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Hernandez Cordero AI, Li X, Yang J, Yang CX, Shaipanich T, MacIsaac JL, Dever K, Kobor MS, Montaner J, Harris M, Guillemi S, Man SFP, Sin DD, Leung JM. DNA Methylation Demonstrates Bronchoalveolar Cell Senescence in People Living with HIV: An Observational Cohort Study. Biomedicines 2024; 12:1261. [PMID: 38927468 PMCID: PMC11201658 DOI: 10.3390/biomedicines12061261] [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: 05/03/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND DNA methylation may be a link between HIV, aging, and the increased risk of lung comorbidities. We investigated whether bronchoalveolar lavage (BAL) cells of people living with HIV (PLWH) demonstrate epigenetic disruptions and advanced epigenetic aging. METHODS BAL cell DNA methylation from 25 PLWH and 16 HIV-uninfected individuals were tested for differential methylation of Alu and LINE-1 sites, markers of aging. We used a weighted gene correlation network analysis to identify HIV- and age-associated co-methylation networks. We tested the effect of HIV on DNA methylation using a robust linear model (false discovery rate < 0.10). RESULTS The BAL cells of PLWH were marked by global hypomethylation in both Alu and LINE-1 elements. Six co-methylated CpG networks were identified that were significantly associated with age; of these, the red module was significantly differentially methylated in PLWH and enriched pathways (e.g., Ras signaling and T-cell receptors). We identified 6428 CpG sites associated with HIV. CONCLUSIONS We have shown here for the first time that alterations in the DNA methylation of BAL cells in the lung with HIV show a pattern of advanced aging. This study strongly supports that HIV may contribute to an increased the risk of lung comorbidities through the epigenetics of aging.
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Affiliation(s)
- Ana I. Hernandez Cordero
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Julie L. MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Kristy Dever
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Shu Fan Paul Man
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
- Edwin S. H. Leong Centre for Healthy Aging, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
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2
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Mathavarajah S, Dellaire G. LINE-1: an emerging initiator of cGAS-STING signalling and inflammation that is dysregulated in disease. Biochem Cell Biol 2024; 102:38-46. [PMID: 37643478 DOI: 10.1139/bcb-2023-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
The cGAS-STING (cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)) axis integrates DNA damage and cellular stress with type I interferon (IFN) signalling to facilitate transcriptional changes underlying inflammatory stress responses. The cGAS-STING pathway responds to cytosolic DNA in the form of double-stranded DNA, micronuclei, and long interspersed nuclear element 1 (L1) retroelements. L1 retroelements are a class of self-propagating non-long terminal repeat transposons that have remained highly active in mammalian genomes. L1 retroelements are emerging as important inducers of cGAS-STING and IFN signalling, which are often dysregulated in several diseases, including cancer. A key repressor of cGAS-STING and L1 activity is the exonuclease three prime repair exonuclease 1 (TREX1), and loss of TREX1 promotes the accumulation of L1. In addition, L1 dysregulation is a common theme among diseases with chronic induction of type I IFN signalling through cGAS-STING, such as Aicardi-Goutières syndrome, Fanconi anemia, and dermatomyositis. Although TREX1 is highly conserved in tetrapod species, other suppressor proteins exist that inhibit L1 retrotransposition. These suppressor genes when mutated are often associated with diseases characterized by unchecked inflammation that is associated with high cGAS-STING activity and elevated levels of L1 expression. In this review, we discuss these interconnected pathways of L1 suppression and their role in the regulation of cGAS-STING and inflammation in disease.
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Affiliation(s)
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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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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4
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Reddam A, Bollati V, Wu H, Favero C, Tarantini L, Hoxha M, Comfort N, Gold DR, Phipatanakul W, Baccarelli AA. Air pollution and human endogenous retrovirus methylation in the school inner-city asthma intervention study. Toxicol Sci 2023; 193:166-174. [PMID: 37042721 PMCID: PMC10230279 DOI: 10.1093/toxsci/kfad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are transposable genomic elements generally repressed through DNA methylation. HERVs can be demethylated and expressed in response to environmental stimuli. Therefore, more research is needed to understand the influence of environmental exposures on HERV methylation. Air pollutants are commonly linked with global hypomethylation, and as HERVs comprise of nearly 8% of repetitive elements in the human genome, our objective was to examine the association between air pollutant exposure and HERV methylation. We investigated 180 students with asthma participating in the School Inner-City Asthma Intervention Study, which evaluated the efficacy of classroom air filters and school-wide pest management on air pollutant/allergen exposure and asthma. Both air pollutants measured in classrooms and asthma outcomes assessed by surveys were collected pre- and post-intervention. Buccal swabs were also collected pre- and post-intervention, and methylation levels from 9 transposable genomic elements (HERV-E, -FRD, -K, -L, -R, -W, -9, and HRES and LINE1) were measured. Adjusting for relevant covariates, the overall air pollutant mixture was cross-sectionally associated with higher HERV-W and lower HERV-L and LINE1 methylation. Coarse PM was cross-sectionally associated with higher HERV-K methylation and CO2 with lower LINE1 methylation. These results suggest that exposure to air pollutants is associated with HERV-W and HERV-K hypermethylation and HERV-L and LINE1 hypomethylation in children with asthma. Future studies are needed to characterize the links between HERV methylation and possible adverse outcomes.
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Affiliation(s)
- Aalekhya Reddam
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Haotian Wu
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Chiara Favero
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Letizia Tarantini
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Mirjam Hoxha
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Nicole Comfort
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Wanda Phipatanakul
- Asthma Clinical Research Center, Boston Children’s Hospital, Boston, Massachusetts 02115, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences; Mailman School of Public Health, Columbia University, New York, New York 10032, USA
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5
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Bai J, Tang L, Luo Y, Han Z, Li C, Sun Y, Sun Q, Lu J, Qiu H, Zhao Z, Huo T, Xiong W, Zhang Q. Vitamin B complex blocks the dust fall PM 2 .5 -induced acute lung injury through DNA methylation in rats. ENVIRONMENTAL TOXICOLOGY 2023; 38:403-414. [PMID: 36282901 DOI: 10.1002/tox.23689] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
This study aimed to explore whether vitamin B complex (folic acid, B6 , and B12 ) could avert DNA methylation changes associated with inflammation induced by acute PM2.5 exposure. Sprague-Dawley rats were administered by gavage with different concentrations of vitamin B complex once a day for 28 days, and then by intratracheal instillation with saline or PM2.5 once every 2 days for three times. Vitamin B continued to be taken during the PM2.5 exposure. Rats were sacrificed 24 h after the last exposure. The results showed that vitamin B complex could block the pathological changes and injury in lungs induced by PM2.5 . Meanwhile, vitamin B complex could prevent the abnormal DNA methylation of IL-4 and IFN-γ to antagonize the imbalance of IL-4/IFN-γ associated with inflammation. It was further found that vitamin B complex could regulate DNA methyltransferases (DNMTs) and increase the S-adenosylmethionine (SAM)/S-Adenosyl-L-homocysteine (SAH) ratio to reverse the hypomethylation of genomic DNA and the abnormal DNA methylation of IL-4 and IFN-γ. In conclusion, vitamin B complex has a protective effect on acute lung injury by attenuating abnormal DNA methylation induced by PM2.5 in rats. This study may provide a new insight into the physiological function of vitamin B to prevent the health effects induced by PM2.5 .
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Affiliation(s)
- Jun Bai
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Lanlan Tang
- School of Public Health, Southwest Medical University, Luzhou, China
- Chengdu Jintang Municipal Center for Disease Control and Prevention, Chengdu, China
| | - Yajun Luo
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Zhixia Han
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Chenwen Li
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Yaochuan Sun
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, China
| | - Qian Sun
- Luzhou Ecological Environment Monitoring Center of Sichuan Province, Luzhou, China
| | - Ji Lu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Hao Qiu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Zhenhu Zhao
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Tingting Huo
- School of Environmental and Resource, Southwest University of Science and Technology, Mianyang, China
| | - Wei Xiong
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Qingbi Zhang
- School of Public Health, Southwest Medical University, Luzhou, China
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6
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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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DENARIYAKOON SIKRIT, PUTTIPANYALEARS CHAROENCHAI, CHATAMRA KRIS, MUTIRANGURA APIWAT. Breast Cancer Sera Changes in Alu Element Methylation Predict Metastatic Disease Progression. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:731-738. [PMID: 36340456 PMCID: PMC9628142 DOI: 10.21873/cdp.10168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND/AIM During metastatic disease development, the cancer-immune system crosstalk induces epigenetic modifications to immune cells, impairing their functions. Recently, Alu elements methylation changes were widely studied in terms of early cancer detection. This study aimed to demonstrate in vitro Alu element methylation changes in peripheral immune cells in a metastatic setting and examine their prognostic values in metastatic breast cancer. MATERIALS AND METHODS Sera from sixteen metastatic cancer patients and sixteen healthy participants were obtained and used to culture normal peripheral immune cells. After 48 h of incubation, the percentage and pattern of Alu element methylation were examined for clinical relevance. RESULTS We found that the Alu element hypomethylation was affected by age in the cancer group. Intriguingly, a decrease in Alu element methylation was found in patients with early progressive disease. Moreover, an increase in unmethylated cytosine (mCuC) loci was related to the poorer prognosis group. Accordingly, the decrease in Alu element methylation and the increase in mCuC loci pattern in peripheral immune cells correlated with poorer prognosis and early progression in metastatic breast cancer. CONCLUSION Alu element hypomethylation in immune cells and their increased mCuC foci were related to the early progression of breast cancer. These warrant the use of Alu element methylation changes for diagnostic and therapeutic purposes in breast cancer.
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Affiliation(s)
- SIKRIT DENARIYAKOON
- Queen Sirikit Centre for Breast Cancer, The Thai Red Cross Society, Bangkok, Thailand
| | - CHAROENCHAI PUTTIPANYALEARS
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - KRIS CHATAMRA
- Queen Sirikit Centre for Breast Cancer, The Thai Red Cross Society, Bangkok, Thailand
| | - APIWAT MUTIRANGURA
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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8
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Hernández Cordero AI, Yang CX, Yang J, Horvath S, Shaipanich T, MacIsaac J, Lin DTS, Kobor MS, Guillemi S, Harris M, Lam W, Lam S, Montaner J, Man SFP, Sin DD, Leung JM. Airway Aging and Methylation Disruptions in HIV-associated Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2022; 206:150-160. [PMID: 35426765 PMCID: PMC9887412 DOI: 10.1164/rccm.202106-1440oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rationale: Age-related diseases like chronic obstructive pulmonary disease (COPD) occur at higher rates in people living with human immunodeficiency virus (PLWH) than in uninfected populations. Objectives: To identify whether accelerated aging can be observed in the airways of PLWH with COPD, manifest by a unique DNA methylation signature. Methods: Bronchial epithelial brushings from PLWH with and without COPD and HIV-uninfected adults with and without COPD (N = 76) were profiled for DNA methylation and gene expression. We evaluated global Alu and LINE-1 methylation and calculated the epigenetic age using the Horvath clock and the methylation telomere length estimator. To identify genome-wide differential DNA methylation and gene expression associated with HIV and COPD, robust linear models were used followed by an expression quantitative trait methylation (eQTM) analysis. Measurements and Main Results: Epigenetic age acceleration and shorter methylation estimates of telomere length were found in PLWH with COPD compared with PLWH without COPD and uninfected patients with and without COPD. Global hypomethylation was identified in PLWH. We identified 7,970 cytosine bases located next to a guanine base (CpG sites), 293 genes, and 9 expression quantitative trait methylation-gene pairs associated with the interaction between HIV and COPD. Actin binding LIM protein family member 3 (ABLIM3) was one of the novel candidate genes for HIV-associated COPD highlighted by our analysis. Conclusions: Methylation age acceleration is observed in the airway epithelium of PLWH with COPD, a process that may be responsible for the heightened risk of COPD in this population. Their distinct methylation profile, differing from that observed in patients with COPD alone, suggests a unique pathogenesis to HIV-associated COPD. The associations warrant further investigation to establish causality.
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Affiliation(s)
- Ana I. Hernández Cordero
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California;,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | | | | | | | | | - Silvia Guillemi
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - Marianne Harris
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - Wan Lam
- British Columbia Cancer, University of British Columbia, Vancouver, British Columbia, Canada; and
| | | | - Julio Montaner
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - S. F. Paul Man
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
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9
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Sunny SK, Zhang H, Relton CL, Ring S, Kadalayil L, Mzayek F, Ewart S, Holloway JW, Arshad SH. Sex-specific longitudinal association of DNA methylation with lung function. ERJ Open Res 2021; 7:00127-2021. [PMID: 34235211 PMCID: PMC8255542 DOI: 10.1183/23120541.00127-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
Investigating whether DNA methylation (DNA-M) at an earlier age is associated with lung function at a later age and whether this relationship differs by sex could enable prediction of future lung function deficit. A training/testing-based technique was used to screen 402 714 cytosine-phosphate-guanine dinucleotide sites (CpGs) to assess the longitudinal association of blood-based DNA-M at ages 10 and 18 years with lung function at 18 and 26 years, respectively, in the Isle of Wight birth cohort (IOWBC). Multivariable linear mixed models were applied to the CpGs that passed screening. To detect differentially methylated regions (DMRs), DMR enrichment analysis was conducted. Findings were further examined in the Avon Longitudinal Study of Parents and Children (ALSPAC). Biological relevance of the identified CpGs was assessed using gene expression data. DNA-M at eight CpGs (five CpGs with forced expiratory volume in 1 s (FEV1) and three CpGs with FEV1/forced vital capacity (FVC)) at an earlier age was associated with lung function at a later age regardless of sex, while at 13 CpGs (five CpGs with FVC, three with FEV1 and five with FEV1/FVC), the associations were sex-specific (p FDR <0.05) in IOWBC, with consistent directions of association in ALSPAC (IOWBC-ALSPAC consistent CpGs). cg16582803 (WNT10A) and cg14083603 (ZGPAT) were replicated in ALSPAC for main and sex-specific effects, respectively. Among IOWBC-ALSPAC consistent CpGs, DNA-M at cg01376079 (SSH3) and cg07557690 (TGFBR3) was associated with gene expression both longitudinally and cross-sectionally. In total, 57 and 170 DMRs were linked to lung function longitudinally in males and females, respectively. CpGs showing longitudinal associations with lung function have the potential to serve as candidate markers in future studies on lung function deficit prediction.
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Affiliation(s)
- Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | | | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Fawaz Mzayek
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Isle of Wight, UK
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10
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Hernandez Cordero AI, Yang CX, Obeidat M, Yang J, MacIsaac J, McEwen L, Lin D, Kobor M, Novak R, Hudson F, Klinker H, Dharan N, Man SP, Sin DD, Kunisaki K, Leung J. DNA methylation is associated with airflow obstruction in patients living with HIV. Thorax 2020; 76:448-455. [PMID: 33443234 PMCID: PMC8070606 DOI: 10.1136/thoraxjnl-2020-215866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022]
Abstract
Introduction People living with HIV (PLWH) suffer from age-related comorbidities such as COPD. The processes responsible for reduced lung function in PLWH are largely unknown. We performed an epigenome-wide association study to investigate whether blood DNA methylation is associated with impaired lung function in PLWH. Methods Using blood DNA methylation profiles from 161 PLWH, we tested the effect of methylation on FEV1, FEV1/FVC ratio and FEV1 decline over a median of 5 years. We evaluated the global methylation of PLWH with airflow obstruction by testing the differential methylation of transposable elements Alu and LINE-1, a well-described marker of epigenetic ageing. Results Airflow obstruction as defined by a FEV1/FVC<0.70 was associated with 1393 differentially methylated positions (DMPs), while 4676 were associated with airflow obstruction based on the FEV1/FVC<lower limit of normal. These DMPs were enriched for biological pathways associated with chronic viral infections. The airflow obstruction group was globally hypomethylated compared with those without airflow obstruction. 103 and 7112 DMPs were associated with FEV1 and FEV1/FVC, respectively. No positions were associated with FEV1 decline. Conclusion A large number of DMPs were associated with airflow obstruction and lung function in a unique cohort of PLWH. Airflow obstruction in even relatively young PLWH is associated with global hypomethylation, suggesting advanced epigenetic ageing compared with those with normal lung function. The disturbance of the epigenetic regulation of key genes not previously identified in non-HIV COPD cohorts could explain the unique risk of COPD in PLWH.
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Affiliation(s)
- Ana I Hernandez Cordero
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Maen Obeidat
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Julie MacIsaac
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, UK
| | - Hartwig Klinker
- Medizinische Klinik und Poliklinik II, Universitatsklinikum Wurzburg, Wurzburg, Germany
| | - Nila Dharan
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sf Paul Man
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine and the Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Janice Leung
- Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
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11
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Sunny SK, Zhang H, Rezwan FI, Relton CL, Henderson AJ, Merid SK, Melén E, Hallberg J, Arshad SH, Ewart S, Holloway JW. Changes of DNA methylation are associated with changes in lung function during adolescence. Respir Res 2020; 21:80. [PMID: 32264874 PMCID: PMC7140357 DOI: 10.1186/s12931-020-01342-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Adolescence is a significant period for the gender-dependent development of lung function. Prior studies have shown that DNA methylation (DNA-M) is associated with lung function and DNA-M at some cytosine-phosphate-guanine dinucleotide sites (CpGs) changes over time. This study examined whether changes of DNA-M at lung-function-related CpGs are associated with changes in lung function during adolescence for each gender, and if so, the biological significance of the detected CpGs. METHODS Genome-scale DNA-M was measured in peripheral blood samples at ages 10 (n = 330) and 18 years (n = 476) from the Isle of Wight (IOW) birth cohort in United Kingdom, using Illumina Infinium arrays (450 K and EPIC). Spirometry was conducted at both ages. A training and testing method was used to screen 402,714 CpGs for their potential associations with lung function. Linear regressions were applied to assess the association of changes in lung function with changes of DNA-M at those CpGs potentially related to lung function. Adolescence-related and personal and family-related confounders were included in the model. The analyses were stratified by gender. Multiple testing was adjusted by controlling false discovery rate of 0.05. Findings were further examined in two independent birth cohorts, the Avon Longitudinal Study of Children and Parents (ALSPAC) and the Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) cohort. Pathway analyses were performed on genes to which the identified CpGs were mapped. RESULTS For females, 42 CpGs showed statistically significant associations with change in FEV1/FVC, but none for change in FEV1 or FVC. No CpGs were identified for males. In replication analyses, 16 and 21 of the 42 CpGs showed the same direction of associations among the females in the ALSPAC and BAMSE cohorts, respectively, with 11 CpGs overlapping across all the three cohorts. Through pathway analyses, significant biological processes were identified that have previously been related to lung function development. CONCLUSIONS The detected 11 CpGs in all three cohorts have the potential to serve as the candidate epigenetic markers for changes in lung function during adolescence in females.
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Affiliation(s)
- Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Faisal I. Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield Bedfordshire, MK43 0AL England
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- Population Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Simon Kebede Merid
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - Jenny Hallberg
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - S. Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Parkhurst Road, Newport, Isle of Wight PO30 5TG UK
| | - Susan Ewart
- Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
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12
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Guerra S, Vasquez MM, Bojang P, Ramos IN, Sherrill DL, Martinez FD, Halonen M, Ramos KS. Serum levels of L1-ORF1p and airflow limitation. ERJ Open Res 2019; 5:00247-2018. [PMID: 31777752 PMCID: PMC6876133 DOI: 10.1183/23120541.00247-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 09/02/2019] [Indexed: 11/22/2022] Open
Abstract
LINE-1 (long interspersed nuclear element-1) is a group of polymorphic DNA sequences in the human genome that mobilise via RNA binding proteins, reverse transcriptase and endonuclease to alter the host genome via mutational insertions, chromosomal rearrangements and reprogramming of gene expression (reviewed by Ramoset al. [1]). Full-length LINE-1 sequences encode two proteins: L1-ORF1p, a 40-kDa protein with nucleic acid binding activity; and L1-ORF2p, a 150-kDa protein with endonuclease and reverse transcriptase activities. The activity of LINE-1 is repressed in somatic tissues via DNA methylation and covalent protein modifications, and reactivated by displacement of retinoblastoma-associated proteins from the regulatory region [2]. Recent studies in our laboratory have implicated LINE-1 as a master regulator of human bronchial epithelial cell phenotypes in experimental in vitro and in vivo models [3]. In a population-based study, higher circulating levels of L1-ORF1p were associated with lower lung function levels and increased risk for airflow limitation among former smokershttp://bit.ly/2ZEIjNv
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Affiliation(s)
- Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.,Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, AZ, USA.,ISGlobal, Barcelona, Spain
| | - Monica M Vasquez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Pasano Bojang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Irma N Ramos
- Dept of Promotion Health Sciences, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Duane L Sherrill
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Marilyn Halonen
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.,Dept of Pharmacology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kenneth S Ramos
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.,Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, AZ, USA.,Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
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13
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DeMeo DL. The Recursive Trek of Epigenetics from the Bench to the Bedside. Predictive Methylation Marks by the Dozen. Am J Respir Crit Care Med 2019; 198:145-146. [PMID: 29585206 DOI: 10.1164/rccm.201803-0477ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Dawn L DeMeo
- 1 Brigham and Women's Hospital Harvard Medical School Boston, Massachusetts
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14
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Gao L, Urman R, Millstein J, Siegmund KD, Dubeau L, Breton CV. Association between AXL promoter methylation and lung function growth during adolescence. Epigenetics 2018; 13:1027-1038. [PMID: 30277126 PMCID: PMC6342069 DOI: 10.1080/15592294.2018.1529517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/19/2018] [Accepted: 09/22/2018] [Indexed: 12/26/2022] Open
Abstract
AXL is one of the TAM (TYRO3, AXL and MERTK) receptor tyrosine kinases and may be involved in airway inflammation. Little is known about how epigenetic changes in AXL may affect lung development during adolescence. We investigated the association between AXL DNA methylation at birth and lung function growth from 10 to 18 years of age in 923 subjects from the Children's Health Study (CHS). DNA methylation from newborn bloodspots was measured at multiple CpG loci across the regulatory regions of AXL using Pyrosequencing. Linear spline mixed-effects models were fitted to assess the association between DNA methylation and 8-year lung function growth. Findings were evaluated for replication in a separate population of 237 CHS subjects using methylation data from the Illumina HumanMethylation450 (HM450) array when possible. A 5% higher average methylation level of the AXL promoter region at birth was associated with a 48.4 ml decrease in mean FEV1 growth from 10 to 18 years of age in the primary study population (95% CI: -100.2, 3.4), and a 53.9 ml decrease in mean FEV1 growth from 11 to 15 years of age in the replication population (95% CI: -104.3, -3.5). One CpG locus in the promoter region, cg10564498, was significantly associated with decreased growth in FEV1, FVC and MMEF from 10 to 18 years of age and the negative associations were observed in a similar age range in the replication population. These findings suggest a potential association between AXL promoter methylation at birth and lower lung function growth during adolescence.
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Affiliation(s)
- Lu Gao
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Robert Urman
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Joshua Millstein
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Louis Dubeau
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Carrie V. Breton
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
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15
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Leng S, Diergaarde B, Picchi MA, Wilson DO, Gilliland FD, Yuan JM, Siegfried JM, Belinsky SA. Gene Promoter Hypermethylation Detected in Sputum Predicts FEV 1 Decline and All-Cause Mortality in Smokers. Am J Respir Crit Care Med 2018; 198:187-196. [PMID: 29437466 PMCID: PMC6058990 DOI: 10.1164/rccm.201708-1659oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
RATIONALE Gene promoter hypermethylation detected in sputum assesses the extent of field cancerization and predicts lung cancer (LC) risk in ever-smokers. A rapid decline of FEV1 is a major driver for development of airway obstruction. OBJECTIVES To assess the effects of methylation of 12 genes on FEV1 decline and of FEV1 decline on subsequent LC incidence using two independent, longitudinal cohorts (i.e., LSC [Lovelace Smokers Cohort] and PLuSS [Pittsburgh Lung Screening Study]). METHODS Gene methylation was measured in sputum using two-stage nested methylation-specific PCR. The linear mixed effects model was used to assess the effects of studied variables on FEV1 decline. MEASUREMENTS AND MAIN RESULTS A dose-dependent relationship between number of genes methylated and FEV1 decline was identified, with smokers with three or more methylated genes having 27.8% and 10.3% faster FEV1 decline than smokers with zero to two methylated genes in the LSC and PLuSS cohort, respectively (all P < 0.01). High methylation in sputum was associated with a shorter latency for LC incidence (log-rank P = 0.0048) and worse all-cause mortality (log-rank P < 0.0001). Smokers with subsequent LC incidence had a more rapid annual decline of FEV1 (by 5.2 ml, P = 0.038) than smoker control subjects. CONCLUSIONS Gene methylation detected in sputum predicted FEV1 decline, LC incidence, and all-cause mortality in smokers. Rapid FEV1 decline may be a risk factor for LC incidence in smokers, which may explain a greater prevalence of airway obstruction seen in patients with LC.
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Affiliation(s)
- Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Cancer Control Research Program and
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Brenda Diergaarde
- Department of Human Genetics and
- Cancer Epidemiology and Prevention Program
- Lung Cancer Program, and
| | - Maria A. Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - David O. Wilson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Frank D. Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, and
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | | | - Steven A. Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Cancer Control Research Program and
- Cancer Genetics and Epigenetics Program, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
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16
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Wang C, Chen R, Shi M, Cai J, Shi J, Yang C, Li H, Lin Z, Meng X, Liu C, Niu Y, Xia Y, Zhao Z, Kan H, Weinberg CR. Possible Mediation by Methylation in Acute Inflammation Following Personal Exposure to Fine Particulate Air Pollution. Am J Epidemiol 2018; 187:484-493. [PMID: 29020142 DOI: 10.1093/aje/kwx277] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/11/2017] [Indexed: 12/23/2022] Open
Abstract
Air pollution may increase cardiovascular and respiratory risk through inflammatory pathways, but evidence for acute effects has been weak and indirect. Between December 2014 and July 2015, we enrolled 36 healthy, nonsmoking college students for a panel study in Shanghai, China, a city with highly variable levels of air pollution. We measured personal exposure to particulate matter with an aerodynamic diameter less than or equal to 2.5 μm (PM2.5) continuously for 72 hours preceding each of 4 clinical visits that included phlebotomy. We measured 4 inflammation proteins and DNA methylation at nearby regulatory cytosine-phosphate-guanine (CpG) loci. We applied linear mixed-effect models to examine associations over various lag times. When results suggested mediation, we evaluated methylation as mediator. Increased PM2.5 concentration was positively associated with all 4 inflammation proteins and negatively associated with DNA methylation at regulatory loci for tumor necrosis factor alpha (TNF-α) and soluble intercellular adhesion molecule-1. A 10-μg/m3 increase in average PM2.5 during the 24 hours preceding blood draw corresponded to a 4.4% increase in TNF-α and a statistically significant decrease in methylation at one of the two studied candidate CpG loci for TNF-α. Epigenetics may play an important role in mediating effects of PM2.5 on inflammatory pathways.
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Affiliation(s)
- Cuicui Wang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Fudan University, Shanghai, China
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Jing Cai
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Jingjin Shi
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Changyuan Yang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Huichu Li
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Zhijing Lin
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Xia Meng
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Cong Liu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Yongjie Xia
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Zhuohui Zhao
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and Key Lab of Health Technology Assessment of the Ministry of Health, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Fudan University, Shanghai, China
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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17
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Bolund ACS, Starnawska A, Miller MR, Schlünssen V, Backer V, Børglum AD, Christensen K, Tan Q, Christiansen L, Sigsgaard T. Lung function discordance in monozygotic twins and associated differences in blood DNA methylation. Clin Epigenetics 2017; 9:132. [PMID: 29299071 PMCID: PMC5740718 DOI: 10.1186/s13148-017-0427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 01/16/2023] Open
Abstract
Background Lung function is an important predictor of morbidity and mortality, with accelerated lung function decline reported to have immense consequences for the world's healthcare systems. The lung function decline across individual's lifetime is a consequence of age-related changes in lung anatomical structure and combination of various environmental factors; however, the exact molecular mechanisms contributing to this decline are not fully understood. DNA methylation is an epigenetic modification that changes across individual's lifetime, as well as allows for interplay between environmental and genetic factors. DNA methylation plays a crucial role in regulation of gene expression, with increasing evidence linking aberrant DNA methylation levels with a number of common human diseases. In this study, we investigated possible associations between genome-wide DNA methylation levels and lung function in 169 pairs of middle-aged monozygotic twins (86 male pairs: mean age (min-max) = 66 years (57-79); 83 female pairs: mean age (min-max) = 66 years (56-78)). The twins were collected from the Danish Twin Registry and were examined at baseline (1998-1999) and follow-up (2008-2011) visits. Using the twin design, we correlated intra-pair differences in cross-sectional and longitudinal lung function with intra-pair blood DNA methylation differences at follow-up by linear regression analyses adjusted for sex, age, BMI, smoking, and blood cell composition measured for each individual with the use of flow cytometry. Results We identified several differentially methylated CpG sites associated with forced expiratory volume the first second (FEV1) and forced vital capacity (FVC). Three probes identified for level of FVC were located in GLIPR1L2 gene (lowest p value = 7.14 × 10-8), involved in innate immunity and tumour-suppressor/pro-oncogenic mechanisms. Change in FEV1 during the 11-year follow-up period was associated with blood DNA methylation level in TRIM27 gene (p value = 1.55 × 10-6), a negative regulator of CD4 T cells, and also involved in cancer development. Several enriched pathways were identified, especially for FEV1, with one being "TGFBR" (Benjamini-Hochbergadjp value = 0.045), the receptor for TGFβ, a growth factor involved in normal lung tissue repair through pro-fibrotic effects. Conclusions Our findings suggest that epigenetic regulation of immunological- and cancer-related genes, as well as TGF-β-receptor-related genes, may be involved in the cross-sectional level and longitudinal change in lung function in middle-aged monozygotic twins.
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Affiliation(s)
- Anneli C. S. Bolund
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Martin R. Miller
- Institute of Occupational and Environmental Medicine, University of Birmingham, Birmingham, UK
| | - Vivi Schlünssen
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Vibeke Backer
- Department of Respiratory Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Kaare Christensen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry and Pharmacology, University Hospital, Odense, Denmark
| | - Qihua Tan
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Institute of Public Health, University of Southern Denmark, Odense, Denmark
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Torben Sigsgaard
- Department of Public Health, Section for Environment Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
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The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
PURPOSE OF REVIEW Metabolic and bariatric surgery (MBS) is considered to be the most effective treatment for obesity. Not only due to the significant weight reduction but also because of the many health benefits associated with it. In the last 5 years, several studies have suggested that epigenetic modifications could be involved in the mechanisms underlying the response to bariatric surgery. In this review, we will compile the different studies (2012-2017) concerning the effect of this surgical procedure on DNA methylation patterns (the most studied epigenetic marker) and its association with metabolic improvement. This is an emerging area, and currently, there are not many studies in the literature. The aim is to show what has been done so far and what the future direction in this emerging area might be. RECENT FINDINGS Recent findings have shown how metabolic and bariatric surgery modifies the DNA methylation profile of the specific genes associated with the pathophysiology of the disease. The studies were performed in morbidly obese subjects, mainly in women, with the aim of reducing weight and improving the obesity-associated comorbidities. DNA methylation has been measured both in specific tissue and in peripheral blood samples. In general, studies about site-specific DNA methylation have shown a change in the methylation profile after surgery, whereas the studies analyzing global DNA methylation are not so conclusive. Summing up, metabolic and bariatric surgery can modify the DNA methylation profile of different genes and contributes to the metabolic health benefits that are often seen after metabolic and bariatric surgery. Although there are still many issues to be resolved, the capacity to revert the DNA methylation profile of specific sites opens a window for searching for target markers to treat obesity-related comorbidities.
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20
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Multiple endpoints to evaluate pristine and remediated titanium dioxide nanoparticles genotoxicity in lung epithelial A549 cells. Toxicol Lett 2017; 276:48-61. [DOI: 10.1016/j.toxlet.2017.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 12/14/2022]
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Machin M, Amaral AFS, Wielscher M, Rezwan FI, Imboden M, Jarvelin MR, Adcock IM, Probst-Hensch N, Holloway JW, Jarvis DL. Systematic review of lung function and COPD with peripheral blood DNA methylation in population based studies. BMC Pulm Med 2017; 17:54. [PMID: 28320365 PMCID: PMC5360084 DOI: 10.1186/s12890-017-0397-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Epigenetic variations in peripheral blood have potential as biomarkers for disease. This systematic review assesses the association of lung function and chronic obstructive pulmonary disease (COPD) with DNA methylation profiles in peripheral blood from population-based studies. METHODS Online databases Medline, Embase, and Web of Science were searched. Google Scholar was searched to identify grey literature. After removing duplicate articles, 1155 articles were independently screened by two investigators. Peer reviewed reports on population-based studies that examined peripheral blood DNA methylation in participants with measured lung function (FEV1, FEV1/FVC ratio) or known COPD status were selected for full-text review. Six articles were suitable for inclusion. Information regarding study characteristics, designs, methodologies and conclusions was extracted. A narrative synthesis was performed based on published results. RESULTS Three of the six articles assessed the association of COPD with DNA methylation, and two of these also included associations with lung function. Overall, five reports examined the association of lung function with DNA methylation profiles. Five of the six articles reported 'significant' results. However, no consistent CpG sites were identified across studies for COPD status or lung function values. CONCLUSIONS DNA methylation patterns in peripheral blood from individuals with reduced lung function or COPD may be different to those in people with normal lung function. However, this systematic review did not find any consistent associations of lung function or COPD with differentially methylated CpG sites. Large studies with a longitudinal design to address reverse causality may prove a more fruitful area of research. TRIAL REGISTRATION PROSPERO 2016: CRD42016037352 .
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Affiliation(s)
| | - André F S Amaral
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK.
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.
| | - Matthias Wielscher
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Marjo-Riitta Jarvelin
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ian M Adcock
- Airways Disease Section, NHLI, Imperial College London, London, UK
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Deborah L Jarvis
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
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Lee J, Kalia V, Perera F, Herbstman J, Li T, Nie J, Qu LR, Yu J, Tang D. Prenatal airborne polycyclic aromatic hydrocarbon exposure, LINE1 methylation and child development in a Chinese cohort. ENVIRONMENT INTERNATIONAL 2017; 99:315-320. [PMID: 28027800 PMCID: PMC5810919 DOI: 10.1016/j.envint.2016.12.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAH) are carcinogenic, neurotoxic environmental pollutants generated during incomplete combustion of fossil fuel and other organic material. PAH exposure has been associated with adverse fetal development and epigenetic alterations in cord blood. Several molecular epidemiology studies have established PAH-DNA adducts as biomarkers of PAH exposure. OBJECTIVES We investigated the relationship between LINE1 DNA methylation and PAH-DNA adduct levels in cord blood, and with neurodevelopmental outcomes. METHODS In Tongliang County, China, the current study enrolled two population-based cohorts of nonsmoking pregnant women before (2002) and after (2005) the closure of a local coal-fired power plant in May 2004. We analyzed cord blood samples collected from mothers in the two cohorts (n=110 from 2002 cohort and n=107 from 2005 cohort) for PAH-DNA adducts and genomic LINE1 DNA methylation. Neurodevelopmental data on children were collected using the Gesell Developmental Scales (GDS) at age 2 and using the Wechsler Intelligence Scale for Children (WISC) at age 5. RESULTS A significant inverse relationship was observed between PAH-DNA adducts and LINE1 DNA methylation (β=-0.010, p<0.038). A significant, positive association between LINE1 methylation and scores on WISC full scale and verbal (β=85.31, p<0.005; β=94.36, p<0.003) but not on the GDS. Mediation analysis did not find LINE1 to be a direct mediator between PAH-DNA adducts and IQ score. CONCLUSION LINE1 methylation in cord blood DNA was a positive predictor of IQ at age 5 and was decreased at higher levels of prenatal PAH exposure measured by PAH-DNA adducts in cord blood. However, the adverse effects of prenatal exposure to PAH on IQ scores did not appear to be directly mediated by altered LINE1 methylation.
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Affiliation(s)
- Joan Lee
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Vrinda Kalia
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Frederica Perera
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Julie Herbstman
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Tingyu Li
- Chirdren's Hospital, Chongqing Medical University, Chongqing, China
| | | | - L R Qu
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jie Yu
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Deliang Tang
- Department of Environmental Health Sciences, Columbia Center for Children's Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, United States.
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Global DNA hypomethylation has no impact on lung function or serum inflammatory and fibrosis cytokines in asbestos-exposed population. Int Arch Occup Environ Health 2017; 90:265-274. [PMID: 28105512 DOI: 10.1007/s00420-017-1195-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 01/02/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE To examine the effect of asbestos exposure on global DNA methylation and determine whether lung function and inflammatory and fibrosis biomarkers are correlated with the methylation state. METHODS A total of 26 healthy subjects without asbestos exposure (Group 1), 47 healthy subjects with exposure (Group 2), and 52 subjects with benign asbestos-related disorders (ARDs) (Group 3) participated in this cross-sectional study. Blood global 5-methylcytosine (5mC) and serum TNF-α, collagen IV, CCL5 and CC16 concentrations were analyzed using enzyme-linked immunosorbent assay-like assays. Spirometric maneuvers were performed to assess lung function. RESULTS Decreased 5mC levels were observed in Groups 2 and 3 compared to Group 1, irrespective of lung function (p < 0.01). There was no significant change in 5mC between Groups 2 and 3. Overall, 5mC was negatively correlated with CCL5 and collagen IV (p < 0.05), but no significant inverse relationship was found between 5mC and CCL5 or collagen IV in each group. Additionally, both 5mC and CC16 were inversely associated with FEV1/FVC% (p = 0.001, adjusted R 2 = 0.145) for non-smokers, and consistently significant inverse relationships were found between CC16 and FEV1/FVC%, independent of asbestos exposure. CONCLUSIONS Asbestos exposure causes global DNA hypomethylation. DNA hypomethylation has no influence on serum biomarkers and lung function in asbestos-exposed population with or without pleural and pulmonary parenchymal abnormalities.
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Xiao FH, Kong QP, Perry B, He YH. Progress on the role of DNA methylation in aging and longevity. Brief Funct Genomics 2016; 15:454-459. [PMID: 27032421 DOI: 10.1093/bfgp/elw009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aging is a major risk factor for individuals' health problems. Moreover, environmental signals have a widespread influence on the aging process. Epigenetic modification, e.g. DNA methylation, represents a link between genetic and environmental signals via the regulation of gene transcription. An abundance of literature indicates that aberrant epigenetic change occurs throughout the aging process at both the cellular and the organismal level. In particular, DNA methylation presents globally decreasing and site-specific increasing in aging. In this review, we focus on the crucial roles of DNA methylation in aging and age-related disease and highlight the great potential of DNA methylation as a therapeutic target in preventing age-related diseases and promoting healthy longevity.
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Abstract
Brochopulmonary dysplasia (BPD) is the most common form of chronic lung disease in infancy. At present, BPD primarily occurs in extremely premature infants (23-28 weeks of gestation) born during the late canalicular/early saccular stage of lung development. This article summarizes the current knowledge of the life course of BPD by emphasizing recent or key articles notating its natural history from the newborn period through adulthood and building the case for a continued focus on its primary prevention.
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Affiliation(s)
- Cindy T McEvoy
- Department of Pediatrics, Oregon Health & Science University, 707 SW Gaines Street, CDRC-P, Portland, OR 97239-3098, USA.
| | - Judy L Aschner
- Department of Pediatrics, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Rosenthal Pavilion, Room 402, 111 East 210th Street, Bronx, NY 10467, USA; Department of Obstetrics & Gynecology and Women's Health, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Rosenthal Pavilion, Room 402, 111 East 210th Street, Bronx, NY 10467, USA
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26
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da Silva RA, Sammartino Mariano F, Planello AC, Line SRP, de Souza AP. HaCaT anchorage blockade leads to oxidative stress, DNA damage and DNA methylation changes. Biochem Biophys Rep 2015; 2:94-102. [PMID: 29124149 PMCID: PMC5668640 DOI: 10.1016/j.bbrep.2015.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/14/2015] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
Cell adhesion plays an important role in neoplastic transformation. Thus, anchorage-independent growth and epithelial-mesenchymal transition, which are features associated to anoikis-resistance, are vital steps in cancer progression and metastatic colonization. Cell attachment loss may induce intracellular oxidative stress, which triggers DNA damage as methylation changes. HaCaT lineage cells were submitted to periods of 1, 3, 5 and 24 h of anchorage blockage with the purpose of study of oxidative stress effect on changes in the DNA methylation pattern, derived from attachment blockade. Through this study, HaCaT anchorage blockage-induced oxidative stress was reported to mediate alterations in global DNA methylation changes and into TP53 gene promoter pattern during anoikis-resistance acquisition. Furthermore, at the first experimental time-periods (1, 3 and 5 h), genome hypermethylation was found; however, genome hypomethylation was observed in later time-periods (24 h) of attachment impediment. The TP 53 methylation analyses were performed after 24 h of replated anoikis-resistance cells and same methylation pattern was observed, occurring an early (1 and 3 h) hypermethylation that was followed by late (5 and 24 h) hypomethylation. However, LINE-1, a marker of genomic instability, was perceived in time-dependent hypomethylation. The mRNA levels of the DNMTs enzymes were influenced by cell attachment blockage, but non-conclusive results were obtained in order to match DNMTs transcription to pattern methylation results. In conclusion, DNA damage was found, leaded by oxidative stress that has come up from HaCaT anchorage blockade, which rises a global genome hypomethylation tendency as consequence, which might denote genomic instability.
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Affiliation(s)
- Rodrigo A da Silva
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Flavia Sammartino Mariano
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Aline C Planello
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Sergio R P Line
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Ana Paula de Souza
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
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27
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DNA methylation analysis of SOCS1, SOCS3, and LINE-1 in microdissected gingival tissue. Clin Oral Investig 2015; 19:2337-44. [DOI: 10.1007/s00784-015-1460-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 03/18/2015] [Indexed: 12/18/2022]
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Dynamic Alu methylation during normal development, aging, and tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:784706. [PMID: 25243180 PMCID: PMC4163490 DOI: 10.1155/2014/784706] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/16/2014] [Indexed: 12/15/2022]
Abstract
DNA methylation primarily occurs on CpG dinucleotides and plays an important role in transcriptional regulations during tissue development and cell differentiation. Over 25% of CpG dinucleotides in the human genome reside within Alu elements, the most abundant human repeats. The methylation of Alu elements is an important mechanism to suppress Alu transcription and subsequent retrotransposition. Decades of studies revealed that Alu methylation is highly dynamic during early development and aging. Recently, many environmental factors were shown to have a great impact on Alu methylation. In addition, aberrant Alu methylation has been documented to be an early event in many tumors and Alu methylation levels have been associated with tumor aggressiveness. The assessment of the Alu methylation has become an important approach for early diagnosis and/or prognosis of cancer. This review focuses on the dynamic Alu methylation during development, aging, and tumor genesis. The cause and consequence of Alu methylation changes will be discussed.
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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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30
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Baptista N, Portinho D, Casarin R, Vale H, Casati M, De Souza A, Andia D. DNA methylation levels of SOCS1 and LINE-1 in oral epithelial cells from aggressive periodontitis patients. Arch Oral Biol 2014; 59:670-8. [DOI: 10.1016/j.archoralbio.2014.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/10/2014] [Accepted: 03/26/2014] [Indexed: 11/28/2022]
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Lepeule J, Bind MAC, Baccarelli AA, Koutrakis P, Tarantini L, Litonjua A, Sparrow D, Vokonas P, Schwartz JD. Epigenetic influences on associations between air pollutants and lung function in elderly men: the normative aging study. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:566-72. [PMID: 24602767 PMCID: PMC4050500 DOI: 10.1289/ehp.1206458] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/04/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Few studies have been performed on pulmonary effects of air pollution in the elderly--a vulnerable population with low reserve capacity--and mechanisms and susceptibility factors for potential effects are unclear. OBJECTIVES We evaluated the lag structure of air pollutant associations with lung function and potential effect modification by DNA methylation (< or ≥ median) at 26 individual CpG sites in nine candidate genes in a well-characterized cohort of elderly men. METHODS We measured forced vital capacity (FVC), forced expiratory volume in 1 sec (FEV1), and blood DNA methylation one to four times between 1999 and 2009 in 776 men from the Normative Aging Study. Air pollution was measured at fixed monitors 4 hr to 28 days before lung function tests. We used linear mixed-effects models to estimate the main effects of air pollutants and effect modification by DNA methylation. RESULTS An interquartile range (IQR) increase in subchronic exposure (3 to 28 days cumulated), but not in acute exposure (during the previous 4 hr, or the current or previous day), to black carbon, total and nontraffic particles with aerodynamic diameter ≤ 2.5 μm (PM2.5), carbon monoxide, and nitrogen dioxide was associated with a 1-5% decrease in FVC and FEV1 (p < 0.05). Slope estimates were greater for FVC than FEV1, and increased with cumulative exposure. The estimates slopes for air pollutants (28 days cumulated) were higher in participants with low (< median) methylation in TLR2 at position 2 and position 5 and high (≥ median) methylation in GCR. CONCLUSIONS Subchronic exposure to traffic-related pollutants was associated with significantly reduced lung function in the elderly; nontraffic pollutants (particles, ozone) had weaker associations. Epigenetic mechanisms related to inflammation and immunity may influence these associations.
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Affiliation(s)
- Johanna Lepeule
- Exposure, Epidemiology, and Risk Program, Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
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Faulk C, Liu K, Barks A, Goodrich JM, Dolinoy DC. Longitudinal epigenetic drift in mice perinatally exposed to lead. Epigenetics 2014; 9:934-41. [PMID: 24786859 DOI: 10.4161/epi.29024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
An understanding of the natural change in DNA methylation over time, defined as "epigenetic drift," will inform the study of environmental effects on the epigenome. This study investigates epigenetic drift in isogenic mice exposed perinatally to lead (Pb) acetate at four concentrations, 0 ppm (control), 2.1 ppm (low), 16 ppm (medium), and 32 ppm (high) prior to conception through weaning, then followed until 10 months of age. Absolute values of DNA methylation in a transposon-associated metastable locus, Cdk5-activator binding protein (Cabp(IAP)), and three imprinted loci (Igf2, Igf2r, and H19) were obtained from tail tissue in paired samples. DNA methylation levels in the controls increased over time at the imprinted Igf2 and Igf2r loci (both P = 0.0001), but not at the imprinted H19 locus or the Cabp(IAP) metastable epiallele. Pb exposure was associated with accelerated DNA hypermethylation in Cabp(IAP) (P = 0.0209) and moderated hypermethylation in Igf2r (P = 0.0447), and with marginally accelerated hypermethylation at H19 (P = 0.0847). In summary, the presence and magnitude of epigenetic drift was locus-dependent, and enhancement of drift was mediated by perinatal Pb exposure, in some, but not all, loci.
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Affiliation(s)
- Christopher Faulk
- Department of Environmental Health Sciences; University of Michigan; Ann Arbor, MI USA
| | - Kevin Liu
- Department of Environmental Health Sciences; University of Michigan; Ann Arbor, MI USA
| | - Amanda Barks
- Department of Environmental Health Sciences; University of Michigan; Ann Arbor, MI USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences; University of Michigan; Ann Arbor, MI USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences; University of Michigan; Ann Arbor, MI USA
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Newman MR, Sykes PJ, Blyth BJ, Bezak E, Lawrence MD, Morel KL, Ormsby RJ. A single whole-body low dose X-irradiation does not affect L1, B1 and IAP repeat element DNA methylation longitudinally. PLoS One 2014; 9:e93016. [PMID: 24676381 PMCID: PMC3968115 DOI: 10.1371/journal.pone.0093016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 02/27/2014] [Indexed: 11/18/2022] Open
Abstract
The low dose radioadaptive response has been shown to be protective against high doses of radiation as well as aging-induced genomic instability. We hypothesised that a single whole-body exposure of low dose radiation would induce a radioadaptive response thereby reducing or abrogating aging-related changes in repeat element DNA methylation in mice. Following sham or 10 mGy X-irradiation, serial peripheral blood sampling was performed and differences in Long Interspersed Nucleic Element 1 (L1), B1 and Intracisternal-A-Particle (IAP) repeat element methylation between samples were assessed using high resolution melt analysis of PCR amplicons. By 420 days post-irradiation, neither radiation- or aging-related changes in the methylation of peripheral blood, spleen or liver L1, B1 and IAP elements were observed. Analysis of the spleen and liver tissues of cohorts of untreated aging mice showed that the 17-19 month age group exhibited higher repeat element methylation than younger or older mice, with no overall decline in methylation detected with age. This is the first temporal analysis of the effect of low dose radiation on repeat element methylation in mouse peripheral blood and the first to examine the long term effect of this dose on repeat element methylation in a radiosensitive tissue (spleen) and a tissue fundamental to the aging process (liver). Our data indicate that the methylation of murine DNA repeat elements can fluctuate with age, but unlike human studies, do not demonstrate an overall aging-related decline. Furthermore, our results indicate that a low dose of ionising radiation does not induce detectable changes to murine repeat element DNA methylation in the tissues and at the time-points examined in this study. This radiation dose is relevant to human diagnostic radiation exposures and suggests that a dose of 10 mGy X-rays, unlike high dose radiation, does not cause significant short or long term changes to repeat element or global DNA methylation.
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Affiliation(s)
- Michelle R. Newman
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Pamela J. Sykes
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Benjamin J. Blyth
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Eva Bezak
- Department of Medical Physics, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Mark D. Lawrence
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Katherine L. Morel
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
| | - Rebecca J. Ormsby
- Flinders Centre for Innovation in Cancer, Flinders University and Medical Centre, Bedford Park, South Australia, Australia
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Wong JYY, De Vivo I, Lin X, Grashow R, Cavallari J, Christiani DC. The association between global DNA methylation and telomere length in a longitudinal study of boilermakers. Genet Epidemiol 2014; 38:254-64. [PMID: 24616077 DOI: 10.1002/gepi.21796] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/24/2013] [Accepted: 01/07/2014] [Indexed: 01/18/2023]
Abstract
The objectives of this study were to determine if global DNA methylation, as reflected in LINE-1 and Alu elements, is associated with telomere length and whether it modifies the rate of telomeric change. A repeated-measures longitudinal study was performed with a panel of 87 boilermaker subjects. The follow-up period was 29 months. LINE-1 and Alu methylation was determined using pyrosequencing. Leukocyte relative telomere length was assessed via real-time qPCR. Linear-mixed models were used to estimate the association between DNA methylation and telomere length. A structural equation model (SEM) was used to explore the hypothesized relationship between DNA methylation, proxies of particulate matter exposure, and telomere length at baseline. There appeared to be a positive association between both LINE-1 and Alu methylation levels, and telomere length. For every incremental increase in LINE-1 methylation, there was a statistically significant 1.0 × 10(-1) (95% CI: 4.6 × 10(-2), 1.5 × 10(-1), P < 0.01) unit increase in relative telomere length, controlling for age at baseline, current and past smoking status, work history, BMI (log kg/m(2) ) and leukocyte differentials. Furthermore, for every incremental increase in Alu methylation, there was a statistically significant 6.2 × 10(-2) (95% CI: 1.0 × 10(-2), 1.1 × 10(-1), P = 0.02) unit increase in relative telomere length. The interaction between LINE-1 methylation and follow-up time was statistically significant with an estimate -9.8 × 10(-3) (95% CI: -1.8 × 10(-2), -1.9 × 10(-3), P = 0.02); suggesting that the rate of telomeric change was modified by the degree of LINE-1 methylation. No statistically significant association was found between the cumulative PM exposure construct, with global DNA methylation and telomere length at baseline.
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Affiliation(s)
- Jason Y Y Wong
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America; Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
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Peng H, Yang M, Chen ZY, Chen P, Guan CX, Xiang XD, Cai S, Chen Y, Fang X. Expression and methylation of mitochondrial transcription factor a in chronic obstructive pulmonary disease patients with lung cancer. PLoS One 2013; 8:e82739. [PMID: 24367550 PMCID: PMC3867397 DOI: 10.1371/journal.pone.0082739] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 10/28/2013] [Indexed: 11/25/2022] Open
Abstract
Background Apoptosis plays a central role in the pathogenesis of chronic obstructive pulmonary disease (COPD), and this process can be regulated by mitochondrial transcription factor A (mtTFA). Epigenetics is involved in the regulation and modification of the genes involved in lung cancer and COPD. In this study, we determined the expression of mtTFA and its methylation levels in the COPD patients with lung cancer. Methods Twenty-one squamous cell lung cancer patients, 11 with COPD and 10 without COPD, undergoing pneumonectomy were enrolled. The apoptotic index (AI) of pulmonary vascular endothelial cells was analyzed by transferase-mediated deoxyuridine triphosphate-biotin nick end labeling assay. The expression of mtTFA mRNA and protein was measured using PCR, immunohistochemistry and Western-blot. Methylation of the mtTFA promoter was detected using bisulfite sequencing PCR. Results Compared to the non-COPD group, the AI was higher, and expression of mtTFA mRNA and protein was lower in the COPD group (P<0.001). Expression of the mtTFA protein was positively correlated with FEV1/Pre (r = 0.892, P<0.001), and negatively correlated with AI (r = −0.749, P<0.001) and smoke index (r = −0.763, P<0.001). Percentage of mtTFA promoter methylation in the COPD patients was significantly higher compared to the non-COPD patients (P<0.05). Conclusion These results suggest that the expression of mtTFA mRNA and protein is down-regulated in the lung tissue from the COPD patients with squamous cell lung cancer, and the level of mtTFA protein is related to apoptosis of pulmonary vascular endothelial cells. Aberrant mtTFA methylation may also play an important role in the pathogenesis of COPD.
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Affiliation(s)
- Hong Peng
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Min Yang
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China ; Human Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Zhi-yong Chen
- Department of Urology, Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Ping Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Cha-xiang Guan
- Physiological Research Center, Xiangya Medical School of Central-South University, Changsha, Hunan, PR China
| | - Xu-dong Xiang
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Shan Cai
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Yan Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital of Central-South University, Changsha, Hunan, PR China
| | - Xiang Fang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Vilahur N, Baccarelli AA, Bustamante M, Agramunt S, Byun HM, Fernandez MF, Sunyer J, Estivill X. Storage conditions and stability of global DNA methylation in placental tissue. Epigenomics 2013; 5:341-8. [PMID: 23750648 DOI: 10.2217/epi.13.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIM The placenta is an informative and easily available tissue for many epidemiological studies. We analyzed the extent to which storage delay affects DNA methylation. MATERIAL & METHODS Biopsies from two placentas were sequentially stored at -80°C after standing at room temperature for 30 min, 1 h, 2 h, 6 h and 24 h. Global DNA methylation was measured by bisulfite pyrosequencing of repetitive elements and the luminometric methylation assay. RESULTS Small changes in global DNA methylation in relation to time-to-storage were observed by pyrosequencing, with a coefficient of variation (COV) of 2.49% (placenta 1) and 2.86% (placenta 2), similar to the mean technical variation observed for pyrosequencing (COV: 1.91 and 1.51%, respectively). A luminometric methylation assay yielded more variable results in the two placentas analyzed, both among time points (COV: 9.13 and 10.35%, respectively) and technical replicates (COV: 11.60 and 9.80%, respectively). CONCLUSION Global DNA methylation is stable at room temperature. However, some techniques to measure methylation might be confounded by DNA degradation caused by a delay in storage.
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Affiliation(s)
- Nadia Vilahur
- Center for Research in Environmental Epidemiology CREAL, Barcelona, Catalonia, Spain.
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Sargurupremraj M, Wjst M. Transposable elements and their potential role in complex lung disorder. Respir Res 2013; 14:99. [PMID: 24093510 PMCID: PMC3851442 DOI: 10.1186/1465-9921-14-99] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/02/2013] [Indexed: 12/19/2022] Open
Abstract
Transposable elements (TEs) are a class of mobile genetic elements (MGEs) that were long regarded as junk DNA, which make up approximately 45% of the genome. Although most of these elements are rendered inactive by mutations and other gene silencing mechanisms, TEs such as long interspersed nuclear elements (LINEs) are still active and translocate within the genome. During transposition, they may create lesions in the genome, thereby acting as epigenetic modifiers. Approximately 65 disease-causing LINE insertion events have been reported thus far; however, any possible role of TEs in complex disorders is not well established. Chronic obstructive pulmonary disease (COPD) is one such complex disease that is primarily caused by cigarette smoking. Although the exact molecular mechanism underlying COPD remains unclear, oxidative stress is thought to be the main factor in the pathogenesis of COPD. In this review, we explore the potential role of oxidative stress in epigenetic activation of TEs such as LINEs and the subsequent cascade of molecular damage. Recent advancements in sequencing and computation have eased the identification of mobile elements. Therefore, a comparative study on the activity of these elements and markers for genome instability would give more insight on the relationship between MGEs and complex disorder such as COPD.
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Affiliation(s)
- Muralidharan Sargurupremraj
- Molecular genetics of lung diseases group, Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, GmbH, Ingolstadter, Landstrasse 1, D-85764, Neuherberg, Munich, Germany.
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