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Marson F, Zampieri M, Verdone L, Bacalini MG, Ravaioli F, Morandi L, Chiarella SG, Vetriani V, Venditti S, Caserta M, Raffone A, Dotan Ben-Soussan T, Reale A. Quadrato Motor Training (QMT) is associated with DNA methylation changes at DNA repeats: A pilot study. PLoS One 2023; 18:e0293199. [PMID: 37878626 PMCID: PMC10599555 DOI: 10.1371/journal.pone.0293199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/07/2023] [Indexed: 10/27/2023] Open
Abstract
The control of non-coding repeated DNA by DNA methylation plays an important role in genomic stability, contributing to health and healthy aging. Mind-body practices can elicit psychophysical wellbeing via epigenetic mechanisms, including DNA methylation. However, in this context the effects of movement meditations have rarely been examined. Consequently, the current study investigates the effects of a specifically structured movement meditation, called the Quadrato Motor Training (QMT) on psychophysical wellbeing and on the methylation level of repeated sequences. An 8-week daily QMT program was administered to healthy women aged 40-60 years and compared with a passive control group matched for gender and age. Psychological well-being was assessed within both groups by using self-reporting scales, including the Meaning in Life Questionnaire [MLQ] and Psychological Wellbeing Scale [PWB]). DNA methylation profiles of repeated sequences (ribosomal DNA, LINE-1 and Alu) were determined in saliva samples by deep-sequencing. In contrast to controls, the QMT group exhibited increased Search for Meaning, decreased Presence of Meaning and increased Positive Relations, suggesting that QMT may lessen the automatic patterns of thinking. In the QMT group, we also found site-specific significant methylation variations in ribosomal DNA and LINE-1 repeats, consistent with increased genome stability. Finally, the correlations found between changes in methylation and psychometric indices (MLQ and PWB) suggest that the observed epigenetic and psychological changes are interrelated. Collectively, the current results indicate that QMT may improve psychophysical health trajectories by influencing the DNA methylation of specific repetitive sequences.
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Affiliation(s)
- Fabio Marson
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
- Neuroimaging Laboratory, Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Loredana Verdone
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Maria Giulia Bacalini
- Brain Aging Laboratory, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Dep. of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Luca Morandi
- Dep. of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Salvatore Gaetano Chiarella
- Institute of Sciences and Technologies of Cognition (ISTC), National Council of Research (CNR), Rome, Italy
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Valerio Vetriani
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Sabrina Venditti
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Micaela Caserta
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Antonino Raffone
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Tal Dotan Ben-Soussan
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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Shen Y, Kioumourtzoglou MA, Wu H, Vokonas P, Spiro A, Navas-Acien A, Baccarelli AA, Gao F. Cohort Network: A Knowledge Graph toward Data Dissemination and Knowledge-Driven Discovery for Cohort Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:8236-8244. [PMID: 37224396 PMCID: PMC10597774 DOI: 10.1021/acs.est.2c08174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Contemporary environmental health sciences draw on large-scale longitudinal studies to understand the impact of environmental exposures and behavior factors on the risk of disease and identify potential underlying mechanisms. In such studies, cohorts of individuals are assembled and followed up over time. Each cohort generates hundreds of publications, which are typically neither coherently organized nor summarized, hence limiting knowledge-driven dissemination. Hence, we propose a Cohort Network, a multilayer knowledge graph approach to extract exposures, outcomes, and their connections. We applied the Cohort Network on 121 peer-reviewed papers published over the past 10 years from the Veterans Affairs (VA) Normative Aging Study (NAS). The Cohort Network visualized connections between exposures and outcomes across different publications and identified key exposures and outcomes, such as air pollution, DNA methylation, and lung function. We demonstrated the utility of the Cohort Network for new hypothesis generation, e.g., identification of potential mediators of exposure-outcome associations. The Cohort Network can be used by investigators to summarize the cohort's research and facilitate knowledge-driven discovery and dissemination.
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Affiliation(s)
- Yike Shen
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Marianthi-Anna Kioumourtzoglou
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Haotian Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, Massachusetts 02130, United States
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Avron Spiro
- VA Normative Aging Study, VA Boston Healthcare System, Boston, Massachusetts 02130, United States
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts 02118, United States
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Feng Gao
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
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Chang WCL, Ghosh J, Cooper HS, Vanderveer L, Schultz B, Zhou Y, Harvey KN, Kaunga E, Devarajan K, Li Y, Jelinek J, Fragoso MF, Sapienza C, Clapper ML. Folic Acid Supplementation Promotes Hypomethylation in Both the Inflamed Colonic Mucosa and Colitis-Associated Dysplasia. Cancers (Basel) 2023; 15:2949. [PMID: 37296911 PMCID: PMC10252136 DOI: 10.3390/cancers15112949] [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: 05/05/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
PURPOSE The purpose of this study was to assess the effect of folic acid (FA) supplementation on colitis-associated colorectal cancer (CRC) using the azoxymethane/dextran sulfate sodium (AOM/DSS) model. METHODS Mice were fed a chow containing 2 mg/kg FA at baseline and randomized after the first DSS treatment to receive 0, 2, or 8 mg/kg FA chow for 16 weeks. Colon tissue was collected for histopathological evaluation, genome-wide methylation analyses (Digital Restriction Enzyme Assay of Methylation), and gene expression profiling (RNA-Seq). RESULTS A dose-dependent increase in the multiplicity of colonic dysplasias was observed, with the multiplicity of total and polypoid dysplasias higher (64% and 225%, respectively) in the 8 mg FA vs. the 0 mg FA group (p < 0.001). Polypoid dysplasias were hypomethylated, as compared to the non-neoplastic colonic mucosa (p < 0.05), irrespective of FA treatment. The colonic mucosa of the 8 mg FA group was markedly hypomethylated as compared to the 0 mg FA group. Differential methylation of genes involved in Wnt/β-catenin and MAPK signaling resulted in corresponding alterations in gene expression within the colonic mucosa. CONCLUSIONS High-dose FA created an altered epigenetic field effect within the non-neoplastic colonic mucosa. The observed decrease in site-specific DNA methylation altered oncogenic pathways and promoted colitis-associated CRC.
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Affiliation(s)
- Wen-Chi L. Chang
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (J.G.); (B.S.)
| | - Harry S. Cooper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
- Department of Pathology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Lisa Vanderveer
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
| | - Bryant Schultz
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (J.G.); (B.S.)
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Kristen N. Harvey
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
| | - Esther Kaunga
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
| | - Karthik Devarajan
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Yuesheng Li
- DNA Sequencing and Genomic Core Facility, National Heart, Lung, and Blood Institute, NIH, 10 Center Drive, Bethesda, MD 20892, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (J.G.); (B.S.)
| | - Mariana F. Fragoso
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (J.G.); (B.S.)
| | - Margie L. Clapper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA (L.V.); (E.K.)
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Xu R, Li S, Wu Y, Yue X, Wong EM, Southey MC, Hopper JL, Abramson MJ, Li S, Guo Y. Wildfire-related PM 2.5 and DNA methylation: An Australian twin and family study. ENVIRONMENT INTERNATIONAL 2023; 171:107704. [PMID: 36542997 DOI: 10.1016/j.envint.2022.107704] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Wildfire-related fine particulate matter (PM2.5) has many adverse health impacts, but its impacts on human epigenome are unknown. We aimed to evaluate the associations between long-term exposure to wildfire-related PM2.5 and blood DNA methylation, and whether the associations differ from those with non-wildfire-related PM2.5. METHODS We studied 479 Australian women comprising 132 twin pairs and 215 of their sisters. Blood-derived DNA methylation was measured using the HumanMethylation450 BeadChip array. Data on 3-year (year of blood collection and previous two years) average wildfire-related and non-wildfire-related PM2.5 at 0.01°×0.01° spatial resolution were created by combining information from satellite observations, chemical transport models, and ground-based observations. Exposure data were linked to each participant's home address, assuming the address did not change during the exposure window. For DNA methylation of each cytosine-guanine dinucleotide (CpG), and for global DNA methylation represented by the average of all measured CpGs or CpGs in repetitive elements, we evaluated their associations with wildfire- or non-wildfire-related PM2.5 using a within-sibship analysis controlling for factors shared between siblings and other important covariates. Differentially methylated regions (DMRs) were defined by comb-p and DMRcate. RESULTS The 3-year average wildfire-related PM2.5 (range: 0.3 to 7.6 µg/m3, mean: 1.6 µg/m3) was negatively, but not significantly (p-values greater than 0.05) associated with all seven global DNA methylation measures. There were 26 CpGs and 33 DMRs associated with wildfire-related PM2.5 (Bonferroni adjusted p-value < 0.05) mapped to 47 genes enriched for pathways related to inflammatory regulation and platelet activation. These genes have been related to many human diseases or phenotypes e.g., cancer, mental disorders, diabetes, obesity, asthma, blood pressure. These CpGs, DMRs and enriched pathways did not overlap with the 1 CpG and 7 DMRs associated with non-wildfire-related PM2.5. CONCLUSIONS Long-term exposure to wildfire-related PM2.5 was associated with various blood DNA methylation signatures in Australian women, and these were distinct from those associated with non-wildfire-related PM2.5.
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Affiliation(s)
- Rongbin Xu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yao Wu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Xu Yue
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Division, Cancer Council Victoria, VIC 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shuai Li
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia.
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Tajbakhsh J, Mortazavi F, Gupta NK. DNA methylation topology differentiates between normal and malignant in cell models, resected human tissues, and exfoliated sputum cells of lung epithelium. Front Oncol 2022; 12:991120. [DOI: 10.3389/fonc.2022.991120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGlobal DNA hypomethylation is a prominent feature of cancer cells including lung cancer, that has not been widely explored towards cancer diagnosis. In this study we assess the comparative distribution of global DNA methylation in normal cells versus cancer cells in various specimen models.MethodsWe used in situ immunofluorescence labeling of overall 5-methylcytosine (5mC) and covisualization of global DNA (gDNA) by 4’,6-diamidino-2-phenylindole (DAPI), confocal microscopy and 3D image analysis to derive 5mC/DAPI colocalization patterns in human cell lines (BEAS-2B, A549, H157) and upper respiratory epithelial cells derived from various sources (i.e., sputum from healthy and cancer patients, and resected tissues from normal parenchyma and lung tumors).ResultsBy introducing 5mC/DAPI colocalization index as a metric we could distinguish between normal epithelial cells and aberrantly hypomethylated cancer cells. Cultured lung cancer cells (H157 and A549) had significantly lower indices compared to normal cells (BEAS-2B). Furthermore, we were able to identify such extensively hypomethylated low-index cells in tumor tissues and the matching sputum from cancer patients. In contrast, the indices of cells derived from sputum of healthy individuals had more similarity to epithelial cells of normal parenchyma and the phenotypically normal BEAS-2B cells.ConclusionsThe results suggest that 5mC topology using high-resolution image cytometry shows potential for identifying hypomethylated cancerous cells in human tissues and amongst normal cells in matching sputum, which may render a valuable surrogate for biopsied tissues. This promising feature deserves further validation in more comprehensive studies.
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Issah I, Arko-Mensah J, Rozek LS, Zarins KR, Agyekum TP, Dwomoh D, Basu N, Batterman S, Robins TG, Fobil JN. Global DNA (LINE-1) methylation is associated with lead exposure and certain job tasks performed by electronic waste workers. Int Arch Occup Environ Health 2021; 94:1931-1944. [PMID: 34148106 DOI: 10.1007/s00420-021-01733-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE This study assessed the associations between blood and urine levels of toxic metals; cadmium (Cd) and lead (Pb), and methylation levels of the LINE-1 gene among e-waste and control populations in Ghana. METHODS The study enrolled 100 male e-waste workers and 51 all-male non-e-waste workers or controls. The concentrations of Cd and Pb were measured in blood and urine using inductively coupled plasma mass spectrometry, while LINE1 methylation levels were assessed by pyrosequencing of bisulfite-converted DNA extracted from whole blood. Single and multiple metals linear regression models were used to determine the associations between metals and LINE1 DNA methylation. RESULTS Blood lead (BPb) and urine lead (UPb) showed higher median concentrations among the e-waste workers than the controls (76.82 µg/L vs 40.25 µg/L, p ≤ 0.001; and 6.89 µg/L vs 3.43 µg/L, p ≤ 0.001, respectively), whereas blood cadmium (BCd) concentration was lower in the e-waste workers compared to the controls (0.59 µg/L vs 0.81 µg/L, respectively, p = 0.003). There was no significant difference in LINE1 methylation between the e-waste and controls (85.16 ± 1.32% vs 85.17 ± 1.11%, p = 0.950). In our single metal linear regression models, BPb was significantly inversely associated with LINE1 methylation in the control group (βBPb = - 0.027, 95% CI - 0.045, - 0.010, p = 0.003). In addition, a weak association between BPb and LINE1 was observed in the multiple metals analysis in the e-waste worker group (βBPb = - 0.005, 95% CI - 0.011, 0.000, p = 0.058). CONCLUSION Continuous Pb exposure may interfere with LINE1 methylation, leading to epigenetic alterations, thus serving as an early epigenetic marker for future adverse health outcomes.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana.
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Duah Dwomoh
- Department of Biostatistics, School of Public Health, University of Ghana, P.O. Box LG13, Accra, Ghana
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
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Liu F, Wang X, Duan C, Zhang J, Li X. Hepatoxicity mechanism of cantharidin-induced liver LO2 cells by LC-MS metabolomics combined traditional approaches. Toxicol Lett 2020; 333:49-61. [PMID: 32726682 DOI: 10.1016/j.toxlet.2020.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Hepatotoxicity induced by Mylabris has been reported in both clinical and animal experiments. Cantharidin (CTD), the main active compound of Mylabris was responsible for the hepatotoxicity, which aroused widespread concern. However, the mechanism of CTD hepatotoxicity remained unclear. In this study, LO2 cells were exposed to two doses of CTD (6.25 and 25 μM) for 12 h, the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were measured. The metabolites in LO2 cells were profiled by LC-MS. Partial least squares discriminant analysis and orthogonal partial least squares discriminant analysis were used for screening potential biomarkers. The MetPA software was used for clustering and pathway analysis. Network pharmacology was used to predict the genes acted with potential biomarkers. Compared with the control group, the levels of ALT, AST, and LDH was significantly increased after CTD treatment. A total of 46 potential biomarkers for hepatotoxicity induced by CTD were identified. And downregulated potential biomarkers reflected the inhibitory effects of CTD toxicity on metabolism of LO2. Moreover, CTD-induced liver toxicity of LO2 cells is mainly related to three pathways: cysteine and methionine metabolism; glutathione metabolism; and glycine, serine, and threonine metabolism. Furtherly, the mRNA expression of CES2, DNMT1, NOS1, NOS3, S1PR2, and CES1 screened by network pharmacology were regulated by CTD. These studies provide valuable mechanistic insights into CTD-associated hepatotoxicity that will aid in the development of therapeutic prevention and treatment options for this liver disease.
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Affiliation(s)
- Fang Liu
- Basic Medical School, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xiaoning Wang
- School of pharmacy, Zunyi Medical University, Zunyi, Guizhou, China
| | - Cancan Duan
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jianyong Zhang
- School of pharmacy, Zunyi Medical University, Zunyi, Guizhou, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China.
| | - Xiaofei Li
- Basic Medical School, Zunyi Medical University, Zunyi, Guizhou, China.
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Ye D, Jiang D, Zhang X, Mao Y. Alu Methylation and Risk of Cancer: A Meta-analysis. Am J Med Sci 2020; 359:271-280. [PMID: 32268941 DOI: 10.1016/j.amjms.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The association between Alu methylation and risk of cancer remains uncertain. This meta-analysis was conducted to elucidate this issue. MATERIALS AND METHODS PubMed and Web of Science up to December 31, 2018, and the reference lists of studies, as well as those presented in relevant meta-analyses and reviews were systematically searched. Standardized mean difference (SMD) in Alu methylation level between cases and controls were pooled using random effects model and assessed heterogeneity between strata by stratified factors using meta-regression model. Sensitivity analysis and publication bias test were also conducted. RESULTS Twenty-five articles, including 2719 cases and 3018 controls were included in the meta-analysis. The significant difference in Alu methylation level between cancer cases and controls was greater in tissue (SMD = -1.89, 95% CI: -2.72, -1.05) than blood (SMD = -0.46, 95% CI: -0.82, -0.09), and heterogeneity was found in materials (P = 0.038). In tissue samples, Alu hypomethylation was found in carcinoma (SMD = -2.50, 95% CI: -3.51, -1.48), while not in non-carcinoma. The inverse associations were consistently found in subgroups stratified by data sources and quality score in tissue samples, and publication year was considered to be the potential source of between-study heterogeneity. Moreover, reduced Alu methylation level was found in the European subgroup, detection method of SIRPH and COBRA, and original data source in blood samples. CONCLUSIONS Alu hypomethylation was associated with increased risk of cancer, which could be a potential biomarker for cancer.
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Affiliation(s)
- Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Danjie Jiang
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xinhan Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Yingying Mao
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China.
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Sándor S, Kubinyi E. Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging. Front Genet 2019; 10:948. [PMID: 31681409 PMCID: PMC6813227 DOI: 10.3389/fgene.2019.00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.
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Affiliation(s)
- Sára Sándor
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
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Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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11
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Gogna P, O'Sullivan DE, King WD. The effect of inflammation-related lifestyle exposures and interactions with gene variants on long interspersed nuclear element-1 DNA methylation. Epigenomics 2018; 10:785-796. [PMID: 29888958 DOI: 10.2217/epi-2017-0164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the relationship between inflammation-related lifestyle factors and long interspersed nuclear element-1 (LINE-1) DNA methylation, and test for interaction by gene variants involved in one-carbon metabolism. PATIENTS & METHODS The study population consisted of 280 individuals undergoing colonoscopy screening. Multivariable linear regression was employed to examine associations of physical activity, BMI and NSAID use with LINE-1 DNA methylation and interactions with MTR and MTHFR gene variants. RESULTS The highest quartile of physical activity compared with the lowest was associated with higher LINE-1 DNA methylation (p = 0.005). Long-term NSAID use and a normal BMI were associated with increased LINE-1 DNA methylation among individuals with the variant MTR allele (p = 0.02; p = 0.03). CONCLUSION This study provides evidence that inflammation-related exposures may influence LINE-1 DNA methylation.
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Affiliation(s)
- Priyanka Gogna
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Dylan E O'Sullivan
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
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12
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Lu S, Niu Z, Chen Y, Tu Q, Zhang Y, Chen W, Tong W, Zhang Z. Repetitive Element DNA Methylation is Associated with Menopausal Age. Aging Dis 2018; 9:435-443. [PMID: 29896431 PMCID: PMC5988598 DOI: 10.14336/ad.2017.0810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/10/2017] [Indexed: 12/21/2022] Open
Abstract
To investigate associations between the age of menopause and the DNA methylation levels of two repetitive elements, Alu and LINE-1, we performed plasma DNA extraction on 161 subjects and serum cell-free DNA extraction on 120 subjects. We grouped women by menopausal age as follows: ≤ 48 years (earlier menopause), ≥ 52 years (later menopause), and 48-52 years (control). The DNA methylation levels of Alu and LINE-1 were measured by MethyLight PCR. The results showed that the DNA methylation levels of both Alu and LINE-1 were inversely correlated with menopausal age in the plasma DNA cohort (r = 0.079, P < 0.001 for Alu; r = 0.045, P = 0.007 for LINE-1) as well as in the serum DNA cohort (r = 0.087, P = 0.001 for Alu; r = 0.041, P = 0.026 for LINE-1). Alu methylation levels in both the plasma and serum DNA cohorts and LINE-1 methylation levels in the plasma cohort were remarkably higher in the earlier menopause group than in the later menopause and control groups (P < 0.01 and P < 0.05, respectively). In the serum DNA cohort, the LINE-1 methylation levels in the later menopause group were significantly lower than that in the earlier menopause group and control group (P < 0.05). Therefore, methylation levels of Alu and LINE-1 were significantly associated with menopausal age. Women with earlier menopause showed hypermethylation in both repetitive elements, while women with later menopause showed hypomethylation. These findings suggest that altered DNA methylation in leukocytes and serum cell-free DNA may represent a biomarker of menopausal age.
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Affiliation(s)
- Sha Lu
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China.,2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Zheng Niu
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Yueming Chen
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Qiaofeng Tu
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Yue Zhang
- 2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Wenli Chen
- 4Department of Obstetrics and Gynecology, the Second People's Hospital of Tonglu, Hangzhou, China
| | - Wenjuan Tong
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Zhifen Zhang
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China.,2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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13
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Davis A, Tao MH, Chen J, Scelo G, Bencko V, Fabianova E, Foretova L, Janout V, Lissowska J, Mates D, Mates IN, Rudnai P, Zaridze D, Boffetta P. No association between global DNA methylation in peripheral blood and lung cancer risk in nonsmoking women: results from a multicenter study in Eastern and Central Europe. Eur J Cancer Prev 2018; 27:1-5. [PMID: 27045934 DOI: 10.1097/cej.0000000000000244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alterations in global DNA methylation have been suggested to play an important role in cancer development. We evaluated the association of global DNA methylation in peripheral blood with the risk of lung cancer in nonsmoking women from six countries in Central and Eastern Europe. This multicenter case-control study included primary, incident lung cancer cases diagnosed from 1998 to 2001 and controls frequency-matched for geographic area, sex, and age. Global methylation was assessed in peripheral blood DNA from 83 nonsmoking female cases and 181 nonsmoking female controls using the luminometric methylation assay (LUMA). Unconditional logistic regression models were used to estimate associations between DNA methylation in the blood and the risk of lung cancer. LUMA methylation level was not associated with the risk of lung cancer in nonsmoking women. Associations were not significantly different according to different strata of age, BMI, alcohol drinking, or second-hand tobacco smoke exposure status. In our study of nonsmoking women, the LUMA methylation level in peripheral blood was not associated with the risk of lung cancer. Our findings do not support an association of global blood DNA methylation with the risk of lung cancer in nonsmoking women.
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Affiliation(s)
- Ann Davis
- Department of Biostatistics and Epidemiology, University of North Texas Health Science Center, Fort Worth, Texas
| | - Meng-Hua Tao
- Department of Biostatistics and Epidemiology, University of North Texas Health Science Center, Fort Worth, Texas
- Institute for Translational Epidemiology
| | - Jia Chen
- Department of Community and Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Vladimir Bencko
- Institute of Hygiene and Epidemiology, First Faculty of Medicine, Charles University in Prague, Prague
| | - Eleonora Fabianova
- Department of Occupational Health, Specialized State Health Institute, Banska Bystrica, Slovakia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Cancer Institute and Medical Faculty of Masaryk University, Brno
| | - Vladimir Janout
- Department of Preventive Medicine, Palacky University of Medicine, Olomouc, Czech Republic
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Cancer Center and M. Sklodowska-Curie Memorial Institute of Oncology, Warsaw, Poland
| | - Dana Mates
- Institute of Hygiene, Public Health, Health Services and Management
| | - Ioan N Mates
- General Surgery Department, "St Mary" Clinical Hospital, University of Medicine and Pharmacy 'Carol Davila' Bucharest, Romania
| | - Peter Rudnai
- National Institute of Environmental Health, Budapest, Hungary
| | - David Zaridze
- Department of Epidemiology and Prevention, Russian N.N. Blokhin Cancer Research Center, Moscow, Russia
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14
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Heßelbach K, Kim GJ, Flemming S, Häupl T, Bonin M, Dornhof R, Günther S, Merfort I, Humar M. Disease relevant modifications of the methylome and transcriptome by particulate matter (PM 2.5) from biomass combustion. Epigenetics 2017; 12:779-792. [PMID: 28742980 PMCID: PMC5739103 DOI: 10.1080/15592294.2017.1356555] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Exposure to particulate matter (PM) is recognized as a major health hazard, but molecular responses are still insufficiently described. We analyzed the epigenetic impact of ambient PM2.5 from biomass combustion on the methylome of primary human bronchial epithelial BEAS-2B cells using the Illumina HumanMethylation450 BeadChip. The transcriptome was determined by the Affymetrix HG-U133 Plus 2.0 Array. PM2.5 induced genome wide alterations of the DNA methylation pattern, including differentially methylated CpGs in the promoter region associated with CpG islands. Gene ontology analysis revealed that differentially methylated genes were significantly clustered in pathways associated with the extracellular matrix, cellular adhesion, function of GTPases, and responses to extracellular stimuli, or were involved in ion binding and shuttling. Differential methylations also affected tandem repeats. Additionally, 45 different miRNA CpG loci showed differential DNA methylation, most of them proximal to their promoter. These miRNAs are functionally relevant for lung cancer, inflammation, asthma, and other PM-associated diseases. Correlation of the methylome and transcriptome demonstrated a clear bias toward transcriptional activation by hypomethylation. Genes that exhibited both differential methylation and expression were functionally linked to cytokine and immune responses, cellular motility, angiogenesis, inflammation, wound healing, cell growth, differentiation and development, or responses to exogenous matter. Disease ontology of differentially methylated and expressed genes indicated their prominent role in lung cancer and their participation in dominant cancer related signaling pathways. Thus, in lung epithelial cells, PM2.5 alters the methylome of genes and noncoding transcripts or elements that might be relevant for PM- and lung-associated diseases.
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Affiliation(s)
- Katharina Heßelbach
- a Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Gwang-Jin Kim
- b Pharmaceutical Bioinformatics, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Stephan Flemming
- b Pharmaceutical Bioinformatics, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Thomas Häupl
- c Department of Rheumatology and Clinical Immunology , Charité University Hospital Berlin , Germany
| | - Marc Bonin
- a Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Regina Dornhof
- a Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Stefan Günther
- d Pharmaceutical Bioinformatics and Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs University Freiburg , Freiburg , Germany
| | - Irmgard Merfort
- a Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Matjaz Humar
- a Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg , Freiburg , Germany
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15
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Han Y, Xu J, Kim J, Wu X, Gu J. Methylation of subtelomeric repeat D4Z4 in peripheral blood leukocytes is associated with biochemical recurrence in localized prostate cancer patients. Carcinogenesis 2017; 38:821-826. [PMID: 28854562 DOI: 10.1093/carcin/bgx064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/28/2017] [Indexed: 01/06/2023] Open
Abstract
Global DNA methylation may affect chromosome structure and genomic stability and is involved in carcinogenesis. In this study, we aimed to investigate whether methylation of pericentromeric repeat NBL2 and subtelomeric repeat D4Z4 in peripheral blood was associated with the aggressiveness of prostate cancer (PCa). We measured the methylation status of different CpG sites of NBL2 and D4Z4 in 795 PCa patients and compared their methylation levels among patients with different Gleason Score at diagnosis. We then analyzed the association of the NBL2 and D4Z4 methylation with the risk of biochemical recurrence (BCR) in patients receiving radical prostatectomy or radiotherapy using a multivariate Cox proportional hazards model. In addition, we used the Kaplan-Meier survival function and log-rank tests to assess BCR-free survival associated with D4Z4 methylation. There was no significant difference in methylation level of NBL2 and D4Z4 between clinically defined aggressive and non-aggressive PCa at diagnosis. However, the methylation of D4Z4 was associated with BCR, while the methylation of NBL2 was not. In tertile analysis, patients in the highest tertile of D4Z4 methylation had an increased risk of BCR (HR = 2.17, 95% CI 1.36-3.48) compared to patients in the lower tertiles after adjustment of age, body mass index, smoking status, pack year, D'Amico risk groups and treatments. Among the four CpG sites in this region, the association was mostly attributable to the methylation of the second CpG site of D4Z4. These data suggest that higher methylation in D4Z4 was associated with worse prognosis of localized PCa patients.
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Affiliation(s)
- Yuyan Han
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Junfeng Xu
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeri Kim
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xifeng Wu
- Department of Epidemiology and Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jian Gu
- To whom correspondence should be addressed. Tel: +713 7928016; Fax: +713 7922145;
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16
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Boyne DJ, Friedenreich CM, McIntyre JB, Courneya KS, King WD. Associations between adiposity and repetitive element DNA methylation in healthy postmenopausal women. Epigenomics 2017; 9:1267-1277. [PMID: 28874065 DOI: 10.2217/epi-2017-0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AIM To describe the association between adiposity and repetitive element DNA methylation in healthy postmenopausal women. PATIENTS & METHODS A cross-sectional study was conducted using baseline information from 289 women who participated in the Alberta Physical Activity and Breast Cancer Prevention trial. RESULTS After adjusting for important confounders, long interspersed nuclear element-1 methylation was positively associated with intra-abdominal fat area (p = 0.03), body fat percent (p = 0.048), fat mass (p = 0.01), waist circumference (p = 0.03), hip circumference (p = 0.001), BMI (p = 0.03), current weight (p = 0.002), weight at age 20 (p = 0.02) and adulthood weight gain (p = 0.03). No significant associations were found between any of the adiposity measures and Alu methylation. CONCLUSION Current and historical adiposity measures are positively associated with long interspersed nuclear element-1 methylation in healthy postmenopausal women.
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Affiliation(s)
- Devon J Boyne
- Department of Cancer Epidemiology & Prevention Research, Cancer Control Alberta, Alberta Health Services, Calgary, AB, Canada.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christine M Friedenreich
- Department of Cancer Epidemiology & Prevention Research, Cancer Control Alberta, Alberta Health Services, Calgary, AB, Canada.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John B McIntyre
- Translational Laboratory, Department of Pathology & Laboratory Medicine, Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Kerry S Courneya
- Faculty of Physical Education & Recreation, University of Alberta, Edmonton, AB, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
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17
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Desai G, Chu L, Guo Y, Myneni AA, Mu L. Biomarkers used in studying air pollution exposure during pregnancy and perinatal outcomes: a review. Biomarkers 2017; 22:489-501. [PMID: 28581828 DOI: 10.1080/1354750x.2017.1339294] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE This review focuses on studies among pregnant women that used biomarkers to assess air pollution exposure, or to understand the mechanisms by which it affects perinatal outcomes. METHODS We searched PubMed and Google scholar databases to find articles. RESULTS AND CONCLUSIONS We found 29 articles, mostly consisting of cohort studies. Interpolation models were most frequently used to assess exposure. The most consistent positive association was between polycyclic aromatic hydrocarbon (PAH) exposure during entire pregnancy and cord blood PAH DNA adducts. Exposure to particulate matter (PM) and nitrogen dioxide (NO2) showed consistent inverse associations with mitochondrial DNA (mtDNA) content, particularly in the third trimester of pregnancy. No single pollutant showed strong associations with all the biomarkers included in this review. C-reactive proteins (CRPs) and oxidative stress markers increased, whereas telomere length decreased with increasing air pollution exposure. Placental global DNA methylation and mtDNA methylation showed contrasting results with air pollution exposure, the mechanism behind which is unclear. Most studies except those on PAH DNA adducts and mtDNA content provided insufficient evidence for characterizing a critical exposure window. Further research using biomarkers is warranted to understand the relationship between air pollution and perinatal outcomes.
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Affiliation(s)
- Gauri Desai
- a Department of Epidemiology and Environmental Health, School of Public Health and Health Professions , The State University of New York (SUNY) at Buffalo , Buffalo , NY , USA
| | - Li Chu
- b Department of Obstetrics and Gynecology , Anzhen Hospital , Beijing , China
| | - Yanjun Guo
- c Department of Obstetrics and Gynecology , Hang Tian General Hospital , Beijing , China
| | - Ajay A Myneni
- a Department of Epidemiology and Environmental Health, School of Public Health and Health Professions , The State University of New York (SUNY) at Buffalo , Buffalo , NY , USA
| | - Lina Mu
- a Department of Epidemiology and Environmental Health, School of Public Health and Health Professions , The State University of New York (SUNY) at Buffalo , Buffalo , NY , USA
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18
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Lu Y, Li S, Zhu S, Gong Y, Shi J, Xu L. Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer. Biol Proced Online 2017; 19:2. [PMID: 28331435 PMCID: PMC5356409 DOI: 10.1186/s12575-017-0051-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.
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Affiliation(s)
- Yan Lu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Shulin/Sl Li
- MD Anderson Cancer Center, the university of Texas, 1840 Old Spanish Trail, Houston, TX USA
| | - Shiguo/Sg Zhu
- Department of Immunology and Pathogenic Biology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai, China
| | - Yabin/Yb Gong
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Jun/J Shi
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Ling/L Xu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
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The RFC1 80G>A, among Common One-Carbon Polymorphisms, Relates to Survival Rate According to DNA Global Methylation in Primary Liver Cancers. PLoS One 2016; 11:e0167534. [PMID: 27936032 PMCID: PMC5147923 DOI: 10.1371/journal.pone.0167534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
Polymorphisms within one-carbon metabolism genes have been largely studied in relation to cancer risk for the function of this pathway in nucleotide synthesis and DNA methylation. Aims of this study were to explore the possible link among several common functional gene polymorphisms within one-carbon metabolism and survival rate in primary liver cancers, i.e., hepatocellular carcinoma and cholangiocarcinoma, and to assess the additional effect of global DNA methylation on survival rate and mortality risk. Forty-seven primary liver cancer patients were genotyped for ten polymorphisms: DHFR 19bp ins/del, TS 2rpt-3rpt, MTHFD1 1958G>A, MTHFR 677C>T, MTR 2756A>G, MTRR 66A>G, RFC1 80G>A, SHMT1 1420C>T, BHMT 716 A>G, TC II 776C>G. Methylation was determined in peripheral blood mononuclear cells (PBMCs) DNA as methylcytosine (mCyt) content using LC/MS/MS. Among the polymorphisms analysed, the RFC1 80G>A (rs1051266) influenced the survival rate in primary liver cancers. The RFC1 80AA was associated to a significantly reduced survival rate (22.2%) as compared to both GG and GA genotypes (61.5% and 76% respectively, p = 0.005). When the cancer patients were stratified according to the mCyt median value as high (>5.34%) or low (≤5.34%), the concomitant presence of AA genotype and low mCyt level led to a significantly worse survival rate as compared to the G allele carriership (p<0.0001) with a higher Hazard Ratio (HR = 6.62, p = 0.001). The subjects carrying the AA genotype in association with high mCyt did not show a significant difference in survival rate as compared with the G allele carriers (p = 0.919). The RFC1 80G>A polymorphism influenced the survival rate, and the presence of RFC1 80AA genotype with low global methylation in PBMCs DNA was associated with poorer prognosis and higher mortality risk, therefore highlighting novel molecular signatures potentially helpful to define prognostic markers for primary liver cancers.
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20
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Kim CH, Lee EK, Choi YJ, An HJ, Jeong HO, Park D, Kim BC, Yu BP, Bhak J, Chung HY. Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Aging Cell 2016; 15:1074-1081. [PMID: 27561685 PMCID: PMC6398531 DOI: 10.1111/acel.12513] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 01/14/2023] Open
Abstract
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq). CpG islands and repetitive regions were hypomethylated, but 5'-UTR, exon, and 3'-UTR hypermethylated in old and OCR rats. The methylation in the promoter and intron regions was decreased in old rats, but increased in OCR rats. Pathway enrichment analysis showed that the hypermethylated promoters in old rats were associated with degenerative phenotypes such as cancer and diabetes. The hypomethylated promoters in old rats related significantly to the chemokine signaling pathway. However, the pathways significantly enriched in old rats were not observed from the differentially methylated promoters in OCR rats. Thus, these findings suggest that short-term CR could partially ameliorate age-related methylation changes in promoters in old rats. From the epigenomic data, we propose that the hypermethylation found in the promoter regions of disease-related genes during aging may indicate increases in susceptibility to age-related diseases. Therefore, the CR-induced epigenetic changes that ameliorate age-dependent aberrant methylation may be important to CR's health- and life-prolonging effects.
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Affiliation(s)
| | - Eun Kyeong Lee
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Yeon Ja Choi
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hye Jin An
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hyeong Oh Jeong
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Daeui Park
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byoung Chul Kim
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byung Pal Yu
- Department of Physiology University of Texas Health Science Center San Antonio TX USA
| | - Jong Bhak
- Biomedical Engineering Ulsan National Institute of Sciences and Technology Ulsan Korea
| | - Hae Yung Chung
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
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21
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Gainetdinov IV, Kapitskaya KY, Rykova EY, Ponomaryova AA, Cherdyntseva NV, Vlassov VV, Laktionov PP, Azhikina TL. Hypomethylation of human-specific family of LINE-1 retrotransposons in circulating DNA of lung cancer patients. Lung Cancer 2016; 99:127-30. [PMID: 27565927 DOI: 10.1016/j.lungcan.2016.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/12/2016] [Accepted: 07/05/2016] [Indexed: 02/06/2023]
Abstract
Circulating DNA has recently gained attention as a fast and non-invasive way to assess tumor biomarkers. Since hypomethylation of LINE-1 repetitive elements was described as one of the key hallmarks of tumorigenesis, we aimed to establish whether the methylation level of LINE-1 retrotransposons changes in cell-surface-bound fraction of circulating DNA (csbDNA) of lung cancer patients. Methylated CpG Island Recovery Assay (MIRA) coupled to qPCR-based quantitation was performed to assess integral methylation level of LINE-1 promoters in csbDNA of non-small cell lung cancer patients (n=56) and healthy controls (n=44). Deep sequencing of amplicons revealed that hypomethylation of LINE-1 promoters in csbDNA of lung cancer patients is more pronounced for the human-specific L1Hs family. Statistical analysis demonstrates significant difference in LINE-1 promoter methylation index between cancer patients and healthy individuals (ROC-curve analysis: n=100, AUC=0.69, p=0.0012) and supports the feasibility of MIRA as a promising non-invasive approach.
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Affiliation(s)
- Ildar V Gainetdinov
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Kristina Yu Kapitskaya
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Elena Yu Rykova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk State, Russia.
| | - Anastasia A Ponomaryova
- Tomsk Cancer Research Institute, National Research Tomsk Polytechnic University, Tomsk, Russia.
| | - Nadezda V Cherdyntseva
- Tomsk Cancer Research Institute, National Research Tomsk State University, Tomsk, Russia.
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
| | - Pavel P Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Academician E.N. Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia Technical University, Novosibirsk, Russia.
| | - Tatyana L Azhikina
- Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Joyce BT, Gao T, Zheng Y, Liu L, Zhang W, Dai Q, Shrubsole MJ, Hibler EA, Cristofanilli M, Zhang H, Yang H, Vokonas P, Cantone L, Schwartz J, Baccarelli A, Hou L. Prospective changes in global DNA methylation and cancer incidence and mortality. Br J Cancer 2016; 115:465-72. [PMID: 27351216 PMCID: PMC4985350 DOI: 10.1038/bjc.2016.205] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/31/2016] [Accepted: 06/07/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Methylation of repetitive elements Alu and LINE-1 in humans is considered a surrogate for global DNA methylation. Previous studies of blood-measured Alu/LINE-1 and cancer risk are inconsistent. METHODS We studied 1259 prospective methylation measurements from blood drawn 1-4 times from 583 participants from 1999 to 2012. We used Cox regression to evaluate time-dependent methylation as a biomarker for cancer risk and mortality, and linear regression to compare mean differences in methylation over time by cancer status and analyse associations between rate of methylation change and cancer. RESULTS Time-dependent LINE-1 methylation was associated with prostate cancer incidence (HR: 1.38, 95% CI: 1.01-1.88) and all-cancer mortality (HR: 1.41, 95% CI: 1.03-1.92). The first measurement of Alu methylation (HR: 1.39, 95% CI: 1.08-1.79) was associated with all-cancer mortality. Participants who ultimately developed cancer had lower mean LINE-1 methylation than cancer-free participants 10+ years pre-diagnosis (P<0.01). Rate of Alu methylation change was associated with all-cancer incidence (HR: 3.62, 95% CI: 1.09-12.10). CONCLUSIONS Our results add longitudinal data on blood Alu and LINE-1 methylation and cancer, and potentially contribute to their use as early-detection biomarkers. Future larger studies are needed and should account for the interval between blood sample collection and cancer diagnosis.
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Affiliation(s)
- Brian T Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-Chicago, 1603 W. Taylor Street, Chicago, IL 60612, USA
| | - Tao Gao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Institute for Public Health and Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Lei Liu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Qi Dai
- Vanderbilt University Medical Center, 2525 West End Avenue, Suite 319, Nashville, TN 37203, USA
| | - Martha J Shrubsole
- Vanderbilt University Medical Center, 2525 West End Avenue, Suite 319, Nashville, TN 37203, USA
| | - Elizabeth A Hibler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Massimo Cristofanilli
- Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, 676 N. St Clair Street, 8th Floor, Chicago, IL 60611, USA
| | - Hu Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA
| | - Hushan Yang
- Department of Medical Oncology, Division of Population Science, Sidney Kimmel Cancer Center, Thomas Jefferson University, 834 Chestnut Street, Suite 314, Philadelphia, PA 19107, USA
| | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, 150 South Huntington Avenue, Boston, MA 02130, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura Cantone
- Molecular Epidemiology and Environmental Epigenetics Laboratory, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, San Barnaba 8, Milan 20122, Italy
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Avenue, Olson Pavilion 8350, Chicago, IL 60611, USA
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23
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Zheng Y, Joyce BT, Colicino E, Liu L, Zhang W, Dai Q, Shrubsole MJ, Kibbe WA, Gao T, Zhang Z, Jafari N, Vokonas P, Schwartz J, Baccarelli AA, Hou L. Blood Epigenetic Age may Predict Cancer Incidence and Mortality. EBioMedicine 2016; 5:68-73. [PMID: 27077113 PMCID: PMC4816845 DOI: 10.1016/j.ebiom.2016.02.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/14/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Biological measures of aging are important for understanding the health of an aging population, with epigenetics particularly promising. Previous studies found that tumor tissue is epigenetically older than its donors are chronologically. We examined whether blood Δage (the discrepancy between epigenetic and chronological ages) can predict cancer incidence or mortality, thus assessing its potential as a cancer biomarker. In a prospective cohort, Δage and its rate of change over time were calculated in 834 blood leukocyte samples collected from 442 participants free of cancer at blood draw. About 3–5 years before cancer onset or death, Δage was associated with cancer risks in a dose-responsive manner (P = 0.02) and a one-year increase in Δage was associated with cancer incidence (HR: 1.06, 95% CI: 1.02–1.10) and mortality (HR: 1.17, 95% CI: 1.07–1.28). Participants with smaller Δage and decelerated epigenetic aging over time had the lowest risks of cancer incidence (P = 0.003) and mortality (P = 0.02). Δage was associated with cancer incidence in a ‘J-shaped’ manner for subjects examined pre-2003, and with cancer mortality in a time-varying manner. We conclude that blood epigenetic age may mirror epigenetic abnormalities related to cancer development, potentially serving as a minimally invasive biomarker for cancer early detection. We prospectively examined blood Δage and its ability to predict cancer risks. Epigenetic age older than chronological age elevated cancer risk. Δage predicted cancer incidence and mortality in a dose-responsive manner. The Δage–cancer relationship was a nonlinear ‘J-shape’ for subjects measured before 2003. Blood-based epigenetic age is a potential biomarker for cancer early detection.
This study studies a way to calculate your body's age, not based on how old you are, but by measuring a number of markers in your blood — called epigenetic age. This paper also looks at how good epigenetic age over time is at predicting whether you'll get cancer, and whether you'll die from it. The authors found that epigenetic age could be good at predicting both of these things, which means that someday it could be developed into a blood test for diagnosing cancer, and for helping patients figure out how long they'll live.
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Affiliation(s)
- Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian T Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois-Chicago, Chicago, IL 60613, USA
| | - Elena Colicino
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lei Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qi Dai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Warren A Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA; Biomedical Informatics Center (NUBIC), Northwestern University Clinical and Translational Sciences Institute (NUCATS), Chicago, IL 60611, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nadereh Jafari
- Genomics Core Facility, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Pantel Vokonas
- VA Boston Healthcare System and Boston University Schools of Public Health and Medicine, Boston, MA 02215, USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Gao T, Joyce BT, Liu L, Zheng Y, Dai Q, Zhang Z, Zhang W, Shrubsole MJ, Tao MH, Schwartz J, Baccarelli A, Hou L. DNA methylation of oxidative stress genes and cancer risk in the Normative Aging Study. Am J Cancer Res 2016; 6:553-561. [PMID: 27186424 PMCID: PMC4859680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023] Open
Abstract
Oxidative stress (OS) is a primary mechanism of carcinogenesis, and methylation of genes related to it may play a role in cancer development. In this study, we examined the prospective association between blood DNA methylation of four oxidative stress genes and cancer incidence. Our study population included a total of 582 participants in the Normative Aging Study (NAS) who had blood drawn during 1-4 visits from 1999-2012 (mean follow up 9.0 years). Promoter DNA methylation of CRAT, iNOS, OGG1 and GCR in blood leukocytes was measured using pyrosequencing. We used Cox regression models to examine prospective associations between cancer incidence and both methylation at the baseline visit and methylation rate of changes over time. Baseline OGG1 methylation was associated with higher risk of all-cancer (HR: 1.43, 95% CI: 1.15-1.78) and prostate cancer (HR: 1.52, 95% CI: 1.03-2.25) incidence. Compared with participants remaining cancer-free, those who eventually developed cancer had significantly accelerated CRAT methylation (p = 0.04) and decelerated iNOS methylation (p<0.01) over time prior to cancer diagnosis. Accelerated CRAT methylation was associated with higher all-cancer incidence (HR: 3.88, 95% CI: 1.06-14.30), whereas accelerated iNOS methylation was associated with lower all-cancer incidence (HR: 0.08, 95% CI 0.02-0.38). Our results suggest that methylation and its dynamic change over time in OS-related genes, including OGG1, CRAT and iNOS, may play an important role in carcinogenesis. These results can potentially facilitate the development of early detection biomarkers and new treatments for a variety of cancers.
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Affiliation(s)
- Tao Gao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-ChicagoChicago, IL, USA 60612
| | - Lei Liu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Qi Dai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashville, TN, USA 37232
| | - Zhou Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Wei Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical CenterNashville, TN, USA 37232
| | - Meng-Hua Tao
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science CenterFort Worth, TX, USA 76107
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public HealthBoston, MA, USA 02115
| | - Andrea Baccarelli
- Department of Environmental Health, Harvard School of Public HealthBoston, MA, USA 02115
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicago, IL, USA 60611
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25
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Tang JT, Wang ZH, Fang JY. Assessing the potential value of long interspersed element-1 hypomethylation in colorectal cancer: evidence from retrospective studies. Onco Targets Ther 2015; 8:3265-76. [PMID: 26604793 PMCID: PMC4640227 DOI: 10.2147/ott.s91941] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND AIMS Long interspersed element-1 (LINE-1) hypomethylation may play an important role in colorectal cancer (CRC). Studies were identified that investigated LINE-1 methylation levels in CRC compared with normal controls. METHODS The random-effects model was used to estimate standardized mean difference with 95% confidence intervals according to the heterogeneity between the studies. We explored the relationship between LINE-1 hypomethylation and microsatellite instability (MSI) status, clinical features, and molecular features in CRC patients using a fixed-effects model. RESULTS A total of 7396 CRC patients were included in the meta-analysis. LINE-1 methylation was significantly lower in CRC patients than in controls (P=0.000). Mean LINE-1 methylation was significantly lower in non-MSI-high than in MSI-high tumors (P=0.000). LINE-1 hypomethylation was found more frequently in patients with a family history compared with those without family history (P=0.002). Patients with left colon cancer had lower LINE-1 methylation than those with right colon cancer (P=0.001). LINE-1 methylation was not associated with body mass index or patient sex. LINE-1 hypomethylation was found in p21 lost tumors (P=0.000). LINE-1 methylation levels were not associated with KRAS or PIK3CA-mutation status. CONCLUSION LINE-1 hypomethylation is a potential biomarker for risk of CRC and associated with various clinical and molecular features of CRC.
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Affiliation(s)
- Jie-Ting Tang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China ; Shanghai Institute of Digestive Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhen-Hua Wang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China ; Shanghai Institute of Digestive Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China ; Shanghai Institute of Digestive Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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26
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Barry KH, Moore LE, Liao LM, Huang WY, Andreotti G, Poulin M, Berndt SI. Prospective study of DNA methylation at LINE-1 and Alu in peripheral blood and the risk of prostate cancer. Prostate 2015; 75:1718-25. [PMID: 26250474 PMCID: PMC4535169 DOI: 10.1002/pros.23053] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/02/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Evidence suggests that global blood DNA methylation levels may be associated with the risk of various cancers, but no studies have evaluated this relationship for prostate cancer. METHODS We used pyrosequencing to quantify DNA methylation levels at the long interspersed nuclear element 1 (LINE-1) and Alu repetitive elements in pre-diagnostic blood samples from 694 prostate cancer cases and 703 controls from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. We evaluated prostate cancer risk associated with the mean methylation level for each element using logistic regression, adjusting for potential confounders. RESULTS We did not observe a significant association with prostate cancer for LINE-1 [odds ratio (OR) for the highest compared to the lowest quartile = 1.01, 95% confidence interval (CI): 0.73-1.39, Ptrend = 0.99] or Alu (OR = 0.94, 95% CI: 0.68-1.29, Ptrend = 0.69) methylation levels overall. However, for Alu, we observed that higher DNA methylation levels were associated with a significant increased risk for those diagnosed 4 or more years after blood draw (OR = 2.26, 95% CI: 1.27-4.00, Ptrend = 4.4 × 10(-3) ). In contrast, there was no association for those diagnosed 2 (OR = 1.13, 95% CI: 0.67-1.90, Ptrend = 0.64) or 3 years after draw (OR = 1.22, 95% CI: 0.71-2.07, Ptrend = 0.32), and a decreased risk for those diagnosed less than 2 years after draw (OR = 0.40, 95% CI: 0.25-0.65, Ptrend = 3.8 × 10(-5) ; Pheterogeneity = 5.3 × 10(-6) ). CONCLUSIONS Although LINE-1 DNA methylation levels were not associated with prostate cancer, we observed an association for Alu that varied by time from blood draw to diagnosis. Our study suggests that elevated Alu blood DNA methylation levels several years before diagnosis may be associated with an increased prostate cancer risk.
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Affiliation(s)
- Kathryn Hughes Barry
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Lee E. Moore
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Linda M. Liao
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Wen-Yi Huang
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Sonja I. Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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27
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Joyce BT, Gao T, Liu L, Zheng Y, Liu S, Zhang W, Penedo F, Dai Q, Schwartz J, Baccarelli AA, Hou L. Longitudinal Study of DNA Methylation of Inflammatory Genes and Cancer Risk. Cancer Epidemiol Biomarkers Prev 2015; 24:1531-8. [PMID: 26265203 DOI: 10.1158/1055-9965.epi-15-0198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/06/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Chronic inflammation plays a key role in cancer etiology. DNA methylation modification, one of the epigenetic mechanisms regulating gene expression, is considered a hallmark of cancer. Human and animal models have identified numerous links between DNA methylation and inflammatory biomarkers. Our objective was to prospectively and longitudinally examine associations between methylation of four inflammatory genes and cancer risk. METHODS We included 795 Normative Aging Study participants with blood drawn one to four times from 1999 to 2012 (median follow-up, 10.6 years). Promoter DNA methylation of IL6, ICAM-1, IFN, and TLR2 in blood leukocytes was measured using pyrosequencing at multiple CpG sites and averaged by gene for data analysis. We used Cox regression models to examine prospective associations of baseline and time-dependent methylation with cancer risk and compared mean methylation differences over time between cancer cases and cancer-free participants. RESULTS Baseline IFN hypermethylation was associated with all-cancer (HR, 1.49; P = 0.04) and prostate cancer incidence (HR, 1.69; P = 0.02). Baseline ICAM-1 and IL6 hypermethylation were associated with prostate cancer incidence (HR, 1.43; P = 0.02; HR, 0.70; P = 0.03, respectively). In our time-dependent analyses, IFN hypermethylation was associated with all-cancer (HR, 1.79; P = 0.007) and prostate cancer (HR, 1.57; P = 0.03) incidence; and ICAM-1 and IL6 hypermethylation were associated with prostate cancer incidence (HR, 1.39; P = 0.02; HR, 0.69; P = 0.03, respectively). We detected significant ICAM-1 hypermethylation in cancer cases (P = 0.0003) 10 to 13 years prediagnosis. CONCLUSION Hypermethylation of IFN and ICAM-1 may play important roles in early carcinogenesis, particularly that of prostate cancer. IMPACT These methylation changes could inform the development of early detection biomarkers and potential treatments of inflammation-related carcinogenesis.
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Affiliation(s)
- Brian Thomas Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Division of Epidemiology/Biostatistics, School of Public Health, University of Illinois-Chicago, Chicago, Illinois.
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lei Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yinan Zheng
- Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Siran Liu
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Frank Penedo
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Qi Dai
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Cappetta M, Berdasco M, Hochmann J, Bonilla C, Sans M, Hidalgo PC, Artagaveytia N, Kittles R, Martínez M, Esteller M, Bertoni B. Effect of genetic ancestry on leukocyte global DNA methylation in cancer patients. BMC Cancer 2015; 15:434. [PMID: 26012346 PMCID: PMC4445803 DOI: 10.1186/s12885-015-1461-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 05/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of genetic variants alone is not enough to explain a complex disease like cancer. Alterations in DNA methylation patterns have been associated with different types of tumor. In order to detect markers of susceptibility for the development of cutaneous melanoma and breast cancer in the Uruguayan population, we integrated genetic and epigenetic information of patients and controls. METHODS We performed two case-control studies that included 49 individuals with sporadic cutaneous melanoma and 73 unaffected controls, and 179 women with sporadic breast cancer and 209 women controls. We determined the level of global leukocyte DNA methylation using relative quantification of 5mdC by HPLC, and we compared methylation levels between cases and controls with nonparametric statistical tests. Since the Uruguayan population is admixed and both melanoma and breast cancer have very high incidences in Uruguay compared to other populations, we examined whether individual ancestry influences global leucocyte DNA methylation status. We carried out a correlation analysis between the percentage of African, European and Native American individual ancestries, determined using 59 ancestry informative markers, and global DNA methylation in all participants. RESULTS We detected global DNA hypomethylation in leukocytes of melanoma and breast cancer patients compared with healthy controls (p < 0.001). Additionally, we found a negative correlation between African ancestry and global DNA methylation in cancer patients (p <0.005). CONCLUSIONS These results support the potential use of global DNA methylation as a biomarker for cancer risk. In addition, our findings suggest that the ancestral genome structure generated by the admixture process influences DNA methylation patterns, and underscore the importance of considering genetic ancestry as a modifying factor in epigenetic association studies in admixed populations such as Latino ones.
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Affiliation(s)
- Mónica Cappetta
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain.
| | - Jimena Hochmann
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Carolina Bonilla
- School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
| | - Pedro C Hidalgo
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
- Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay.
| | - Nora Artagaveytia
- Departamento Básico de Medicina, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Rick Kittles
- Department of Surgery and Public Health, University of Arizona, Tucson, USA.
| | - Miguel Martínez
- Cátedra de Dermatología, Hospital de Clínicas "Manuel Quintela", Universidad de la República, Montevideo, Uruguay.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Blood Telomere Length Attrition and Cancer Development in the Normative Aging Study Cohort. EBioMedicine 2015; 2:591-6. [PMID: 26288820 PMCID: PMC4535161 DOI: 10.1016/j.ebiom.2015.04.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 11/12/2022] Open
Abstract
Background Accelerated telomere shortening may cause cancer via chromosomal instability, making it a potentially useful biomarker. However, publications on blood telomere length (BTL) and cancer are inconsistent. We prospectively examined BTL measures over time and cancer incidence. Methods We included 792 Normative Aging Study participants with 1–4 BTL measurements from 1999 to 2012. We used linear mixed-effects models to examine BTL attrition by cancer status (relative to increasing age and decreasing years pre-diagnosis), Cox models for time-dependent associations, and logistic regression for cancer incidence stratified by years between BTL measurement and diagnosis. Findings Age-related BTL attrition was faster in cancer cases pre-diagnosis than in cancer-free participants (pdifference = 0.017); all participants had similar age-adjusted BTL 8–14 years pre-diagnosis, followed by decelerated attrition in cancer cases resulting in longer BTL three (p = 0.003) and four (p = 0.012) years pre-diagnosis. Longer time-dependent BTL was associated with prostate cancer (HR = 1.79, p = 0.03), and longer BTL measured ≤ 4 years pre-diagnosis with any (OR = 3.27, p < 0.001) and prostate cancers (OR = 6.87, p < 0.001). Interpretation Age-related BTL attrition was faster in cancer cases but their age-adjusted BTL attrition began decelerating as diagnosis approached. This may explain prior inconsistencies and help develop BTL as a cancer detection biomarker. Normal, age-related telomere attrition is faster in subjects who later developed cancer. Telomere attrition began decelerating before cancer diagnosis, resulting in longer telomeres 3–4 years pre-diagnosis. Longer telomeres measured within four years of diagnosis were associated with all-cancer incidence.
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Karami S, Andreotti G, Liao LM, Pfeiffer RM, Weinstein SJ, Purdue MP, Hofmann JN, Albanes D, Mannisto S, Moore LE. LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk. Epigenetics 2015; 10:282-92. [PMID: 25647181 DOI: 10.1080/15592294.2015.1006505] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96-1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00-2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46-4.63). A significant interaction for smoking was also detected (P-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07-1.60). In a pooled analysis of PLCO and ATBC male smokers (281 cases/755 controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34-2.67, P-value: 3 x 10(-4)); a trend was also observed by methylation quartile (P-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
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Affiliation(s)
- Sara Karami
- a Division of Cancer Epidemiology and Genetics (DCEG); US National Cancer Institute (NCI); National Institutes of Health (NIH); Department of Health and Human Services (DHHS) ; Rockville , MD USA
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Abstract
Hepatocellular carcinoma (HCC) is the third most common cause of cancer death worldwide. Hepatocarcinogenesis is a complex, multistep process. It is now recognized that HCC is a both genetic and epigenetic disease; genetic and epigenetic components cooperate at all stages of hepatocarcinogenesis. Epigenetic changes involve aberrant DNA methylation, posttranslational histone modifications and aberrant expression of microRNAs all of which can affect the expression of oncogenes, tumor suppressor genes and other tumor-related genes and alter the pathways in cancer development. Several risk factors for HCC, including hepatitis B and C virus infections and exposure to the chemical carcinogen aflatoxin B1 have been found to influence epigenetic changes. Their interactions could play an important role in the initiation and progression of HCC. Discovery and detection of biomarkers for epigenetic changes is a promising area for early diagnosis and risk prediction of HCC.
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Affiliation(s)
- Yujing Zhang
- Department of Environmental Health Sciences, Mailman School of Public Health and Cancer Center of Columbia University, Room 1608, 630 West 168th Street, New York, NY, 10032, USA,
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Keller M, Kralisch S, Rohde K, Schleinitz D, Dietrich A, Schön MR, Gärtner D, Lohmann T, Dreßler M, Tönjes A, Stumvoll M, Kovacs P, Fasshauer M, Blüher M, Böttcher Y. Global DNA methylation levels in human adipose tissue are related to fat distribution and glucose homeostasis. Diabetologia 2014; 57:2374-83. [PMID: 25145546 DOI: 10.1007/s00125-014-3356-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/23/2014] [Indexed: 12/31/2022]
Abstract
AIMS/HYPOTHESIS Epigenetic alterations may influence the metabolic pathways involved in human obesity. We hypothesised that global DNA methylation levels in adipose tissue might be associated with obesity and related phenotypes. METHODS We measured global DNA methylation levels in paired samples of subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (OVAT) from 51 individuals, and in leucocytes from 559 Sorbs, a population from Germany, using LUminometric Methylation Assay (LUMA). To further investigate the underlying mechanisms of the observed associations, we measured global methylation levels in 3T3-L1 adipocytes exposed to glucose, insulin and lipids. RESULTS Global methylation levels (±SD) were significantly higher in OVAT (74.27% ± 2.2%) compared with SAT (71.97% ± 2.4%; paired t test, p < 1 × 10(-9)). Furthermore, global methylation levels in SAT were positive correlates of measures of fat distribution (waist measurement, WHR) and glucose homeostasis (HbA1c) (all p < 0.015 after accounting for multiple testing and covariates). Global methylation levels in the German Sorb cohort were associated with glucose homeostasis, but this association did not withstand adjustment for covariates. Exposure of 3T3-L1 adipocytes to insulin, palmitate and glucose decreased global methylation levels 1 h after treatment relative to controls. CONCLUSIONS/INTERPRETATION Our data suggest that the variability in global methylation in adipose tissue might be related to alterations in glucose metabolism.
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Affiliation(s)
- Maria Keller
- Medical Faculty, IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
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Wagner W, Weidner CI, Lin Q. Do age-associated DNA methylation changes increase the risk of malignant transformation? Bioessays 2014; 37:20-4. [DOI: 10.1002/bies.201400063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Carola I. Weidner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
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Barchitta M, Quattrocchi A, Maugeri A, Vinciguerra M, Agodi A. LINE-1 hypomethylation in blood and tissue samples as an epigenetic marker for cancer risk: a systematic review and meta-analysis. PLoS One 2014; 9:e109478. [PMID: 25275447 PMCID: PMC4183594 DOI: 10.1371/journal.pone.0109478] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/31/2014] [Indexed: 01/07/2023] Open
Abstract
Objective A systematic review and a meta-analysis were carried out in order to summarize the current published studies and to evaluate LINE-1 hypomethylation in blood and other tissues as an epigenetic marker for cancer risk. Methods A systematic literature search in the Medline database, using PubMed, was conducted for epidemiological studies, published before March 2014. The random-effects model was used to estimate weighted mean differences (MDs) with 95% Confidence Intervals (CIs). Furthermore, subgroup analyses were conducted by sample type (tissue or blood samples), cancer types, and by assays used to measure global DNA methylation levels. The Cochrane software package Review Manager 5.2 was used. Results A total of 19 unique articles on 6107 samples (2554 from cancer patients and 3553 control samples) were included in the meta-analysis. LINE-1 methylation levels were significantly lower in cancer patients than in controls (MD: −6.40, 95% CI: −7.71, −5.09; p<0.001). The significant difference in methylation levels was confirmed in tissue samples (MD −7.55; 95% CI: −9.14, −65.95; p<0.001), but not in blood samples (MD: −0.26, 95% CI: −0.69, 0.17; p = 0.23). LINE-1 methylation levels were significantly lower in colorectal and gastric cancer patients than in controls (MD: −8.33; 95% CI: −10.56, −6.10; p<0.001 and MD: −5.75; 95% CI: −7.75, −3.74; p<0.001) whereas, no significant difference was observed for hepatocellular cancer. Conclusions The present meta-analysis adds new evidence to the growing literature on the role of LINE-1 hypomethylation in human cancer and demonstrates that LINE-1 methylation levels were significantly lower in cancer patients than in control samples, especially in certain cancer types. This result was confirmed in tissue samples, both fresh/frozen or FFPE specimens, but not in blood. Further studies are needed to better clarify the role of LINE-1 methylation in specific subgroups, considering both cancer and sample type, and the methods of measurement.
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Affiliation(s)
| | | | - Andrea Maugeri
- Department GF Ingrassia, University of Catania, Catania, Italy
| | - Manlio Vinciguerra
- University College London, Institute for Liver and Digestive Health, Royal Free Campus, London, United Kingdom
- Gastroenterology Unit, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- * E-mail: (AA); (MV)
| | - Antonella Agodi
- Department GF Ingrassia, University of Catania, Catania, Italy
- * E-mail: (AA); (MV)
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Li J, Huang Q, Zeng F, Li W, He Z, Chen W, Zhu W, Zhang B. The prognostic value of global DNA hypomethylation in cancer: a meta-analysis. PLoS One 2014; 9:e106290. [PMID: 25184628 PMCID: PMC4153632 DOI: 10.1371/journal.pone.0106290] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/29/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Aberrant methylation of the global genome has been investigated as a prognostic indicator in various cancers, but the results are controversial and ambiguous. METHODS AND FINDINGS This meta-analysis presents pooled estimates of the evidence to elucidate this issue. We searched the electronic databases: PubMed, Embase, ISI Web of Science and the Cochrane library (up to August 2013) to identify all of the relevant studies. The association between the level of surrogates' indexes of genome-wide hypomethylation (LINE-1, Alu and Sat-α) and the overall survival (OS) of cancer patients was examined. In addition, the pooled hazard ratios (HRs) with their 95% confidence interval (95%CI) were calculated to estimate the influences through fixed-effects and random-effects model. Finally, twenty studies with total population of 5447 met the inclusion criteria. The results indicate that the summary HRs for the studies employing LINE-1, Alu, and Sat-α repetitive elements also show that the global DNA hypomethylation have significant desirable effects on the tumour prognostic value. The pooled HRs (and CIs) of LINE-1, Alu and Sat-α were 1.83 (1.38-2.44), 2.00 (1.16-3.45), and 2.92 (1.04-8.25), with a heterogeneity measure index of I2 (and p-value) shows of 66.6% (p = 0.001), 57.1% (p = 0.053) and 68.2% (p = 0.076) respectively. The meta-regression and subgroup analysis indicated that the percentage of hypomethylated sample of cancer patients is one source of heterogeneity. CONCLUSION Our meta-analysis findings support the hypothesis that the global DNA hypomethylation is associated with a detrimental prognosis in tumour patients.
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Affiliation(s)
- Jinhui Li
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, P.R. China
| | - Qingyuan Huang
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Fangfang Zeng
- Department of Epidemiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Medical Statistics & Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wenxue Li
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, P.R. China
| | - Zhini He
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wen Chen
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
| | - Wei Zhu
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, P.R. China
| | - Bo Zhang
- Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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37
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Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol 2014; 24:686-94. [PMID: 25103681 DOI: 10.1016/j.tcb.2014.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 02/06/2023]
Abstract
Age is a major risk factor for cancer. Alterations in DNA methylation, histone modifications, chromatin structure, and epigenetic regulatory mechanisms are prominent hallmarks of both the aging process and cancer. Intriguingly--or possibly coincidentally--several chromatin features are common between aging and cancer. Here we ask whether, and if so how, aging-associated chromatin modifications contribute to tumor susceptibility and tumorigenesis.
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Affiliation(s)
- Linda Zane
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Guo L, Byun HM, Zhong J, Motta V, Barupal J, Zheng Y, Dou C, Zhang F, McCracken JP, Diaz A, Marco SG, Colicino S, Schwartz J, Wang S, Hou L, Baccarelli AA. Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:322-35. [PMID: 24436168 PMCID: PMC4426495 DOI: 10.1002/em.21838] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 01/06/2013] [Accepted: 01/06/2014] [Indexed: 05/21/2023]
Abstract
There is compelling evidence that particulate matter (PM) increases lung cancer risk by triggering systemic inflammation, and leukocyte DNA hypomethylation. However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which display a greater propensity to mutate, and are often hypomethylated in cancer patients, have never been investigated in individuals exposed to PM. We measured methylation of three tandem repeats (SATα, NBL2, and D4Z4) by polymerase chain reaction-pyrosequencing on blood samples from truck drivers and office workers (60 per group) in Beijing, China. We used lightweight monitors to measure personal PM2.5 (PM with aerodynamic diameter ≤2.5 µm) and elemental carbon (a tracer of PM from vehicular traffic). Ambient PM10 data were obtained from air quality measuring stations. Overall, an interquartile increase in personal PM2.5 and ambient PM10 levels was associated with a significant covariate-adjusted decrease in SATα methylation (-1.35% 5-methyl cytosine [5mC], P = 0.01; and -1.33%5mC; P = 0.01, respectively). Effects from personal PM2.5 and ambient PM10 on SATα methylation were stronger in truck drivers (-2.34%5mC, P = 0.02; -1.44%5mC, P = 0.06) than office workers (-0.95%5mC, P = 0.26; -1.25%5mC, P = 0.12, respectively). Ambient PM10 was negatively correlated with NBL2 methylation in truck drivers (-1.38%5mC, P = 0.03) but not in office workers (1.04%5mC, P = 0.13). Our result suggests that PM exposure is associated with hypomethylation of selected tandem repeats. Measuring tandem-repeat hypomethylation in easy-to-obtain blood specimens might identify individuals with biological effects and potential cancer risk from PM exposure.
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Affiliation(s)
- Liqiong Guo
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Sciences and Engineering, Nankai University, Tianjin, China
- Correspondence to: Liqiong Guo, Nankai University, College of Environmental Sciences and Engineering, Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin 300071, Tel. +86(186)-9804-6908,
| | - Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Jia Zhong
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Valeria Motta
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
- Center for Molecular and Genetic Epidemiology, Department of Environmental and Occupational Health, Ca’Granda Ospedale Maggiore Policlinico IRCCS Foundation, Universita degli Studi di Milano, Milan, Italy
| | - Jitendra Barupal
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Yinan Zheng
- Driskill Graduate Program (DGP) in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Chang Dou
- Department of Safety Engineering, China Institute of Industrial Health, Beijing, China
| | - Feiruo Zhang
- Department of Occupational and Environmental Health, Peking University Health Science Center, Beijing, China
| | - John P. McCracken
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Anaité Diaz
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Sanchez-Guerra Marco
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Silvia Colicino
- Center for Molecular and Genetic Epidemiology, Department of Environmental and Occupational Health, Ca’Granda Ospedale Maggiore Policlinico IRCCS Foundation, Universita degli Studi di Milano, Milan, Italy
| | - Joel Schwartz
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Sheng Wang
- Department of Occupational and Environmental Health, Peking University Health Science Center, Beijing, China
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Andrea A. Baccarelli
- Laboratory of Environmental Epigenetics, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
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Wei L, Liu S, Su Z, Cheng R, Bai X, Li X. LINE-1 hypomethylation is associated with the risk of coronary heart disease in Chinese population. Arq Bras Cardiol 2014; 102:481-8. [PMID: 24918913 PMCID: PMC4051451 DOI: 10.5935/abc.20140054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/12/2013] [Accepted: 12/13/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Global methylation level in blood leukocyte DNA has been associated with the risk of coronary heart disease (CHD), with inconsistent results in various populations. Similar data are lacking in Chinese population where different genetic, lifestyle and environmental factors may affect DNA methylation and its risk relationship with CHD. OBJECTIVES To examine whether global methylation is associated with the risk of CHD in Chinese population. METHODS A total of 334 cases with CHD and 788 healthy controls were included. Global methylation in blood leukocyte DNA was estimated by analyzing LINE-1 repeats using bisulfite pyrosequencing. RESULTS In an initial analysis restricted to control subjects, LINE-1 level reduced significantly with aging, elevated total cholesterol, and diagnosis of diabetes. In the case-control analysis, reduced LINE-1 methylation was associated with increased risk of CHD; analysis by quartile revealed odds ratios (95%CI) of 0.9 (0.6-1.4), 1.9 (1.3-2.9) and 2.3 (1.6-3.5) for the third, second and first (lowest) quartile (Ptrend < 0.001), respectively, compared to the fourth (highest) quartile. Lower ( CONCLUSION LINE-1 hypomethylation is associated with the risk of CHD in Chinese population. Potential CHD risk factors such as older age, elevated total cholesterol, and diagnosis of diabetes may have impact on global DNA methylation, whereby exerting their effect on CHD risk.
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Affiliation(s)
- Li Wei
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin
Medical University, Harbin - China
| | - Shuchuan Liu
- Department of Hematology, The First Affiliated Hospital of Harbin
Medical University, Harbin - China
| | - Zhendong Su
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin
Medical University, Harbin - China
| | - Rongchao Cheng
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin
Medical University, Harbin - China
| | - Xiuping Bai
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin
Medical University, Harbin - China
| | - Xueqi Li
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin
Medical University, Harbin - China
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Hou L, Zhang X, Zheng Y, Wang S, Dou C, Guo L, Byun HM, Motta V, McCracken J, Díaz A, Kang CM, Koutrakis P, Bertazzi PA, Li J, Schwartz J, Baccarelli AA. Altered methylation in tandem repeat element and elemental component levels in inhalable air particles. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:256-65. [PMID: 24273195 PMCID: PMC4001244 DOI: 10.1002/em.21829] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/31/2013] [Indexed: 05/20/2023]
Abstract
Exposure to particulate matter (PM) has been associated with lung cancer risk in epidemiology investigations. Elemental components of PM have been suggested to have critical roles in PM toxicity, but the molecular mechanisms underlying their association with cancer risks remain poorly understood. DNA methylation has emerged as a promising biomarker for environmental-related diseases, including lung cancer. In this study, we evaluated the effects of PM elemental components on methylation of three tandem repeats in a highly exposed population in Beijing, China. The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. On two days separated by 1-2 weeks, we measured blood DNA methylation of SATα, NBL2, D4Z4, and personal exposure to eight elemental components in PM2.5 , including aluminum (Al), silicon (Si), sulfur (S), potassium (K), calcium (Ca) titanium (Ti), iron (Fe), and zinc (Zn). We estimated the associations of individual elemental component with each tandem-repeat methylation in generalized estimating equations (GEE) models adjusted for PM2.5 mass and other covariates. Out of the eight examined elements, NBL2 methylation was positively associated with concentrations of Si [0.121, 95% confidence interval (CI): 0.030; 0.212, False Discovery Rate (FDR) = 0.047] and Ca (0.065, 95%CI: 0.014; 0.115, FDR = 0.047) in truck drivers. In office workers, SATα methylation was positively associated with concentrations of S (0.115, 95% CI: 0.034; 0.196, FDR = 0.042). PM-associated differences in blood tandem-repeat methylation may help detect biological effects of the exposure and identify individuals who may eventually experience higher lung cancer risk.
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Affiliation(s)
- Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- The Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Xiao Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Yinan Zheng
- Driskill Graduate Program (DGP) in Life Sciences, Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA
| | - Sheng Wang
- Department of Occupational and Environmental Health, Peking University Health Science Center, Beijing, China
| | - Chang Dou
- Department of Safety Engineering, China Institute of Industrial Health, Beijing, China
| | - Liqiong Guo
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Sciences and Engineering, Nankai University, Tianjin, China
| | - Hyang-Min Byun
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Valeria Motta
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - John McCracken
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Anaité Díaz
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Choong-Min Kang
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Petros Koutrakis
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Pier Alberto Bertazzi
- Department of Clinical Sciences and Community Health - DISCCO, Università degli Studi di Milano and Fondazione IRCCS Ca' Granda Maggiore Policlinico Hospital, Milan, Italy
| | - Jingyun Li
- Beijing Institute of Occupational Medicine for Chemical Industry, Beijing, China
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
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Shen F, Huang W, Qi JH, Yuan BF, Huang JT, Zhou X, Feng YQ, Liu YJ, Liu SM. Association of 5-methylcytosine and 5-hydroxymethylcytosine with mitochondrial DNA content and clinical and biochemical parameters in hepatocellular carcinoma. PLoS One 2013; 8:e76967. [PMID: 24143196 PMCID: PMC3797098 DOI: 10.1371/journal.pone.0076967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/30/2013] [Indexed: 01/24/2023] Open
Abstract
Increasing epidemiological evidence has indicated that inherited variations of mitochondrial DNA (mtDNA) copy number affect the genetic susceptibility of many malignancies in a tumour-specific manner and that DNA methylation also plays an important role in controlling gene expression during the differentiation and development of hepatocellular carcinoma (HCC). Our previous study demonstrated that HCC tissues showed a lower 5-hydroxymethylcytosine (5-hmC) content when compared to tumour-adjacent tissues, but the relationship among 5-hmC, 5-methylcytosine (5-mC) and mtDNA content in HCC patients is still unknown. This study aimed to clarify the correlation among mtDNA content, 5-mC and 5-hmC by quantitative real-time PCR and liquid chromatography tandem mass spectrometry analysis. We demonstrated that 5-hmC correlated with tumour size [odds ratio (OR) 0.847, 95% confidence interval (CI) 0.746–0.962, P = 0.011], and HCC patients with a tumour size ≥5.0 cm showed a lower 5-hmC content and higher levels of fasting plasma aspartate aminotransferase, the ratio of alanine amiotransferase to aspartate aminotransferase, γ-glutamyltransferase, alpha-fetoprotein than those with a tumour size <5 cm (all P<0.05). We further revealed that the mtDNA content of HCC tumour tissues was 225.97(105.42, 430.54) [median (25th Percentile, 75th Percentile)] and was negatively correlated with 5-mC content (P = 0.035), but not 5-hmC content, in genomic DNA from HCC tumour tissues.
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Affiliation(s)
- Fan Shen
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wei Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Jia-Hui Qi
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Jing-Tao Huang
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xin Zhou
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei, China
| | - Ying-Juan Liu
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Song-Mei Liu
- Center for Gene Diagnosis, Medical Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- * E-mail:
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Inoue-Choi M, Nelson HH, Robien K, Arning E, Bottiglieri T, Koh WP, Yuan JM. Plasma S-adenosylmethionine, DNMT polymorphisms, and peripheral blood LINE-1 methylation among healthy Chinese adults in Singapore. BMC Cancer 2013; 13:389. [PMID: 23957506 PMCID: PMC3765398 DOI: 10.1186/1471-2407-13-389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 08/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Global hypomethylation of repetitive DNA sequences is believed to occur early in tumorigenesis. There is a great interest in identifying factors that contribute to global DNA hypomethylation and associated cancer risk. We tested the hypothesis that plasma S-adenosylmethionine (SAM) level alone or in combination with genetic variation in DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) was associated with global DNA methylation extent at long interspersed nucleotide element-1 (LINE-1) sequences. METHODS Plasma SAM level and LINE-1 DNA methylation index were measured using stored blood samples collected from 440 healthy Singaporean Chinese adults during 1994-1999. Genetic polymorphisms of 13 loci in DNMT1, DNMT3A and DNMT3B were determined. RESULTS LINE-1 methylation index was significantly higher in men than in women (p = 0.001). LINE-1 methylation index was positively associated with plasma SAM levels (p ≤ 0.01), with a plateau at approximately 78% of LINE-1 methylation index (55 nmol/L plasma SAM) in men and 77% methylation index (50 nmol/L plasma SAM) in women. In men only, the T allele of DNMT1 rs21124724 was associated with a statistically significantly higher LINE-1 methylation index (ptrend = 0.001). The DNMT1 rs2114724 genotype modified the association between plasma SAM and LINE-1 methylation index at low levels of plasma SAM in men. CONCLUSIONS Circulating SAM level was associated with LINE-1 methylation status among healthy Chinese adults. The DNMT1 genetic polymorphism may exert a modifying effect on the association between SAM and LINE-1 methylation status in men, especially when plasma SAM level is low. Our findings support a link between plasma SAM and global DNA methylation status at LINE-1 sequences.
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Affiliation(s)
- Maki Inoue-Choi
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Heather H Nelson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, USA
| | - Kim Robien
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, USA
- Department of Epidemiology and Biostatistics, George Washington University, Washington, USA
| | - Erland Arning
- Institute of Metabolic Disease, Baylor Research Institute, Dallas, USA
| | | | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jian-Min Yuan
- Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, USA
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43
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DeMarini DM. Genotoxicity biomarkers associated with exposure to traffic and near-road atmospheres: a review. Mutagenesis 2013; 28:485-505. [DOI: 10.1093/mutage/get042] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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44
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Byun HM, Motta V, Panni T, Bertazzi PA, Apostoli P, Hou L, Baccarelli AA. Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants. Part Fibre Toxicol 2013; 10:28. [PMID: 23855992 PMCID: PMC3717285 DOI: 10.1186/1743-8977-10-28] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 07/05/2013] [Indexed: 02/07/2023] Open
Abstract
Background Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies. Results High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose–response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‒interaction=0.003) and benzene (p‒interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02). Conclusions The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation to airborne pollutants.
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Affiliation(s)
- Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA.
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45
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Walters RJ, Williamson EJ, English DR, Young JP, Rosty C, Clendenning M, Walsh MD, Parry S, Ahnen DJ, Baron JA, Win AK, Giles GG, Hopper JL, Jenkins MA, Buchanan DD. Association between hypermethylation of DNA repetitive elements in white blood cell DNA and early-onset colorectal cancer. Epigenetics 2013; 8:748-55. [PMID: 23804018 DOI: 10.4161/epi.25178] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Changes in the methylation levels of DNA from white blood cells (WBCs) are putatively associated with an elevated risk for several cancers. The aim of this study was to investigate the association between colorectal cancer (CRC) and the methylation status of three DNA repetitive elements in DNA from peripheral blood. WBC DNA from 539 CRC cases diagnosed before 60 years of age and 242 sex and age frequency-matched healthy controls from the Australasian Colorectal Cancer Family Registry were assessed for methylation across DNA repetitive elements Alu, LINE-1 and Sat2 using MethyLight. The percentage of methylated reference (PMR) of cases and controls was calculated for each marker. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using multivariable logistic regression adjusted for potential confounders. CRC cases demonstrated a significantly higher median PMR for LINE-1 (p < 0.001), Sat2 (p < 0.001) and Alu repeats (p = 0.02) when compared with controls. For each of the DNA repetitive elements, individuals with PMR values in the highest quartile were significantly more likely to have CRC compared with those in the lowest quartile (LINE-1 OR = 2.34, 95%CI = 1.48-3.70; p < 0.001, Alu OR = 1.83, 95%CI = 1.17-2.86; p = 0.01, Sat2 OR = 1.72, 95%CI = 1.10-2.71; p = 0.02). When comparing the OR for the PMR of each marker across subgroups of CRC, only the Alu marker showed a significant difference in the 5-fluoruracil treated and nodal involvement subgroups (both p = 0.002). This association between increasing methylation levels of three DNA repetitive elements in WBC DNA and early-onset CRC is novel and may represent a potential epigenetic biomarker for early CRC detection.
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Affiliation(s)
- Rhiannon J Walters
- Cancer and Population Studies Group; Queensland Institute of Medical Research; Herston, QLD Australia
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46
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Stembalska A, Leszczyński P, Gil J, Ramsey D, Pitala G, Maciejczyk A, Frączek M. Global DNA methylation status in laryngeal cancer. Head Neck 2013; 36:419-24. [DOI: 10.1002/hed.23315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2013] [Indexed: 01/25/2023] Open
Affiliation(s)
| | - Przemysław Leszczyński
- Department of Genetics; Wroclaw Medical University; Wroclaw Poland
- Department of Biology and Medical Parasitology; Wroclaw Medical University; Wroclaw Poland
| | - Justyna Gil
- Department of Genetics; Wroclaw Medical University; Wroclaw Poland
| | - David Ramsey
- Department of Mathematics and Statistics; University of Limerick; Limerick Ireland
| | - Grzegorz Pitala
- Department of Clinical Otolaryngology; 4th Military Hospital; Wroclaw Wroclaw Poland
| | | | - Marcin Frączek
- Department of Otolaryngology; Wroclaw Medical University; Wroclaw Poland
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Brennan K, Flanagan JM. Is there a link between genome-wide hypomethylation in blood and cancer risk? Cancer Prev Res (Phila) 2012; 5:1345-57. [PMID: 23135621 DOI: 10.1158/1940-6207.capr-12-0316] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer cells display widespread genetic and epigenetic abnormalities, but the contribution to disease risk, particularly in normal tissue before disease, is not yet established. Genome-wide hypomethylation occurs frequently in tumors and may facilitate chromosome instability, aberrant transcription and transposable elements reactivation. Several epidemiologic case-control studies have reported genomic hypomethylation in peripheral blood of cancer patients, suggesting a systemic effect of hypomethylation on disease predisposition, which may be exploited for biomarker development. However, more recent studies have failed to reproduce this. Here, we report a meta-analysis, indicating a consistent inverse association between genomic 5-methylcytosine levels and cancer risk [95% confidence interval (CI), 1.2-6.1], but no overall risk association for studies using surrogates for genomic methylation, including methylation at the LINE-1 repetitive element (95% CI, 0.8-1.7). However, studies have been highly heterogeneous in terms of experimental design, assay type, and analytical methods. We discuss the limitations of the current approaches, including the low interindividual variability of surrogate assays such as LINE1 and the importance of using prospective studies to investigate DNA methylation in disease risk. Insights into genomic location of hypomethylation, from recent whole genome, high-resolution methylome maps, will help address this interesting and clinically important question.
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Affiliation(s)
- Kevin Brennan
- Epigenetics Unit, Department of Surgery and Cancer, Hammersmith Hospital, Imperial College, London, United Kingdom
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48
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Jung AY, Botma A, Lute C, Blom HJ, Ueland PM, Kvalheim G, Midttun Ø, Nagengast F, Steegenga W, Kampman E. Plasma B vitamins and LINE-1 DNA methylation in leukocytes of patients with a history of colorectal adenomas. Mol Nutr Food Res 2012; 57:698-708. [PMID: 23132835 DOI: 10.1002/mnfr.201200069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 07/23/2012] [Accepted: 09/10/2012] [Indexed: 12/21/2022]
Abstract
SCOPE Low concentrations of folate, other B vitamins, and methionine are associated with colorectal cancer risk, possibly by changing DNA methylation patterns. Here, we examine whether plasma concentrations of B vitamins and methionine are associated with methylation of long interspersed nuclear element-1 (LINE-1) among those at high risk of colorectal cancer, i.e. patients with at least one histologically confirmed colorectal adenoma (CRA) in their life. METHODS AND RESULTS We used LINE-1 bisulfite pyrosequencing to measure global DNA methylation levels in leukocytes of 281 CRA patients. Multivariable linear regression was used to assess associations between plasma B vitamin concentrations and LINE-1 methylation levels. Plasma folate was inversely associated with LINE-1 methylation in CRA patients, while plasma methionine was positively associated with LINE-1 methylation. CONCLUSION This study does not provide evidence that in CRA patients, plasma folate concentrations are positively related to LINE-1 methylation in leukocytes but does suggest a direct association between plasma methionine and LINE-1 methylation in leukocytes.
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Affiliation(s)
- Audrey Y Jung
- Department of Epidemiology, Biostatistics, and HTA, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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Lange NE, Sordillo J, Tarantini L, Bollati V, Sparrow D, Vokonas P, Zanobetti A, Schwartz J, Baccarelli A, Litonjua AA, DeMeo DL. Alu and LINE-1 methylation and lung function in the normative ageing study. BMJ Open 2012; 2:e001231. [PMID: 23075571 PMCID: PMC3488751 DOI: 10.1136/bmjopen-2012-001231] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 09/06/2012] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES To investigate the association between methylation of transposable elements Alu and long-interspersed nuclear elements (LINE-1) and lung function. DESIGN Cohort study. SETTING Outpatient Veterans Administration facilities in greater Boston, Massachusetts, USA. PARTICIPANTS Individuals from the Veterans Administration Normative Aging Study, a longitudinal study of aging in men, evaluated between 1999 and 2007. The majority (97%) were white. PRIMARY AND SECONDARY OUTCOME MEASURES Primary predictor was methylation, assessed using PCR-pyrosequencing after bisulphite treatment. Primary outcome was lung function as assessed by spirometry, performed according to American Thoracic Society/European Respiratory Society guidelines at the same visit as the blood draws. RESULTS In multivariable models adjusted for age, height, body mass index (BMI), pack-years of smoking, current smoking and race, Alu hypomethylation was associated with lower forced expiratory volume in 1 s (FEV(1)) (β=28 ml per 1% change in Alu methylation, p=0.017) and showed a trend towards association with a lower forced vital capacity (FVC) (β=27 ml, p=0.06) and lower FEV(1)/FVC (β=0.3%, p=0.058). In multivariable models adjusted for age, height, BMI, pack-years of smoking, current smoking, per cent lymphocytes, race and baseline lung function, LINE-1 hypomethylation was associated with more rapid decline of FEV(1) (β=6.9 ml/year per 1% change in LINE-1 methylation, p=0.005) and of FVC (β=9.6 ml/year, p=0.002). CONCLUSIONS In multiple regression analysis, Alu hypomethylation was associated with lower lung function, and LINE-1 hypomethylation was associated with more rapid lung function decline in a cohort of older and primarily white men from North America. Future studies should aim to replicate these findings and determine if Alu or LINE-1 hypomethylation may be due to specific and modifiable environmental exposures.
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Affiliation(s)
- Nancy E Lange
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine Harvard Medical School, Boston, Massachusetts, USA
| | - Joanne Sordillo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine Harvard Medical School, Boston, Massachusetts, USA
| | - Letizia Tarantini
- Department of Environmental and Occupational Health, Center of Molecular and Genetic Epidemiology, Università degli Studi di Milano and IRCCS Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Bollati
- Department of Environmental and Occupational Health, Center of Molecular and Genetic Epidemiology, Università degli Studi di Milano and IRCCS Maggiore Policlinico Hospital, Milan, Italy
| | - David Sparrow
- Veterans Administration Boston Healthcare System and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Pantel Vokonas
- Veterans Administration Boston Healthcare System and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Antonella Zanobetti
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Andrea Baccarelli
- Department of Environmental and Occupational Health, Center of Molecular and Genetic Epidemiology, Università degli Studi di Milano and IRCCS Maggiore Policlinico Hospital, Milan, Italy
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine Harvard Medical School, Boston, Massachusetts, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine Harvard Medical School, Boston, Massachusetts, USA
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50
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Peluso M, Bollati V, Munnia A, Srivatanakul P, Jedpiyawongse A, Sangrajrang S, Piro S, Ceppi M, Bertazzi PA, Boffetta P, Baccarelli AA. DNA methylation differences in exposed workers and nearby residents of the Ma Ta Phut industrial estate, Rayong, Thailand. Int J Epidemiol 2012; 41:1753-60; discussion 1761-3. [PMID: 23064502 DOI: 10.1093/ije/dys129] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Adverse biological effects from airborne pollutants are a primary environmental concern in highly industrialized areas. Recent studies linked air pollution exposures with altered blood Deoxyribo-nucleic acid (DNA) methylation, but effects from industrial sources and underlying biological mechanisms are still largely unexplored. METHODS The Ma Ta Phut industrial estate (MIE) in Rayong, Thailand hosts one of the largest steel, oil refinery and petrochemical complexes in south-eastern Asia. We measured a panel of blood DNA methylation markers previously associated with air pollution exposures, including repeated elements [long interspersed nuclear element-1 (LINE-1) and Alu] and genes [p53, hypermethylated-in-cancer-1 (HIC1), p16 and interleukin-6 (IL-6)], in 67 MIE workers, 65 Ma Ta Phut residents and 45 rural controls. To evaluate the role of DNA damage and oxidation, we correlated DNA methylation measures with bulky DNA and 3-(2-deoxy-β-D-erythro-pentafuranosyl)pyrimido[1,2-α]purin-10(3H)-one deoxyguanosine (M(1)dG) adducts. RESULTS In covariate-adjusted models, MIE workers, compared with rural residents, showed lower LINE-1 (74.8% vs 78.0%; P < 0.001), p53 (8.0% vs 15.7%; P < 0.001) and IL-6 methylation (39.2% vs 45.0%; P = 0.027) and higher HIC1 methylation (22.2% vs 15.3%, P < 0.001). For all four markers, Ma Ta Phut residents exhibited methylation levels intermediate between MIE workers and rural controls (LINE-1, 75.7%, P < 0.001; p53, 9.0%, P < 0.001; IL-6, 39.8%, P = 0.041; HIC1, 17.8%, P = 0.05; all P-values vs rural controls). Bulky DNA adducts showed negative correlation with p53 methylation (P = 0.01). M(1)dG showed negative correlations with LINE-1 (P = 0.003) and IL-6 methylation (P = 0.05). CONCLUSIONS Our findings indicate that industrial exposures may induce alterations of DNA methylation patterns detectable in blood leucocyte DNA. Correlation of DNA adducts with DNA hypomethylation suggests potential mediation by DNA damage.
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Affiliation(s)
- Marco Peluso
- Cancer Risk Factor Branch, Cancer Prevention and Research Institute, Florence, Italy
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