Maldonado L, Goldberg R, Brait M, Sidransky D, Illei P, Baras A, Vij N, Hoque MO. Expression of GULP1 in bronchial epithelium is associated with the progression of emphysema in chronic obstructive pulmonary disease. Respir Med 2017; 124:72-78. [DOI: 10.1016/j.rmed.2017.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 11/16/2022]
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16
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Brait M, Banerjee M, Maldonado L, Ooki A, Loyo M, Guida E, Izumchenko E, Mangold L, Humphreys E, Rosenbaum E, Partin A, Sidransky D, Hoque MO. Promoter methylation of MCAM, ERα and ERβ in serum of early stage prostate cancer patients. Oncotarget 2017; 8:15431-15440. [PMID: 28147335 PMCID: PMC5362497 DOI: 10.18632/oncotarget.14873] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/31/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Prostate cancer (PC) is the second most common cancer among men worldwide. Currently, the most common non-invasive approach for screening and risk assessment of PC is measuring the level of serum prostate-specific antigen (PSA). However, the sensitivity of PSA is 42.8 % and specificity is 41.1%. As a result, the serum PSA test leads to numerous unneeded biopsies. Therefore, a rigorous search for biomarkers for early detection of PC is ongoing. In this study, we aim to assess a panel of epigenetic markers in an intend to develop an early detection test for PC. RESULTS The sensitivity and specificity of hypermethylation of MCAM was 66% and 73% respectively which is an improvement from the sensitivity and specificity of PSA. Considering a combination marker panel of MCAM, ERα and ERβ increased the sensitivity to 75% and the specificity became 70% for the minimally invasive early detection test of PC. MATERIALS AND METHODS Sixteen primary matched tumor and serum were analyzed by quantitative methylation specific PCR (QMSP) to determine analytical and clinical sensitivity of the genes tested (SSBP2, MCAM, ERα, ERβ, APC, CCND2, MGMT, GSTP1, p16 and RARβ2). Additionally, serum samples from eighty four cases of PC, thirty controls and seven cases diagnosed as high grade Prostatic Intraepithelial Neoplasia (HGPIN) were analyzed. CONCLUSIONS Promoter methylation of MCAM, ERα and ERβ have a potential to be utilized as biomarker for the early detection of prostate PC as their sensitivity and specificity seem to be better than serum PSA in our cohort of samples. After robust validation in a larger prospective cohort, our findings may reduce the numbers of unwarranted prostate biopsies.
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Affiliation(s)
- Mariana Brait
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mithu Banerjee
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leonel Maldonado
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, University of South Alabama Medical Center, Mobile, Alabama, USA
| | - Akira Ooki
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Myriam Loyo
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elisa Guida
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Evgeny Izumchenko
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leslie Mangold
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth Humphreys
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eli Rosenbaum
- Department of Urological Oncology, Davidoff Center, Beilinson Hospital, Eliahu Hakim, Ramat Aviv, Israel
| | - Alan Partin
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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17
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Shen J, Song R, Wan J, Huff C, Fang S, Lee JE, Zhao H. Global methylation of blood leukocyte DNA and risk of melanoma. Int J Cancer 2017; 140:1503-1509. [PMID: 28006848 DOI: 10.1002/ijc.30577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/10/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Global DNA methylation, possibly influenced by lifestyle and environmental factors, has been suggested to play an active role in carcinogenesis. However, its role in melanoma has rarely been explored. The aims of this study were to evaluate the relationship between melanoma risk and levels of 5-methylcytosine (5-mC), a marker for global DNA methylation, in blood leukocyte DNA, and to determine whether this 5-mC level is influenced by pigmentation and sun exposure. This case-control study included 540 melanoma cases and 540 healthy controls. Overall, melanoma cases had significantly lower levels of 5-mC% than healthy controls (median: 3.24 vs. 3.91, p < 0.001). The significant difference between two groups did not differ by pigmentation or sun exposure. Among healthy controls, however, those who had fair skin color (p = 0.041) or light or no tanning after prolonged sun exposure (p = 0.031) or used a sunlamp (p = 0.028) had lower levels of 5-mC% than their counterparts. In addition, those with an intermediate or high phenotypic index, an indicator of cutaneous cancer susceptibility, had 2.58-fold greater likelihood of having a low level of 5-mC% [odds ratio (OR): 2.58; 95% confidence interval (CI): 1.72, 3.96] than those with a low phenotypic index. Lower levels of 5-mC% were associated with a 1.25-fold greater risk of melanoma (OR: 1.25; 95% CI: 1.08, 1.37). A significant dose-response relationship was observed in quartile analysis (p = 0.001). Our results suggest that global hypomethylation in blood leukocyte DNA is associated with increased risk of melanoma and that the level of methylation is influenced by pigmentation and sun exposure.
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Affiliation(s)
- Jie Shen
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Renduo Song
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jie Wan
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Chad Huff
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Shenying Fang
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jeffrey E Lee
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Hua Zhao
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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18
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Kuzmina NS, Lapteva NS, Rubanovich AV. Hypermethylation of gene promoters in peripheral blood leukocytes in humans long term after radiation exposure. ENVIRONMENTAL RESEARCH 2016; 146:10-17. [PMID: 26708527 DOI: 10.1016/j.envres.2015.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Some human genes known to undergo age-related promoter hypermethylation. These epigenetic modifications are similar to those occurring in the course of certain diseases, e.g. some types of cancer, which in turn may also associate with age. Given external genotoxic factors may additionally contribute to hypermethylation, this study was designed to analyzes, using methylation-sensitive polymerase chain reaction (PCR), the CpG island hypermethylation in RASSF1A, CDKN2A (including p16/INK4A and p14/ARF) and GSTP1 promoters in peripheral blood leukocytes of individuals exposed to ionizing radiation long time ago. One hundred and twenty-four irradiated subjects (24-77 years old at sampling: 83 Chernobyl Nuclear Power Plant clean-up workers, 21 nuclear workers, 20 residents of territories with radioactive contamination) and 208 unirradiated volunteers (19-77 years old at sampling) were enrolled. In addition, 74 non-exposed offspring (2-51 years old at sampling) born to irradiated parents were examined. The frequency of individuals displaying promoter methylation of at least one gene in exposed group was significantly higher as compared to the control group (OR=5.44, 95% CI=2.62-11.76, p=3.9×10(-7)). No significant difference was found between the frequency of subjects with the revealed promoter methylation in the group of offspring born to irradiated parents and in the control group. The increase in the number of methylated loci of RASSF1A and p14/ARF was associated with age (β=0.242; p=1.7×10(-5)). In contrast, hypermethylation of p16/INK4A and GSTP1 genes correlated with the fact of radiation exposure only (β=0.290; p=1.7×10(-7)). The latter finding demonstrates that methylation changes in blood leukocytes of healthy subjects exposed to radiation resemble those reported in human malignancies. Additional studies are required to identify the dose-response of epigenetic markers specifically associating with radiation-induced premature aging and/or with the development of age-associated cancer and non-cancer diseases.
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Affiliation(s)
- Nina S Kuzmina
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Nellya Sh Lapteva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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19
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Michailidi C, Hayashi M, Datta S, Sen T, Zenner K, Oladeru O, Brait M, Izumchenko E, Baras A, VandenBussche C, Argos M, Bivalacqua TJ, Ahsan H, Hahn NM, Netto GJ, Sidransky D, Hoque MO. Involvement of epigenetics and EMT-related miRNA in arsenic-induced neoplastic transformation and their potential clinical use. Cancer Prev Res (Phila) 2015; 8:208-21. [PMID: 25586904 PMCID: PMC4355280 DOI: 10.1158/1940-6207.capr-14-0251] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Exposure to toxicants leads to cumulative molecular changes that overtime increase a subject's risk of developing urothelial carcinoma. To assess the impact of arsenic exposure at a time progressive manner, we developed and characterized a cell culture model and tested a panel of miRNAs in urine samples from arsenic-exposed subjects, urothelial carcinoma patients, and controls. To prepare an in vitro model, we chronically exposed an immortalized normal human bladder cell line (HUC1) to arsenic. Growth of the HUC1 cells was increased in a time-dependent manner after arsenic treatment and cellular morphology was changed. In a soft agar assay, colonies were observed only in arsenic-treated cells, and the number of colonies gradually increased with longer periods of treatment. Similarly, invaded cells in an invasion assay were observed only in arsenic-treated cells. Withdrawal of arsenic treatment for 2.5 months did not reverse the tumorigenic properties of arsenic-treated cells. Western blot analysis demonstrated decreased PTEN and increased AKT and mTOR in arsenic-treated HUC1 cells. Levels of miR-200a, miR-200b, and miR-200c were downregulated in arsenic-exposed HUC1 cells by quantitative RT-PCR. Furthermore, in human urine, miR-200c and miR-205 were inversely associated with arsenic exposure (P = 0.005 and 0.009, respectively). Expression of miR-205 discriminated cancer cases from controls with high sensitivity and specificity (AUC = 0.845). Our study suggests that exposure to arsenic rapidly induces a multifaceted dedifferentiation program and miR-205 has potential to be used as a marker of arsenic exposure as well as a maker of early urothelial carcinoma detection.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Apoptosis
- Arsenic/adverse effects
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Case-Control Studies
- Cell Movement
- Cell Proliferation
- Cell Transformation, Neoplastic/chemically induced
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Cohort Studies
- DNA Methylation
- Epigenesis, Genetic/genetics
- Epithelial-Mesenchymal Transition
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Immunoenzyme Techniques
- Male
- MicroRNAs/analysis
- MicroRNAs/genetics
- Middle Aged
- Neoplasm Invasiveness
- PTEN Phosphohydrolase/genetics
- PTEN Phosphohydrolase/metabolism
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- TOR Serine-Threonine Kinases/genetics
- TOR Serine-Threonine Kinases/metabolism
- Urinary Bladder/drug effects
- Urinary Bladder/metabolism
- Urinary Bladder/pathology
- Urinary Bladder Neoplasms/drug therapy
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/pathology
- Young Adult
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Affiliation(s)
- Christina Michailidi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Masamichi Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sayantan Datta
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Tanusree Sen
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Kaitlyn Zenner
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Oluwadamilola Oladeru
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Alexander Baras
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | | | - Maria Argos
- Department of Health Studies, The University of Chicago, Chicago, Illinois
| | | | - Habibul Ahsan
- Department of Health Studies, The University of Chicago, Chicago, Illinois. Departments of Medicine and Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois
| | - Noah M Hahn
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland
| | - George J Netto
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland. Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Mohammad Obaidul Hoque
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland. Department of Urology, Johns Hopkins University, Baltimore, Maryland. Department of Oncology, Johns Hopkins University, Baltimore, Maryland.
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20
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Gene promoter methylation and DNA repair capacity in monozygotic twins with discordant smoking habits. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 779:57-64. [DOI: 10.1016/j.mrgentox.2015.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/11/2014] [Accepted: 01/13/2015] [Indexed: 11/24/2022]
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21
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Larijani L, Madjd Z, Samadikuchaksaraei A, Younespour S, Zham H, Rakhshan A, Mohammadi F, Rahbari A, Moradi A. Methylation of O6-methyl guanine methyltransferase gene promoter in meningiomas--comparison between tumor grades I, II, and III. Asian Pac J Cancer Prev 2014; 15:33-8. [PMID: 24528051 DOI: 10.7314/apjcp.2014.15.1.33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meningiomas are the second most common primary intracranial tumors after gliomas. Epigenetic biomarkers such as DNA methylation, which is found in many tumors and is thus important in tumorigenesis can help diagnose meningiomas and predict response to adjuvant chemotherapy. We investigated aberrant O6- methyl guanine methyltransferase (MGMT) methylation in meningiomas. MATERIALS AND METHODS Sixty-one patients were classified according to the WHO grading, and MGMT promoter methylation status was examined via the methylation-Specific PCR(MSP) method. RESULTS MGMT promoter methylation was found in 22.2% of grade I, 35% of grade I with atypical features, 36% of grade II, and 42.9% of grade III tumors. CONCLUSIONS There was an increase, albeit not statistically significant, in MGMT methylation with a rise in the tumor grade. Higher methylation levels were also observed in the male gender.
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Affiliation(s)
- Leila Larijani
- Department of Biology, School of Basic Sciences, Science and Research Branch Islamic Azad University (IAU), Tehran, Iran E-mail :
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22
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The study of hypermethylation in blood leukocytes of irradiated parents and their children. Open Life Sci 2014. [DOI: 10.2478/s11535-014-0333-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
AbstractBackground: Accumulation of evidence about the epigenetic regulation of genome function suggests the necessity to explore new aspects of the genotoxic action of radiation on the human body. Methodology: A methylation-sensitive PCR assay was used to analyze promoter methylation of p16/CDKN2A, p14/ARF, RASSF1A and GSTP1 genes in blood leukocytes from 103 unirradiated volunteers and 104 irradiated subjects (83 Chernobyl Nuclear Power Plant liquidators and 21 nuclear specialists). Additionally, 21 families whose fathers were nuclear specialists were examined. Results: A significantly elevated frequency of individuals with abnormal methylation of p16/CDKN2A and GSTP1 genes was revealed in the exposed group compared to the control group (p = 0.0097 and p = 0.005, respectively). The occurrence of promoter methylation of RASSF1A gene significantly correlated with aging both in the control group (r = 0, 213; p = 0.006) and in the exposed individuals (r = 0, 212; p = 0,031). No methylated genes were found in the offspring of control families. Conclusion: Our study showed for the fist time that prolonged radiation exposure at low and medium doses is associated with hypermethylation of genes involved in the basic protective functions of cells; an effect that is persistent in blood leukocytes for significant periods after irradiation.
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23
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Kagohara LT, Schussel JL, Subbannayya T, Sahasrabuddhe N, Lebron C, Brait M, Maldonado L, Valle BL, Pirini F, Jahuira M, Lopez J, Letelier P, Brebi-Mieville P, Ili C, Pandey A, Chatterjee A, Sidransky D, Guerrero-Preston R. Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in Chile. Future Oncol 2014; 11:233-49. [PMID: 25066711 PMCID: PMC4332836 DOI: 10.2217/fon.14.165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM The aim of the study was to evaluate the use of global and gene-specific DNA methylation changes as potential biomarkers for gallbladder cancer (GBC) in a cohort from Chile. MATERIAL & METHODS DNA methylation was analyzed through an ELISA-based technique and quantitative methylation-specific PCR. RESULTS Global DNA Methylation Index (p = 0.02) and promoter methylation of SSBP2 (p = 0.01) and ESR1 (p = 0.05) were significantly different in GBC when compared with cholecystitis. Receiver curve operator analysis revealed promoter methylation of APC, CDKN2A, ESR1, PGP9.5 and SSBP2, together with the Global DNA Methylation Index, had 71% sensitivity, 95% specificity, a 0.97 area under the curve and a positive predictive value of 90%. CONCLUSION Global and gene-specific DNA methylation may be useful biomarkers for GBC clinical assessment.
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Affiliation(s)
- Luciane Tsukamoto Kagohara
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Juliana L Schussel
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oral Medicine, Post Graduation Program in Dentistry, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Cynthia Lebron
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Mariana Brait
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Leonel Maldonado
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Blanca L Valle
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Francesca Pirini
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Martha Jahuira
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jaime Lopez
- Universidad de La Frontera, Facultad de Medicina, Departamento de Anatomía Patológica, Laboratorio Patología Molecular, BIOREN-CEGIN, Temuco, Chile
| | - Pablo Letelier
- Universidad de La Frontera, Facultad de Medicina, Departamento de Anatomía Patológica, Laboratorio Patología Molecular, BIOREN-CEGIN, Temuco, Chile
- Escuela Ciencias de la Salud, Universidad Católica de Temuco, Temuco, Chile
| | - Priscilla Brebi-Mieville
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Universidad de La Frontera, Facultad de Medicina, Departamento de Anatomía Patológica, Laboratorio Patología Molecular, BIOREN-CEGIN, Temuco, Chile
| | - Carmen Ili
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Universidad de La Frontera, Facultad de Medicina, Departamento de Anatomía Patológica, Laboratorio Patología Molecular, BIOREN-CEGIN, Temuco, Chile
| | - Akhilesh Pandey
- McKusick–Nathans Institute of Genetic Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aditi Chatterjee
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Institute of Bioinformatics, Whitefield, Bangalore 560066, Karnataka, India
| | - David Sidransky
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology–Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- University of Puerto Rico School of Medicine, Department of Obstetrics & Gynecology, San Juan, Puerto Rico
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Abstract
DNA methylation is a significant regulator of gene expression, and its role in carcinogenesis recently has been a subject of remarkable interest. The aim of this review is to analyze the mechanism and cell regulatory effects of both hypo- and hyper-DNA methylation on cancer. In this review, we report new developments and their implications regarding the effects of DNA methylation on cancer development. Indeed, alteration of the pattern of DNA methylation has been a constant finding in cancer cells of the same type and differences in the pattern of DNA methylation not only occur in a variety of tumor types, but also in developmental processes Furthermore, the pattern of histone modification appears to be a predicator of the risk of recurrence of human cancers. It is well known that hypermethylation represses transcription of the promoter sections of tumor-suppressor genes leading to gene silencing. However, hypomethylation also has been identified as a cause of oncogenesis. Furthermore, experiments concerning the mechanism of methylation and its control have led to the discovery of many regulatory enzymes and proteins. This review reports on methods developed for the detection of 5-hydroxymethylcytosine methylation at the 5-methylcytosine of protein domains in the CpG context compared to non-methylated DNA, histone modification, and microRNA change.
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Physical activity and differential methylation of breast cancer genes assayed from saliva: a preliminary investigation. Ann Behav Med 2014; 45:89-98. [PMID: 23054940 DOI: 10.1007/s12160-012-9411-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Individuals who exercise are at lower risk for breast cancer and have better post-diagnosis outcomes. The biological mechanisms behind this association are unclear, but DNA methylation has been suggested. METHODS We developed a composite measure of DNA methylation across 45 CpG sites on genes selected a priori. We examined the association of this measure to self-reported physical activity and objectively measured cardiovascular fitness in a sample of healthy nonsmoking adults (n = 64) in an exercise promotion intervention. RESULTS Individuals who were more physically fit and who exercised more minutes per week had lower levels of DNA methylation. Those who increased their minutes of physical activity over 12 months experienced decreases in DNA methylation. CONCLUSIONS DNA methylation may be a mechanism linking exercise and cancer incidence and could serve as a biomarker for behavioral intervention trials. Studies with larger samples, objectively measured exercise, and more cancer-related markers are needed.
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DONG SHANGWEN, ZHANG PENG, LIANG SHAOJIE, WANG SHUO, SUN PEI, WANG YUANGUO. The role of the retinoblastoma protein-interacting zinc finger gene 1 tumor suppressor gene in human esophageal squamous cell carcinoma cells. Oncol Lett 2013; 6:1656-1662. [PMID: 24260060 PMCID: PMC3833985 DOI: 10.3892/ol.2013.1608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/16/2013] [Indexed: 01/06/2023] Open
Abstract
The tumor suppressor protein retinoblastoma protein-interacting zinc finger gene 1 (RIZ1) is downregulated in several types of cancer, including esophageal squamous cell carcinoma (ESCC). The present study used two in vitro methods to re-express RIZ1 in the human ESCC TE13 cell line in order to induce apoptosis. RIZ1 was re-expressed in the TE13 cells by reintroducing the gene through transfection or by removal of transcriptional repression through treatment with a DNA methyltransferase (DNMT) inhibitor. To reintroduce the gene, the open reading frame of the RIZ1 gene was inserted into the eukaryotic expression pcDNA3.1(+) vector and pcDNA3.1(+)/RIZ1 was purified and transfected into the TE13 ESCC cells. Removing transcriptional repression involved treating the TE13 cells with 5-aza-2'-deoxycytidine (5-aza-CdR), a DNMT inhibitor. RIZ1 mRNA and protein expression were determined by quantitative polymerase chain reaction (qPCR) and western blotting. The rate of apoptosis of the cells was determined by flow cytometry. A recombinant eukaryotic human RIZ1 expression plasmid, pcDNA3.1(+)/RIZ1, was constructed and confirmed by sequencing. RIZ1 mRNA and protein expression increased in pcDNA3.1(+)/RIZ1 stably transfected cells. Treatment with 5-aza-CdR for 48 and 72 h resulted in increased RIZ1 protein expression and increased the rate of apoptosis in the TE13 cells (P<0.01). In conclusion, transfection of the TE13 cells with the eukaryotic pcDNA3.1(+)/RIZ1 expression vector and reversal of transcriptional repression of RIZ1 using 5-aza-CdR demonstrate that it is possible to re-express RIZ1 in TE13 cells. Furthermore, the re-expression of RIZ1 led to an increased rate of apoptosis and this method may provide new therapeutic possibilities.
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Affiliation(s)
- SHANGWEN DONG
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - PENG ZHANG
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - SHAOJIE LIANG
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - SHUO WANG
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - PEI SUN
- Tianjin Institute of Endocrinology, Tianjin Medical University, Heping, Tianjin 300070, P.R. China
| | - YUANGUO WANG
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
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27
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Feng X, Ren C, Zhou W, Liu W, Zeng L, Li G, Wang L, Li M, Zhu B, Yao K, Jiang X. Promoter hypermethylation along with LOH, but not mutation, contributes to inactivation of DLC-1
in nasopharyngeal carcinoma. Mol Carcinog 2013; 53:858-70. [DOI: 10.1002/mc.22044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/08/2013] [Accepted: 04/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Xiangling Feng
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Caiping Ren
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Wen Zhou
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Weidong Liu
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Liang Zeng
- Department of Pathology; Hunan Tumor Hospital; Changsha, Hunan, P.R. China
| | - Guifei Li
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Lei Wang
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Min Li
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Bin Zhu
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
| | - Kaitai Yao
- Key Laboratory for Carcinogenesis of Chinese Ministry of Health, Key Laboratory for Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Cancer Research Institute, Xiangya School of Medicine; Central South University; Changsha, Hunan, P.R. China
- Cancer Research Institute; Southern Medical University; Guangzhou, Guangdong, P.R. China
| | - Xingjun Jiang
- Department of Neurosurgery; Xiangya Hospital, Central South University; Changsha, Hunan, P.R. China
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Ostrow KL, Michailidi C, Guerrero-Preston R, Hoque MO, Greenberg A, Rom W, Sidransky D. Cigarette smoke induces methylation of the tumor suppressor gene NISCH. Epigenetics 2013; 8:383-8. [PMID: 23503203 DOI: 10.4161/epi.24195] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We have previously identified a putative tumor suppressor gene, NISCH, whose promoter is methylated in lung tumor tissue as well as in plasma obtained from lung cancer patients. NISCH was observed to be more frequently methylated in smoker lung cancer patients than in non-smoker lung cancer patients. Here, we investigated the effect of tobacco smoke exposure on methylation of the NISCH gene. We tested methylation of NISCH after oral keratinocytes were exposed to mainstream and side stream cigarette smoke extract in culture. Methylation of the promoter region of the NISCH gene was also evaluated in plasma obtained from lifetime non-smokers and light smokers (<20 pack/year), with and without lung tumors, and heavy smokers (20+ pack/year) without disease. Promoter methylation of NISCH was tested by quantitative fluorogenic real-time PCR in all samples. Promoter methylation of NISCH occurred after exposure to mainstream tobacco smoke as well as to side stream tobacco smoke in normal oral keratinocyte cell lines. NISCH methylation was also detected in 68% of high-risk, heavy smokers without detectable tumors. Interestingly, in light smokers, NISCH methylation was present in 69% of patients with lung cancer and absent in those without disease. Our pilot study indicates that tobacco smoke induces methylation changes in the NISCH gene promoter before any detectable cancer. Methylation of the NISCH gene was also found in lung cancer patients' plasma samples. After confirming these findings in longitudinally collected plasma samples from high-risk populations (such as heavy smokers), examining patients for hypermethylation of the NISCH gene may aid in identifying those who should undergo additional screening for lung cancer.
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Affiliation(s)
- Kimberly Laskie Ostrow
- Department of Otolaryngology; Head and Neck Cancer Research Division; Johns Hopkins School of Medicine; Baltimore, MD USA
| | - Christina Michailidi
- Department of Otolaryngology; Head and Neck Cancer Research Division; Johns Hopkins School of Medicine; Baltimore, MD USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology; Head and Neck Cancer Research Division; Johns Hopkins School of Medicine; Baltimore, MD USA
| | - Mohammad O Hoque
- Department of Otolaryngology; Head and Neck Cancer Research Division; Johns Hopkins School of Medicine; Baltimore, MD USA
| | | | - William Rom
- Department of Medicine; New York University; New York, NY USA
| | - David Sidransky
- Department of Otolaryngology; Head and Neck Cancer Research Division; Johns Hopkins School of Medicine; Baltimore, MD USA
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Knox SS, Ochs MF. Implications of systemic dysfunction for the etiology of malignancy. GENE REGULATION AND SYSTEMS BIOLOGY 2013; 7:11-22. [PMID: 23440603 PMCID: PMC3572920 DOI: 10.4137/grsb.s10943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The current approach to treatment in oncology is to replace the generally cytotoxic chemotherapies with pharmaceutical treatment which inactivates specific molecular targets associated with cancer development and progression. The goal is to limit cellular damage to pathways perceived to be directly responsible for the malignancy. Its underlying assumptions are twofold: (1) that individual pathways are the cause of malignancy; and (2) that the treatment objective should be destruction-either of the tumor or the dysfunctional pathway. However, the extent to which data actually support these assumptions has not been directly addressed. Accumulating evidence suggests that systemic dysfunction precedes the disruption of specific genetic/molecular pathways in most adult cancers and that targeted treatments such as kinase inhibitors may successfully treat one pathway while generating unintended changes to other, non-targeted pathways. This article discusses (1) the systemic basis of malignancy; (2) better profiling of pre-cancerous biomarkers associated with elevated risk so that preventive lifestyle modifications can be instituted early to revert high-risk epigenetic changes before tumors develop; (3) a treatment emphasis in early stage tumors that would target the restoration of systemic balance by strengthening the body's innate defense mechanisms; and (4) establishing better quantitative models of systems to capture adequate complexity for predictability at all stages of tumor progression.
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Affiliation(s)
- Sarah S. Knox
- West Virginia University School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University School of Medicine
| | - Michael F. Ochs
- Division of Oncology Biostatistics and Bioinformatics, Departments of Oncology and Health Science Informatics, Johns Hopkins University
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30
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Dorak MT, Karpuzoglu E. Gender differences in cancer susceptibility: an inadequately addressed issue. Front Genet 2012; 3:268. [PMID: 23226157 PMCID: PMC3508426 DOI: 10.3389/fgene.2012.00268] [Citation(s) in RCA: 272] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/06/2012] [Indexed: 12/25/2022] Open
Abstract
The gender difference in cancer susceptibility is one of the most consistent findings in cancer epidemiology. Hematologic malignancies are generally more common in males and this can be generalized to most other cancers. Similar gender differences in non-malignant diseases including autoimmunity, are attributed to hormonal or behavioral differences. Even in early childhood, however, where these differences would not apply, there are differences in cancer incidence between males and females. In childhood, few cancers are more common in females, but overall, males have higher susceptibility. In Hodgkin lymphoma, the gender ratio reverses toward adolescence. The pattern that autoimmune disorders are more common in females, but cancer and infections in males suggests that the known differences in immunity may be responsible for this dichotomy. Besides immune surveillance, genome surveillance mechanisms also differ in efficiency between males and females. Other obvious differences include hormonal ones and the number of X chromosomes. Some of the differences may even originate from exposures during prenatal development. This review will summarize well-documented examples of gender effect in cancer susceptibility, discuss methodological issues in exploration of gender differences, and present documented or speculated mechanisms. The gender differential in susceptibility can give important clues for the etiology of cancers and should be examined in all genetic and non-genetic association studies.
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Affiliation(s)
- M Tevfik Dorak
- Robert Stempel College of Public Health and Social Work, Florida International University Miami, FL, USA
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31
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Sturgeon SR, Balasubramanian R, Schairer C, Muss HB, Ziegler RG, Arcaro KF. Detection of promoter methylation of tumor suppressor genes in serum DNA of breast cancer cases and benign breast disease controls. Epigenetics 2012; 7:1258-67. [PMID: 22986510 DOI: 10.4161/epi.22220] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Tumors are capable of shedding DNA into the blood stream. This shed DNA may be recovered from serum or plasma. The objective of this study was to evaluate whether pyrosequencing promoter DNA in a panel of 12 breast cancer-related genes (APC, BRCA1, CCND2, CDH1, ESR1, GSTP1, HIN1, P16, RARβ, RASSF1, SFRP1 and TWIST) to measure the degree of methylation would lead to a useful serum-based marker of breast cancer. Serum was obtained from women who were about to undergo a breast biopsy or mastectomy at three hospitals from 1977 to 1987 in Grand Rapids, MI USA. We compared the methylation status of 12 genes in serum DNA obtained from three groups of postmenopausal women (mean age at blood collection: 63.0 y; SD 9.9; range 35-91): breast cancer cases with lymph node-positive disease (n = 241); breast cancer cases with lymph node-negative disease (n = 63); and benign breast disease control subjects (n = 234). Overall, median levels of promoter methylation were low, typically below 5%, for all genes in all study groups. For all genes, median levels of methylation were higher (by 3.3 to 47.6%) in lymph node-positive breast cancer cases than in the controls. Comparing mean methylation level between lymph-node positive cases and controls, the most statistically significant findings, after adjustment of the false-positive rate (q-value), were for TWIST (p = 0.04), SFRP1 (p = 0.16), ESR1 (p = 0.17), P16 (p = 0.19) and APC (p = 0.19). For two of these four genes (TWIST, P16), the median methylation level was also highest in lymph-node positive cases, intermediate in lymph node-negative cases and lowest in the controls. The percent of study subjects with mean methylation scores ≥ 5% was higher among lymph node-positive cases than controls for ten genes, and significantly higher for HIN1 and TWIST (22.0 vs. 12.2%, p = 0.04 and 37.9 vs. 24.5%, p = 0.004, respectively). Despite relatively consistent variation in methylation patterns among groups, these modest differences did not provide sufficient ability to distinguish between cases and controls in a clinical setting.
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Affiliation(s)
- Susan R Sturgeon
- Division of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA.
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32
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Li L, Choi JY, Lee KM, Sung H, Park SK, Oze I, Pan KF, You WC, Chen YX, Fang JY, Matsuo K, Kim WH, Yuasa Y, Kang D. DNA methylation in peripheral blood: a potential biomarker for cancer molecular epidemiology. J Epidemiol 2012; 22:384-94. [PMID: 22863985 PMCID: PMC3798632 DOI: 10.2188/jea.je20120003] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aberrant DNA methylation is associated with cancer development and progression. There are several types of specimens from which DNA methylation pattern can be measured and evaluated as an indicator of disease status (from normal biological process to pathologic condition) and even of pharmacologic response to therapy. Blood-based specimens such as cell-free circulating nucleic acid and DNA extracted from leukocytes in peripheral blood may be a potential source of noninvasive cancer biomarkers. In this article, we describe the characteristics of blood-based DNA methylation from different biological sources, detection methods, and the factors affecting DNA methylation. We provide a comprehensive literature review of blood-based DNA methylation as a cancer biomarker and focus on the study of DNA methylation using peripheral blood leukocytes. Although DNA methylation patterns measured in peripheral blood have great potential to be useful and informative biomarkers of cancer risk and prognosis, large systematic and unbiased prospective studies that consider biological plausibility and data analysis issues will be needed in order to develop a clinically feasible blood-based assay.
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Affiliation(s)
- Lian Li
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
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33
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Brait M, Loyo M, Rosenbaum E, Ostrow KL, Markova A, Papagerakis S, Zahurak M, Goodman SM, Zeiger M, Sidransky D, Umbricht CB, Hoque MO. Correlation between BRAF mutation and promoter methylation of TIMP3, RARβ2 and RASSF1A in thyroid cancer. Epigenetics 2012; 7:710-9. [PMID: 22694820 DOI: 10.4161/epi.20524] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Our aim was to comprehensively analyze promoter hypermethylation of a panel of novel and known methylation markers for thyroid neoplasms and to establish their relationship with BRAF mutation and clinicopathologic parameters of thyroid cancer. A cohort of thyroid tumors, consisting of 44 cancers and 44 benign thyroid lesions, as well as 15 samples of adjacent normal thyroid tissue, was evaluated for BRAF mutation and promoter hypermethylation. Genes for quantitative methylation specific PCR (QMSP) were selected by a candidate gene approach. Twenty-two genes were tested: TSHR, RASSF1A, RARβ2, DAPK, hMLH1, ATM, S100, p16, CTNNB1, GSTP1, CALCA, TIMP3, TGFßR2, THBS1, MINT1, CTNNB1, MT1G, PAK3, NISCH, DCC, AIM1 and KIF1A. The PCR-based "mutector assay" was used to detect BRAF mutation. All p values reported are two sided. Considerable overlap was seen in the methylation markers among the different tissue groups. Significantly higher methylation frequency and level were observed for KIF1A and RARß2 in cancer samples compared with benign tumors. A negative correlation between BRAF mutation and RASSF1A methylation, and a positive correlation with RARß2 methylation were observed in accordance with previous results. In addition, positive correlation with TIMP3 and a marginal correlation with DCC methylation were observed. The present study constitutes a comprehensive promoter methylation profile of thyroid neoplasia and shows that results must be analyzed in a tissue-specific manner to identify clinically useful methylation markers. Integration of genetic and epigenetic changes in thyroid cancer will help identify relevant biologic pathways that drive its development.
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Affiliation(s)
- Mariana Brait
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agusti A, Anderson W, Lomas DA, Demeo DL. Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome. Hum Mol Genet 2012; 21:3073-82. [PMID: 22492999 DOI: 10.1093/hmg/dds135] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The impact of cigarette smoking can persist for extended periods following smoking cessation and may involve epigenetic reprogramming. Changes in DNA methylation associated with smoking may help to identify molecular pathways that contribute to the latency between exposure and disease onset. Cross-sectional cohort data from subjects in the International COPD Genetics Network (n = 1085) and the Boston Early-Onset COPD study (n = 369) were analyzed as the discovery and replication cohorts, respectively. Genome-wide methylation data on 27 578 CpG sites in 14 475 genes were obtained on DNA from peripheral blood leukocytes using the Illumina HumanMethylation27K Beadchip in both cohorts. We identified 15 sites significantly associated with current smoking, 2 sites associated with cumulative smoke exposure, and, within the subset of former smokers, 3 sites associated with time since quitting cigarettes. Two loci, factor II receptor-like 3 (F2RL3) and G-protein-coupled receptor 15 (GPR15), were significantly associated in all three analyses and were validated by pyrosequencing. These findings (i) identify a novel locus (GPR15) associated with cigarette smoking and (ii) suggest the existence of dynamic, site-specific methylation changes in response to smoking which may contribute to the extended risks associated with cigarette smoking that persist after cessation.
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Affiliation(s)
- Emily S Wan
- Channing Laboratory and the Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115, USA.
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35
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Abstract
To elucidate the effect of cigarette smoke on developing lung cancer among individuals, numerous genetic and epigenetic factors related to cigarette smoke-induced lung cancers have been widely investigated and a various genes, loci and pathways have been identified as candidates to date. However, the importance of these molecular alterations in the initiation and progression of lung cancer still remains imprecise and different molecules altered in lung cancer are being used for stratification of patients for targeted therapy. There are a number of molecular pathways involved in the development of lung cancer, and environmental factors related to these alterations are still unclear. Furthermore, various genetic alterations determined by candidate gene approach have not been re-evaluated for their functional significance together with epigenetic alterations in the same population. Accumulated evidence suggested that lung cancer in ever smokers and never smokers follow distinct molecular pathways and may therefore respond to distinct therapy. Therefore, additional studies will be essential to re-evaluate the individual risk of developing lung cancer based on the combination of genetic and epigenetic alterations and to set up a guideline to assess the individual risk for lung cancer and for its prevention.
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Affiliation(s)
- Shahnaz Begum
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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36
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Ehrlich S, Walton E, Roffman JL, Weiss D, Puls I, Doehler N, Burghardt R, Lehmkuhl U, Hillemacher T, Muschler M, Frieling H. Smoking, but not malnutrition, influences promoter-specific DNA methylation of the proopiomelanocortin gene in patients with and without anorexia nervosa. CANADIAN JOURNAL OF PSYCHIATRY. REVUE CANADIENNE DE PSYCHIATRIE 2012; 57:168-76. [PMID: 22398003 DOI: 10.1177/070674371205700306] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Our pilot study evaluates the impact of environmental factors, such as nutrition and smoking status, on epigenetic patterns in a disease-associated gene. METHOD We measured the effects of malnutrition and cigarette smoking on proopiomelanocortin (POMC) promoter-specific DNA methylation in female patients with and without anorexia nervosa (AN). POMC and its derived peptides (alpha melanocyte stimulating hormone and adrenocorticotropic hormone) are implicated in stress and feeding response. Promoter-specific DNA methylation of the POMC gene was determined in peripheral blood mononuclear cells of 54 healthy female control subjects, 40 underweight patients with AN, and 21 weight-restored patients with AN using bisulfite sequencing. Malnutrition was characterized by plasma leptin. RESULTS POMC promoter-specific DNA methylation was not affected by diagnosis or nutritional status but significantly negatively associated with cigarette smoking. CONCLUSIONS Although malnutrition may be expected to reduce DNA methylation through its effects on one-carbon metabolism, our negative results are in line with several in vitro and clinical studies that did not show a direct relation between gene-specific DNA methylation and folate levels. In contrast, smoking has been repeatedly reported to alter DNA methylation of specific genes and should be controlled for in future epigenetic studies.
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Affiliation(s)
- Stefan Ehrlich
- Dresden University of Technology, Department of Child and Adolescent Psychiatry, Translational Developmental Neuroscience Section, Dresden, Germany.
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37
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Altmann S, Murani E, Metges CC, Schwerin M, Wimmers K, Ponsuksili S. Effect of gestational protein deficiency and excess on hepatic expression of genes related to cell cycle and proliferation in offspring from late gestation to finishing phase in pig. Mol Biol Rep 2012; 39:7095-104. [DOI: 10.1007/s11033-012-1541-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/24/2012] [Indexed: 12/20/2022]
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Zhang B, Zhu W, Yang P, Liu T, Jiang M, He ZN, Zhang SX, Chen WQ, Chen W. Cigarette smoking and p16INK4α gene promoter hypermethylation in non-small cell lung carcinoma patients: a meta-analysis. PLoS One 2011; 6:e28882. [PMID: 22174919 PMCID: PMC3236763 DOI: 10.1371/journal.pone.0028882] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/16/2011] [Indexed: 12/31/2022] Open
Abstract
Background Aberrant methylation of promoter DNA and transcriptional repression of specific tumor suppressor genes play an important role in carcinogenesis. Recently, many studies have investigated the association between cigarette smoking and p16INK4α gene hypermethylation in lung cancer, but could not reach a unanimous conclusion. Methods and Findings Nineteen cross-sectional studies on the association between cigarette smoking and p16INK4α methylation in surgically resected tumor tissues from non-small cell lung carcinoma (NSCLC) patients were identified in PubMed database until June 2011. For each study, a 2×2 cross-table was extracted. In total, 2,037 smoker and 765 nonsmoker patients were pooled with a fixed-effects model weighting for the inverse of the variance. Overall, the frequency of p16INK4α hypermethylation was higher in NSCLC patients with smoking habits than that in non-smoking patients (OR = 2.25, 95% CI = 1.81–2.80). The positive association between cigarette smoking and p16INK4α hypermethylation was similar in adenocarcinoma and squamous-cell carcinoma. In the stratified analyses, the association was stronger in Asian patients and in the studies with larger sample sizes. Conclusion Cigarette smoking is positively correlated to p16INK4α gene hypermethylation in NSCLC patients.
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Affiliation(s)
- Bo Zhang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhu
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Ping Yang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Tao Liu
- Faculty of Biostatistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Institute of Public Health, Guangzhou, China
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Mei Jiang
- Faculty of Biostatistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Ni He
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shi-Xin Zhang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wei-Qing Chen
- Faculty of Biostatistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- * E-mail: (W-QC); (WC)
| | - Wen Chen
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
- * E-mail: (W-QC); (WC)
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Abstract
BACKGROUND It remains important to understand the biology and identify biomarkers for less studied cancers like testicular cancer. The purpose of this study was to determine the methylation frequency of several cancer-related genes in different histological types of testicular cancer and normal testis tissues (NT). METHODS DNA was isolated from 43 seminomas (SEs), 14 non-SEs (NSEs) and 23 NT, and was assayed for promoter methylation status of 15 genes by quantitative methylation-specific PCR. The methylation status was evaluated for an association with cancer, and between SEs and NSEs. RESULTS We found differential methylation pattern in SEs and NSEs. MGMT, VGF, ER-β and FKBP4 were predominately methylated in NSEs compared with SEs. APC and hMLH1 are shown to be significantly more methylated in both subtypes in comparison with NT. When combining APC, hMLH1, ER-β and FKBP4, it is possible to identify 86% of the NSEs, whereas only 7% of the SEs. CONCLUSIONS Our results indicate that the methylation profile of cancer-associated genes in testicular cancer correlates with histological types and show cancer-specific pattern for certain genes. Further methylation analysis, in a larger cohort is needed to elucidate their role in testicular cancer development and potential for therapy, early detection and disease monitoring.
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Yang P, Ma J, Zhang B, Duan H, He Z, Zeng J, Zeng X, Li D, Wang Q, Xiao Y, Liu C, Xiao Q, Chen L, Zhu X, Xing X, Li Z, Zhang S, Zhang Z, Ma L, Wang E, Zhuang Z, Zheng Y, Chen W. CpG site-specific hypermethylation of p16INK4α in peripheral blood lymphocytes of PAH-exposed workers. Cancer Epidemiol Biomarkers Prev 2011; 21:182-90. [PMID: 22028397 DOI: 10.1158/1055-9965.epi-11-0784] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sufficient epidemiologic evidence shows an etiologic link between polycyclic aromatic hydrocarbons (PAH) exposure and lung cancer risk. While the genetic modifications have been found in PAH-exposed population, it is unclear whether gene-specific methylation involves in the process of PAH-associated biologic consequence. METHODS Sixty-nine PAH-exposed workers and 59 control subjects were recruited. Using bisulfite sequencing, we examined the methylation status of p16(INK4α) promoter in peripheral blood lymphocytes (PBL) from PAH-exposed workers and in benzo(a)pyrene (BaP)-transformed human bronchial epithelial (HBE) cells. The relationships between p16(INK4α) methylation and the level of urinary 1-hydroxypyrene (1-OHP) or the frequency of cytokinesis block micronucleus (CBMN) were analyzed. RESULTS Compared with the control group, PAH-exposed workers exhibited higher levels of urinary 1-OHP (10.62 vs. 2.52 μg/L), p16(INK4α) methylation (7.95% vs. 1.14% for 22 "hot" CpG sites), and CBMN (7.28% vs. 2.92%) in PBLs. p16(INK4α) hypermethylation in PAH-exposed workers exhibited CpG site specificity. Among the 35 CpG sites we analyzed, 22 were significantly hypermethylated. These 22 hypermethylated CpG sites were positively correlated to levels of urinary 1-OHP and CBMN in PBLs. Moreover, the hypermethylation and suppression of p16 expression was also found in BaP-transformed HBER cells. CONCLUSION PAH exposure induced CpG site-specific hypermethylation of p16(INK4α) gene. The degree of p16(INK4α) methylation was associated with the levels of DNA damage and internal exposure. IMPACT p16(INK4α) hypermethylation might be an essential biomarker for the exposure to PAHs and for early diagnosis of cancer.
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Affiliation(s)
- Ping Yang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
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Sundar IK, Rahman I. Vitamin d and susceptibility of chronic lung diseases: role of epigenetics. Front Pharmacol 2011; 2:50. [PMID: 21941510 PMCID: PMC3171063 DOI: 10.3389/fphar.2011.00050] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/10/2011] [Indexed: 02/06/2023] Open
Abstract
Vitamin D deficiency is linked to accelerated decline in lung function, increased inflammation, and reduced immunity in chronic lung diseases. Epidemiological studies have suggested that vitamin D insufficiency is associated with low lung function in susceptible subjects who are exposed to higher levels of environmental agents (airborne particulates). Recent studies have highlighted the role of vitamin D and vitamin D receptor (VDR) in regulation of several genes that are involved in inflammation, immunity, cellular proliferation, differentiation, and apoptosis. Vitamin D has also been implicated in reversal of steroid resistance and airway remodeling, which are the hallmarks of chronic obstructive pulmonary disease (COPD) and severe asthma. VDR protein level is decreased in lungs of patients with COPD. VDR deficient mice develop an abnormal lung phenotype with characteristics of COPD, such as airspace enlargement and decline in lung function associated with increased lung inflammatory cellular influx, and immune-lymphoid aggregates formation. Dietary vitamin D may regulate epigenetic events, in particular on genes which are responsible for COPD susceptibility. Active metabolite of vitamin D, 1,25-dihydroxyvitamin D3 plays an essential role in cellular metabolism and differentiation via its nuclear receptor (VDR) that cooperates with several other chromatin modification enzymes (histone acetyltransferases and histone deacetylases), thereby mediating complex epigenetic events in vitamin D signaling and metabolism. This review provides an update on the current knowledge and understanding on vitamin D, and susceptibility of chronic lung diseases in relation to the possible role of epigenetics in its molecular action. Understanding the molecular epigenetic mechanism of vitamin D/VDR would provide rationale for dietary vitamin D-mediated intervention in prevention and management of chronic lung diseases linked with vitamin D deficiency.
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Affiliation(s)
- Isaac K Sundar
- Lung Biology and Disease Program, Department of Environmental Medicine, University of Rochester Medical Center Rochester, NY, USA
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Abstract
Long-term supplementation with folic acid may improve cognitive performance in older individuals. The relationship between folate status and cognitive performance might be mediated by changes in methylation capacity, as methylation reactions are important for normal functioning of the brain. Although aberrant DNA methylation has been implicated in neurodevelopmental disorders, the relationship between DNA methylation status and non-pathological cognitive functioning in human subjects has not yet been investigated. The present study investigated the associations between global DNA methylation and key domains of cognitive functioning in healthy older adults. Global DNA methylation, defined as the percentage of methylated cytosine to total cytosine, was measured in leucocytes by liquid chromatography-MS/MS, in 215 men and women, aged 50-70 years, who participated in the Folic Acid and Carotid Intima-Media Thickness (FACIT) study (clinical trial registration number NCT00110604). Cognitive performance was assessed by means of the Visual Verbal Word Learning Task, the Stroop Colour-Word Interference Test, the Concept Shifting Test, the Letter-Digit Substitution Test and the Verbal Fluency Test. Using hierarchical linear regression analyses adjusted for age, sex, level of education, alcohol consumption, smoking status, physical activity, erythrocyte folate concentration and 5,10-methylenetetrahydrofolate reductase 677 C → T genotype, we found that global DNA methylation was not related to cognitive performance on any of the domains measured. The present study results do not support the hypothesis that global DNA methylation, as measured in leucocytes, might be associated with cognitive functioning in healthy older individuals.
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Abstract
Dietary exposures can have consequences for health years or decades later and this raises questions about the mechanisms through which such exposures are 'remembered' and how they result in altered disease risk. There is growing evidence that epigenetic mechanisms may mediate the effects of nutrition and may be causal for the development of common complex (or chronic) diseases. Epigenetics encompasses changes to marks on the genome (and associated cellular machinery) that are copied from one cell generation to the next, which may alter gene expression, but which do not involve changes in the primary DNA sequence. These include three distinct, but closely inter-acting, mechanisms including DNA methylation, histone modifications and non-coding microRNAs (miRNA) which, together, are responsible for regulating gene expression not only during cellular differentiation in embryonic and foetal development but also throughout the life-course. This review summarizes the growing evidence that numerous dietary factors, including micronutrients and non-nutrient dietary components such as genistein and polyphenols, can modify epigenetic marks. In some cases, for example, effects of altered dietary supply of methyl donors on DNA methylation, there are plausible explanations for the observed epigenetic changes, but to a large extent, the mechanisms responsible for diet-epigenome-health relationships remain to be discovered. In addition, relatively little is known about which epigenomic marks are most labile in response to dietary exposures. Given the plasticity of epigenetic marks and their responsiveness to dietary factors, there is potential for the development of epigenetic marks as biomarkers of health for use in intervention studies.
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Affiliation(s)
- J A McKay
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
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Hutajulu SH, Indrasari SR, Indrawati LPL, Harijadi A, Duin S, Haryana SM, Steenbergen RDM, Greijer AE, Middeldorp JM. Epigenetic markers for early detection of nasopharyngeal carcinoma in a high risk population. Mol Cancer 2011; 10:48. [PMID: 21535891 PMCID: PMC3114786 DOI: 10.1186/1476-4598-10-48] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 05/02/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Undifferentiated nasopharyngeal carcinoma (NPC) is strongly related to Epstein-Barr virus (EBV) infection, allowing aberrant antibodies against EBV and viral DNA load as screening tools in high risk populations. Methylation analysis in the promoter of tumor suppressor genes (TSGs) may serve as a complementary marker for identifying early cases. This study determined methylation status of multiple TSGs and evaluated whether it may improve early detection. METHODS Nasopharyngeal brushings were taken from 53 NPC patients, 22 high risk subjects and 25 healthy EBV carriers. Corresponding NPC paraffin tissue was included. DNA was bisulfite-modified preceding analysis by methylation-specific PCR (MSP). Ten TSGs were studied. RESULTS NPC paraffin and brushing DNA revealed an 81.8% concordance so that MSP analysis was done using either one of both specimens. NPC samples showed methylation for individual TSGs (DAPK1 79.2%, CDH13 77.4%, DLC1 76.9%, RASSF1A 75.5%, CADM1 69.8%, p16 66.0%, WIF1 61.2%, CHFR 58.5%, RIZ1 56.6% and RASSF2A 29.2%). High risk individuals, having elevated EBV IgA and viral load, showed high frequency of methylation of CDH13, DAPK1, DLC1 and CADM1, but low frequency of methylation of p16 and WIF1 and undetectable methylation of RASSF1A, CHFR, RIZ1 and RASSF2A. Healthy subjects showed similar patterns as high risk individuals. A combination of RASSF1A and p16 gave good discrimination between NPC and non-NPC, but best results were combined analysis of five methylation markers (RASSF1A, p16, WIF1, CHFR and RIZ1) with detection rate of 98%. CONCLUSION Multiple marker MSP is proposed as a complementary test for NPC risk assessment in combination with EBV-based markers.
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Affiliation(s)
- Susanna H Hutajulu
- Faculty of Medicine/Dr Sardjito Hospital, Universitas Gadjah Mada,Yogyakarta, Indonesia
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Hypermethylation of CCND2 May Reflect a Smoking-Induced Precancerous Change in the Lung. JOURNAL OF ONCOLOGY 2011; 2011:950140. [PMID: 21577262 PMCID: PMC3090638 DOI: 10.1155/2011/950140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/12/2011] [Accepted: 01/26/2011] [Indexed: 11/25/2022]
Abstract
It remains unknown whether tobacco smoke induces DNA hypermethylation as an early event in carcinogenesis or as a late event, specific to overt cancer tissue. Using MethyLight assays, we analyzed 316 lung tissue samples from 151 cancer-free subjects (121 ever-smokers and 30 never-smokers) for hypermethylation of 19 genes previously observed to be hypermethylated in nonsmall cell lung cancers. Only APC (39%), CCND2 (21%), CDH1 (7%), and RARB (4%) were hypermethylated in >2% of these cancer-free subjects. CCND2 was hypermethylated more frequently in ever-smokers (26%) than in never-smokers (3%). CCND2 hypermethylation was also associated with increased age and upper lobe sample location. APC was frequently hypermethylated in both ever-smokers (41%) and never-smokers (30%). BVES, CDH13, CDKN2A (p16), CDKN2B, DAPK1, IGFBP3, IGSF4, KCNH5, KCNH8, MGMT, OPCML, PCSK6, RASSF1, RUNX, and TMS1 were rarely hypermethylated (<2%) in all subjects. Hypermethylation of CCND2 may reflect a smoking-induced precancerous change in the lung.
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Pirouzpanah S, Taleban FA, Atri M, Abadi AR, Mehdipour P. The effect of modifiable potentials on hypermethylation status of retinoic acid receptor-beta2 and estrogen receptor-alpha genes in primary breast cancer. Cancer Causes Control 2010; 21:2101-11. [PMID: 20711807 DOI: 10.1007/s10552-010-9629-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 07/30/2010] [Indexed: 02/08/2023]
Abstract
Epigenetic silencing of retinoic acid receptor-beta2 (RARbeta2) and estrogen receptor-alpha (ERalpha) expressions have been revealed to be important in the development of approaches for diagnosis and therapy of breast cancer. We aimed to explore the correlation of some potential factors with the hypermethylation status of RARbeta2 and ERalpha genes among Iranian breast cancer patients. The hypermethylation status was investigated in 137 dissected tissues from primary breast cancer patients through methylation-specific PCR. Overall, the methylation frequencies of RARbeta2 and ERalpha genes were observed in 36.5 and 51.1% of participants, respectively. The hypermethylated RARbeta2 was associated with younger age at diagnosis and negative family history of breast cancer. The hypermethylation of ERalpha was correlated positively with smoking, duration of estradiol exposure, ER-negativity in tumors and body mass index (at 5 years ago). The plasma levels of folate and vitamin B(12) were inversely related to the hypermethylation status of ERalpha, after controlling for covariates. The risk of ERalpha hypermethylation was increased with high plasma level of total homocysteine. In conclusion, our data provide new insights into the possible effect of some lifestyle-related factors on the aberrant methylation drift of ERalpha and RARbeta2 genes in breast cancer.
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Affiliation(s)
- Saeed Pirouzpanah
- Department of Human Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University M.C., Tehran 19395-4741, Iran.
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McHale CM, Zhang L, Hubbard AE, Smith MT. Toxicogenomic profiling of chemically exposed humans in risk assessment. Mutat Res 2010; 705:172-83. [PMID: 20382258 PMCID: PMC2928857 DOI: 10.1016/j.mrrev.2010.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 04/01/2010] [Indexed: 12/13/2022]
Abstract
Gene-environment interactions contribute to complex disease development. The environmental contribution, in particular low-level and prevalent environmental exposures, may constitute much of the risk and contribute substantially to disease. Systematic risk evaluation of the majority of human chemical exposures, has not been conducted and is a goal of regulatory agencies in the U.S. and worldwide. With the recent recognition that toxicological approaches more predictive of effects in humans are required for risk assessment, in vitro human cell line data as well as animal data are being used to identify toxicity mechanisms that can be translated into biomarkers relevant to human exposure studies. In this review, we discuss how data from toxicogenomic studies of exposed human populations can inform risk assessment, by generating biomarkers of exposure, early effect, and/or susceptibility, elucidating mechanisms of action underlying exposure-related disease, and detecting response at low doses. Good experimental design incorporating precise, individual exposure measurements, phenotypic anchors (pre-disease or traditional toxicological markers), and a range of relevant exposure levels, is necessary. Further, toxicogenomic studies need to be designed with sufficient power to detect true effects of the exposure. As more studies are performed and incorporated into databases such as the Comparative Toxicogenomics Database (CTD) and Chemical Effects in Biological Systems (CEBS), data can be mined for classification of newly tested chemicals (hazard identification), and, for investigating the dose-response, and inter-relationship among genes, environment and disease in a systems biology approach (risk characterization).
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Affiliation(s)
- Cliona M. McHale
- School of Public Health, Division of Environmental Health Sciences, University of California, Berkeley, CA 94720
| | - Luoping Zhang
- School of Public Health, Division of Environmental Health Sciences, University of California, Berkeley, CA 94720
| | - Alan E. Hubbard
- School of Public Health, Division of Biostatistics, University of California, Berkeley, CA 94720
| | - Martyn T. Smith
- School of Public Health, Division of Environmental Health Sciences, University of California, Berkeley, CA 94720
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Liu J, Hutchison K, Perrone-Bizzozero N, Morgan M, Sui J, Calhoun V. Identification of genetic and epigenetic marks involved in population structure. PLoS One 2010; 5:e13209. [PMID: 20949057 PMCID: PMC2951359 DOI: 10.1371/journal.pone.0013209] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/11/2010] [Indexed: 12/31/2022] Open
Abstract
Population structure is well known as a prevalent and important factor in genetic studies, but its relevance in epigenetics is unclear. Very little is known about the affected epigenetic markers and their connections with genetics. In this study we assessed the impact of population diversity on genome wide single nucleotide polymorphisms (SNPs) and DNA methylation levels in 196 participants from five ethnic groups, using principle and independent component analyses. Three population stratification factors (PSFs) were identified in the genomic SNP dataset, accounting for a relatively large portion of total variance (6%). In contrast, only one PSF was identified in genomic methylation dataset accounting for 0.2% of total variance. This methylation PSF, however, was significantly correlated with the largest SNP PSF (r = 0.72, p<1E-23). We then investigated the top contributing markers in these two linked PSFs. The SNP PSF predominantly consists of 8 SNPs from three genes, SLC45A2, HERC2 and CTNNA2, known to encode skin/hair/eye color. The methylation PSF includes 48 methylated sites in 44 genes coding for basic molecular functions, including transcription regulation, DNA binding, cytokine, and transferase activity. Among them, 8 sites are either hypo- or hyper-methylated correlating to minor alleles of SNPs in the SNP PSF. We found that the genes in SNP and methylation PSFs share common biological processes including sexual/multicellular organism reproduction, cell-cell signaling and cytoskeleton organization. We further investigated the transcription regulatory network operating at these genes and identified that most of genes closely interact with ID2, which encodes for a helix-loop-helix inhibitor of DNA binding. Overall, our results show a significant correlation between genetic and epigenetic population stratification, and suggest that the interrelationship between genetic and epigenetic population structure is mediated via complex multiple gene interactions in shared biological processes, through possibly, SNP-dependent modulation and ID2 repressor function.
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Affiliation(s)
- Jingyu Liu
- The Mind Research Network, Albuquerque, New Mexico, United States of America.
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Aguilera O, Fernández AF, Muñoz A, Fraga MF. Epigenetics and environment: a complex relationship. J Appl Physiol (1985) 2010; 109:243-51. [PMID: 20378707 DOI: 10.1152/japplphysiol.00068.2010] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The epigenomes of higher organisms constantly change over time. Many of these epigenetic changes are necessary to direct normal cellular development and differentiation in the developing organism. However, developmental abnormalities may occur in response to inappropriate epigenetic signaling that occurs secondarily to still poorly understood causes. In addition to genetic and stochastic influences on epigenetic processes, epigenetic variation can arise as a consequence of environmental factors. Here we review the effects of such environmental factors on the epigenomes of higher organisms. We discuss the possible impact of epigenetic changes on physiological and pathophysiological processes, depending in part on whether these changes occur during embryonic development or adulthood.
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Affiliation(s)
- Oscar Aguilera
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
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