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Gim JA. A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research. Int J Mol Sci 2022; 23:5963. [PMID: 35682641 PMCID: PMC9180925 DOI: 10.3390/ijms23115963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
Improvements in next-generation sequencing (NGS) technology and computer systems have enabled personalized therapies based on genomic information. Recently, health management strategies using genomics and big data have been developed for application in medicine and public health science. In this review, I first discuss the development of a genomic information management system (GIMS) to maintain a highly detailed health record and detect diseases by collecting the genomic information of one individual over time. Maintaining a health record and detecting abnormal genomic states are important; thus, the development of a GIMS is necessary. Based on the current research status, open public data, and databases, I discuss the possibility of a GIMS for clinical use. I also discuss how the analysis of genomic information as big data can be applied for clinical and research purposes. Tremendous volumes of genomic information are being generated, and the development of methods for the collection, cleansing, storing, indexing, and serving must progress under legal regulation. Genetic information is a type of personal information and is covered under privacy protection; here, I examine the regulations on the use of genetic information in different countries. This review provides useful insights for scientists and clinicians who wish to use genomic information for healthy aging and personalized medicine.
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Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
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2
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Saelens BE, Meenan RT, Keast EM, Frank LD, Young DR, Kuntz JL, Dickerson JF, Fortmann SP. Transit Use and Health Care Costs: A Cross-sectional Analysis. JOURNAL OF TRANSPORT & HEALTH 2022; 24:101294. [PMID: 34926159 PMCID: PMC8682981 DOI: 10.1016/j.jth.2021.101294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
INTRODUCTION Greater transit use is associated with higher levels of physical activity, which is associated with lower health risks and better health outcomes. However, there is scant evidence about whether health care costs differ based on level of transit ridership. METHODS A sample (n=947) of members of Kaiser Permanente in the Portland, Oregon area were surveyed in 2015 about their typical use of various modes of travel including transit. Electronic medical record-derived health care costs were obtained among these members for the prior three years. Analysis examined proportional costs between High transit users (3+ days/week), Low transit users (1-2 days/week), and Non-users adjusting for age and sex, and then individually (base models) and together for demographic and health status variables. RESULTS In separate base models across individual covariates, High transit users had lower total health care costs (59-69% of Non-user's costs) and medication costs (31-37% of Non-users' costs) than Non-users. Low transit users also had lower total health care (69%-76% of Non-users' costs) and medication costs (43-57% transit of Non-user's costs) than Non-users. High transit users' outpatient costs were also lower (77-82% of Non-users). In fully-adjusted models, total health care and medication costs were lower among High transit users' (67% and 39%) and Low transit users' (75% and 48%) compared to Non-users, but outpatient costs did not differ by transit use. CONCLUSIONS Findings have implications for the potential cost benefit of encouraging and supporting more transit use, although controlled longitudinal and experimental evidence is needed to confirm findings and understand mechanisms.
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Affiliation(s)
- B E Saelens
- Seattle Children's Research Institute and the Department of Pediatrics at the University of Washington, 1920 Terry Avenue, Seattle, Washington USA 98101
| | - R T Meenan
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, Oregon USA 97227-1098
| | - E M Keast
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, Oregon USA 97227-1098
| | - L D Frank
- Urban Design 4 Health, Inc., Rochester, NY and Health & Community Design Lab, Schools of Population and Public Health and Community and Regional Planning, University of British Columbia, 433 - 6333 Memorial Road Vancouver, BC Canada V6T 1Z2
| | - D R Young
- Center for Research & Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave, Pasadena, CA U.S. 91101
| | - J L Kuntz
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, Oregon USA 97227-1098
| | - J F Dickerson
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, Oregon USA 97227-1098
| | - S P Fortmann
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, Oregon USA 97227-1098
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Światowy WJ, Drzewiecka H, Kliber M, Sąsiadek M, Karpiński P, Pławski A, Jagodziński PP. Physical Activity and DNA Methylation in Humans. Int J Mol Sci 2021; 22:ijms222312989. [PMID: 34884790 PMCID: PMC8657566 DOI: 10.3390/ijms222312989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022] Open
Abstract
Physical activity is a strong stimulus influencing the overall physiology of the human body. Exercises lead to biochemical changes in various tissues and exert an impact on gene expression. Exercise-induced changes in gene expression may be mediated by epigenetic modifications, which rearrange the chromatin structure and therefore modulate its accessibility for transcription factors. One of such epigenetic mark is DNA methylation that involves an attachment of a methyl group to the fifth carbon of cytosine residue present in CG dinucleotides (CpG). DNA methylation is catalyzed by a family of DNA methyltransferases. This reversible DNA modification results in the recruitment of proteins containing methyl binding domain and further transcriptional co-repressors leading to the silencing of gene expression. The accumulation of CpG dinucleotides, referred as CpG islands, occurs at the promoter regions in a great majority of human genes. Therefore, changes in DNA methylation profile affect the transcription of multiple genes. A growing body of evidence indicates that exercise training modulates DNA methylation in muscles and adipose tissue. Some of these epigenetic markers were associated with a reduced risk of chronic diseases. This review summarizes the current knowledge about the influence of physical activity on the DNA methylation status in humans.
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Affiliation(s)
- Witold Józef Światowy
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (H.D.); (M.K.); (P.P.J.)
- Correspondence: ; Tel.: +48-618-546-513
| | - Hanna Drzewiecka
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (H.D.); (M.K.); (P.P.J.)
| | - Michalina Kliber
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (H.D.); (M.K.); (P.P.J.)
| | - Maria Sąsiadek
- Department of Genetics, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.S.); (P.K.)
| | - Paweł Karpiński
- Department of Genetics, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.S.); (P.K.)
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland;
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (H.D.); (M.K.); (P.P.J.)
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Hwang S, Kang D, Lee M, Byeon JY, Park H, Park D, Kim K, Lee S, Chu SH, Kim NK, Jeon JY. Changes in DNA methylation after 6‐week exercise training in colorectal cancer survivors: A preliminary study. Asia Pac J Clin Oncol 2020; 18:52-60. [DOI: 10.1111/ajco.13482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/04/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Seo‐Hyeon Hwang
- Exercise Medicine Center for Diabetes and Cancer Patients Institute of Convergence of Science (ICONS) Yonsei University Seoul South Korea
- Department of Sport Industry Studies Yonsei University Seoul South Korea
| | - Dong‐Woo Kang
- Behavioural Medicine Laboratory, Faculty of Kinesiology, Sport, and Recreation University of Alberta Edmonton AB Canada
| | - Mi‐Kyung Lee
- Exercise Medicine Center for Diabetes and Cancer Patients Institute of Convergence of Science (ICONS) Yonsei University Seoul South Korea
- Department of Sport Industry Studies Yonsei University Seoul South Korea
| | - Ji Yong Byeon
- Department of Sport Industry Studies Yonsei University Seoul South Korea
| | - Hanui Park
- Department of Sport Industry Studies Yonsei University Seoul South Korea
| | - Dong‐Hyuk Park
- Department of Sport Industry Studies Yonsei University Seoul South Korea
| | - Kyung‐Chul Kim
- Department of healthy aging Gangnam Major Clinic Seoul South Korea
| | - Seung‐Tae Lee
- Department of Laboratory Medicine Yonsei University College of Medicine Seoul South Korea
| | - Sang Hui Chu
- Department of Clinical Nursing Science, College of Nursing, Biobehavioural Research Center Yonsei University Nursing Policy Research Institute Seoul South Korea
| | - Nam Kyu Kim
- Department of Surgery Yonsei University College of Medicine Seoul South Korea
| | - Justin Y. Jeon
- Exercise Medicine Center for Diabetes and Cancer Patients Institute of Convergence of Science (ICONS) Yonsei University Seoul South Korea
- Department of Sport Industry Studies Yonsei University Seoul South Korea
- Cancer Prevention Center Shinchon Severance Hospital Seoul South Korea
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Hibler E, Huang L, Andrade J, Spring B. Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation. Clin Epigenetics 2019; 11:133. [PMID: 31506096 PMCID: PMC6737702 DOI: 10.1186/s13148-019-0707-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Studies demonstrate the impact of diet and physical activity on epigenetic biomarkers, specifically DNA methylation. However, no intervention studies have examined the combined impact of dietary and activity changes on the blood epigenome. The objective of this study was to examine the impact of the Make Better Choices 2 (MBC2) healthy diet and activity intervention on patterns of epigenome-wide DNA methylation. The MBC2 study was a 9-month randomized controlled trial among adults aged 18-65 with non-optimal levels of health behaviors. The study compared three 12-week interventions to (1) simultaneously increase exercise and fruit/vegetable intake, while decreasing sedentary leisure screen time; (2) sequentially increase fruit/vegetable intake and decrease leisure screen time first, then increase exercise; (3) increase sleep and decrease stress (control). We collected blood samples at baseline, 3 and 9 months, and measured DNA methylation using the Illumina EPIC (850 k) BeadChip. We examined region-based differential methylation patterns using linear regression models with the false discovery rate of 0.05. We also conducted pathway analysis using gene ontology (GO), KEGG, and IPA canonical pathway databases. RESULTS We found no differences between the MBC2 population (n = 340) and the subsample with DNA methylation measured (n = 68) on baseline characteristics or the impact of the intervention on behavior change. We identified no differentially methylated regions at baseline between the control versus intervention groups. At 3 versus 9 months, we identified 154 and 298 differentially methylated regions, respectively, between controls compared to pooled samples from sequential and simultaneous groups. In the GO database, we identified two gene ontology terms related to hemophilic cell adhesion and cell-cell adhesion. In IPA analysis, we found pathways related to carcinogenesis including PI3K/AKT, Wnt/β-catenin, sonic hedgehog, and p53 signaling. We observed an overlap between 3 and 9 months, including the GDP-L-fucose biosynthesis I, methylmalonyl metabolism, and estrogen-mediated cell cycle regulation pathways. CONCLUSIONS The results demonstrate that the MBC2 diet and physical activity intervention impacts patterns of DNA methylation in gene regions related to cell cycle regulation and carcinogenesis. Future studies will examine DNA methylation as a biomarker to identify populations that may particularly benefit from incorporating health behavior change into plans for precision prevention.
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Affiliation(s)
- Elizabeth Hibler
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 North Lakeshore Drive, Chicago, IL, 60611, USA.
| | - Lei Huang
- Center for Research Informatics, Biological Sciences Division, University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, Biological Sciences Division, University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
| | - Bonnie Spring
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 North Lakeshore Drive, Chicago, IL, 60611, USA
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Food consumption and its association with leisure-time physical activity and active commuting in Brazilian workers. Eur J Clin Nutr 2019; 74:314-321. [PMID: 31253877 DOI: 10.1038/s41430-019-0454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND/OBJECTIVES An in-depth understanding of the relationship between food consumption and physical activity is relevant since these behaviours could influence each other, while both have an effect on obesity and chronic diseases. In this context, the aim of this study was to investigate the effect of various combinations of food consumption (fruits, vegetables, sweets and snacks) on the associations with PA domains (leisure and commute) among Brazilian industrial workers. SUBJECTS/METHODS This is part of a cross-sectional national survey developed in Brazil using data from the "Lifestyle and Leisure Habits of Industrial Workers" project. A total of 52,774 workers (response rate: 90.6%) responded to a validated questionnaire about the frequency of their consumption of fruit, vegetables, sweets and snacks, their practice of LTPA and active commuting. The answers were analysed by multilevel regression, controlled by sociodemographic behaviour and the presence of hypertension, diabetes and overweight. RESULTS Workers with a simultaneously adequate consumption of fruit, vegetables, sweets and snacks were 2.29 (1.74; 2.99 p-value < 0.001) more likely to perform LTPA. In the full model, there was no association among any of the combinations of food consumption and active commuting. CONCLUSION A better food consumption behaviour was reported among workers who practiced leisure physical activity when compared to those who did not.
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Boyne DJ, O'Sullivan DE, Olij BF, King WD, Friedenreich CM, Brenner DR. Physical Activity, Global DNA Methylation, and Breast Cancer Risk: A Systematic Literature Review and Meta-analysis. Cancer Epidemiol Biomarkers Prev 2018; 27:1320-1331. [PMID: 29991518 DOI: 10.1158/1055-9965.epi-18-0175] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/16/2018] [Accepted: 07/04/2018] [Indexed: 11/16/2022] Open
Abstract
The extent to which physical activity reduces breast cancer risk through changes in global DNA methylation is unknown. We systematically identified studies that investigated the association between: (i) physical activity and global DNA methylation; or (ii) global DNA methylation and breast cancer risk. Associations were quantified using random-effects models. Heterogeneity was investigated through subgroup analyses and the Q-test and I 2 statistics. Twenty-four studies were reviewed. We observed a trend between higher levels of physical activity and higher levels of global DNA methylation [pooled standardized mean difference = 0.19; 95% confidence interval (CI), -0.03-0.40; P = 0.09] which, in turn, had a suggestive association with a reduced breast cancer risk (pooled relative risk = 0.70; 95% CI, 0.49-1.02; P = 0.06). In subgroup analyses, a positive association between physical activity and global DNA methylation was observed among studies assessing physical activity over long periods of time (P = 0.02). Similarly, the association between global DNA methylation and breast cancer was statistically significant for prospective cohort studies (P = 0.007). Despite the heterogeneous evidence base, the literature suggests that physical activity reduces the risk of breast cancer through increased global DNA methylation. This study is the first to systematically overview the complete biologic pathway between physical activity, global DNA methylation, and breast cancer. Cancer Epidemiol Biomarkers Prev; 27(11); 1320-31. ©2018 AACR.
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Affiliation(s)
- Devon J Boyne
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Dylan E O'Sullivan
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Branko F Olij
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada.,Department of Public Health, Erasmus MC-University Medical Center Rotterdam, the Netherlands
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Christine M Friedenreich
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada.,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Darren R Brenner
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada. .,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Boyne DJ, King WD, Brenner DR, McIntyre JB, Courneya KS, Friedenreich CM. Aerobic exercise and DNA methylation in postmenopausal women: An ancillary analysis of the Alberta Physical Activity and Breast Cancer Prevention (ALPHA) Trial. PLoS One 2018; 13:e0198641. [PMID: 29953441 PMCID: PMC6023230 DOI: 10.1371/journal.pone.0198641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/22/2018] [Indexed: 12/17/2022] Open
Abstract
Physical activity is associated with a lower risk of breast, colon, and endometrial cancer. Epigenetic mechanisms such as changes in DNA methylation may help to explain these protective effects. We assessed the impact of a one year aerobic exercise intervention on DNA methylation biomarkers believed to play a role in carcinogenesis. The Alberta Physical Activity and Breast Cancer Prevention (ALPHA) Trial was a two-armed randomized controlled trial in 320 healthy, inactive, postmenopausal women with no history of cancer. In an ancillary analysis, frozen blood samples (n = 256) were reassessed for levels of DNA methylation within LINE-1 and Alu repeats as well as within the promoter regions of APC, BRCA1, RASSF1, and hTERT genes. Differences between the exercise and control arm at 12-months, after adjusting for baseline values, were estimated within an intent-to-treat and per-protocol analysis using linear regression. No significant differences in DNA methylation between the exercise and control arms were observed. In an exploratory analysis, we found that the prospective change in estimated VO2max was negatively associated with RASSF1 methylation in a dose-response manner (p-trend = 0.04). A year-long aerobic exercise intervention does not affect LINE-1, Alu, APC, BRCA1, RASSF1, or hTERT methylation in healthy, inactive, postmenopausal women. Changes in DNA methylation within these genomic regions may not mediate the association between physical activity and cancer in healthy postmenopausal women. Additional research is needed to validate our findings with RASSF1 methylation. Trial Registration: ClinicalTrials.gov NCT00522262.
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Affiliation(s)
- Devon J. Boyne
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Will D. King
- Department of Public Health Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Darren R. Brenner
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - John B. McIntyre
- Translational Laboratory, Tom Baker Cancer Centre, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kerry S. Courneya
- Faculty of Physical Education and Recreation, University of Alberta, Edmonton, Alberta, Canada
| | - Christine M. Friedenreich
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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Gogna P, O'Sullivan DE, King WD. The effect of inflammation-related lifestyle exposures and interactions with gene variants on long interspersed nuclear element-1 DNA methylation. Epigenomics 2018; 10:785-796. [PMID: 29888958 DOI: 10.2217/epi-2017-0164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the relationship between inflammation-related lifestyle factors and long interspersed nuclear element-1 (LINE-1) DNA methylation, and test for interaction by gene variants involved in one-carbon metabolism. PATIENTS & METHODS The study population consisted of 280 individuals undergoing colonoscopy screening. Multivariable linear regression was employed to examine associations of physical activity, BMI and NSAID use with LINE-1 DNA methylation and interactions with MTR and MTHFR gene variants. RESULTS The highest quartile of physical activity compared with the lowest was associated with higher LINE-1 DNA methylation (p = 0.005). Long-term NSAID use and a normal BMI were associated with increased LINE-1 DNA methylation among individuals with the variant MTR allele (p = 0.02; p = 0.03). CONCLUSION This study provides evidence that inflammation-related exposures may influence LINE-1 DNA methylation.
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Affiliation(s)
- Priyanka Gogna
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Dylan E O'Sullivan
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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Preliminary indications of the effect of a brief yoga intervention on markers of inflammation and DNA methylation in chronically stressed women. Transl Psychiatry 2016; 6:e965. [PMID: 27898068 PMCID: PMC5290356 DOI: 10.1038/tp.2016.234] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/20/2016] [Accepted: 09/29/2016] [Indexed: 01/17/2023] Open
Abstract
Yoga is associated with reduced stress and increased well-being, although the molecular basis for these benefits is not clear. Mounting evidence implicates the immune response, with current studies focused on protein immune markers (such as cytokines) in clinical populations. To explore the molecular impact, this pilot study uses a subsample (n=28) from a randomised waitlist control trial investigating the impact of an 8-week yoga intervention in a community population of women reporting psychological distress (N=116). We measured interleukin-6 (IL-6), tumour necrosis factor (TNF) and C-reactive protein (CRP) protein levels, and the DNA methylation of these genes and the global indicator, LINE-1. Correlations between these and psychological variables were explored, identifying moderate correlations with CRP protein levels, and methylation of IL-6, CRP and LINE-1. Many cytokine samples were below detection, however a Mann-Whitney U demonstrated a trend of moderate between-group effect for elevated IL-6 in the yoga group. Methylation analyses applied cross-sectional and non-controlled longitudinal analyses. Waist-to-height ratio and age were covaried. We demonstrated reduced methylation of the TNF region in the yoga group relative to the waitlist control group. No other genes demonstrated a significant difference. Longitudinal analysis further supported these results. This study is one of the first to explore yoga and immunological markers in a non-clinical population, and is the first study to explore DNA methylation. These findings indicate that further research into molecular impact of yoga on markers of immune function is warranted, with larger studies required.
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Sener IN, Lee RJ, Elgart Z. Potential Health Implications and Health Cost Reductions of Transit-Induced Physical Activity. JOURNAL OF TRANSPORT & HEALTH 2016; 3:133-140. [PMID: 27347481 PMCID: PMC4917017 DOI: 10.1016/j.jth.2016.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Transit has the potential to increase an individual's level of physical activity due to the need to walk or bike at the beginning and end of each trip. Consideration of these health benefits would allow transit proponents to better demonstrate its true costs and benefits. In light of transit's potential health-related impacts, this study contributes to the growing discussion in the emerging field of health and transportation by providing a review of the current level of understanding and evidence related to the physical activity implications of transit use and its associated health cost benefits. Findings from the review revealed that transit use is associated with increased levels of physical activity and improved health outcomes, but the magnitude of these effects is uncertain. There were few studies that estimated the health care cost savings of transit systems, and those that did tended to be imprecise and simplistic. Objective physical activity measures and frequency-based transit measures would allow for greater consistency across studies and help more directly attribute physical activity gains to transit ridership. Additionally, research in this area would benefit from disaggregate estimation techniques and more robust health datasets that can be better linked with existing transit data.
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Affiliation(s)
- Ipek N. Sener
- Texas A&M Transportation Institute, 505 E. Huntland Dr., Suite 455, Austin, TX 78752, USA
| | - Richard J. Lee
- Texas A&M Transportation Institute, 505 E. Huntland Dr., Suite 455, Austin, TX 78752, USA
| | - Zachary Elgart
- Texas A&M Transportation Institute, 701 North Post Oak Rd., Suite 430, Houston, TX 77024, USA
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Epigenetics and Colorectal Neoplasia: the Evidence for Physical Activity and Sedentary Behavior. CURRENT COLORECTAL CANCER REPORTS 2015; 11:388-396. [PMID: 27212896 DOI: 10.1007/s11888-015-0296-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studies demonstrate that regular physical activity and, more recently, limited sedentary behavior are associated with reduced risk of colorectal neoplasia. However, the biological mechanisms of action for physical activity versus sedentary behavior are not clear. Epigenetic variation is suggested as a potential mechanism that would allow for independent, or possibly even synergistic, effects of activity and inactivity on colorectal epithelium. We describe the evidence for epigenetic variation as a link between physical activity and sedentary behavior in colorectal neoplasia risk. There are few studies that directly evaluate this relationship. However, the growing literature describes a variety of gene targets influenced by activity that are also important to colorectal neoplasia etiology. Future studies may identify epigenetic markers with translational significance in identifying high-risk individuals or those for whom a personalized activity regimen could significantly alter the methylation signature in colon epithelial cells, and thus future risk of colorectal cancer.
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Brown WM. Exercise-associated DNA methylation change in skeletal muscle and the importance of imprinted genes: a bioinformatics meta-analysis. Br J Sports Med 2015; 49:1567-78. [PMID: 25824446 DOI: 10.1136/bjsports-2014-094073] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Epigenetics is the study of processes--beyond DNA sequence alteration--producing heritable characteristics. For example, DNA methylation modifies gene expression without altering the nucleotide sequence. A well-studied DNA methylation-based phenomenon is genomic imprinting (ie, genotype-independent parent-of-origin effects). OBJECTIVE We aimed to elucidate: (1) the effect of exercise on DNA methylation and (2) the role of imprinted genes in skeletal muscle gene networks (ie, gene group functional profiling analyses). DESIGN Gene ontology (ie, gene product elucidation)/meta-analysis. DATA SOURCES 26 skeletal muscle and 86 imprinted genes were subjected to g:Profiler ontology analysis. Meta-analysis assessed exercise-associated DNA methylation change. DATA EXTRACTION g:Profiler found four muscle gene networks with imprinted loci. Meta-analysis identified 16 articles (387 genes/1580 individuals) associated with exercise. Age, method, sample size, sex and tissue variation could elevate effect size bias. DATA SYNTHESIS Only skeletal muscle gene networks including imprinted genes were reported. Exercise-associated effect sizes were calculated by gene. Age, method, sample size, sex and tissue variation were moderators. RESULTS Six imprinted loci (RB1, MEG3, UBE3A, PLAGL1, SGCE, INS) were important for muscle gene networks, while meta-analysis uncovered five exercise-associated imprinted loci (KCNQ1, MEG3, GRB10, L3MBTL1, PLAGL1). DNA methylation decreased with exercise (60% of loci). Exercise-associated DNA methylation change was stronger among older people (ie, age accounted for 30% of the variation). Among older people, genes exhibiting DNA methylation decreases were part of a microRNA-regulated gene network functioning to suppress cancer. CONCLUSIONS Imprinted genes were identified in skeletal muscle gene networks and exercise-associated DNA methylation change. Exercise-associated DNA methylation modification could rewind the 'epigenetic clock' as we age. TRIAL REGISTRATION NUMBER CRD42014009800.
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Voisin S, Eynon N, Yan X, Bishop DJ. Exercise training and DNA methylation in humans. Acta Physiol (Oxf) 2015; 213:39-59. [PMID: 25345837 DOI: 10.1111/apha.12414] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/14/2014] [Accepted: 10/18/2014] [Indexed: 12/17/2022]
Abstract
The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as trainability do not only depend on the genetic code, but also on epigenetic signals. Epigenetic signals play an important role in the modulation of gene expression, through mechanisms such as DNA methylation and histone modifications. There is an emerging evidence to show that physical activity influences DNA methylation in humans. The present review aims to summarize current knowledge on the link between DNA methylation and physical activity in humans. We have critically reviewed the literature and only papers focused on physical activity and its influence on DNA methylation status were included; a total of 25 papers were selected. We concluded that both acute and chronic exercises significantly impact DNA methylation, in a highly tissue- and gene-specific manner. This review also provides insights into the molecular mechanisms of exercise-induced DNA methylation changes, and recommendations for future research.
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Affiliation(s)
- S. Voisin
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
| | - N. Eynon
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne Vic. Australia
| | - X. Yan
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne Vic. Australia
| | - D. J. Bishop
- Institute of Sport, Exercise and Active Living (ISEAL); Victoria University; Melbourne Vic. Australia
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Saelens BE, Vernez Moudon A, Kang B, Hurvitz PM, Zhou C. Relation between higher physical activity and public transit use. Am J Public Health 2014; 104:854-9. [PMID: 24625142 DOI: 10.2105/ajph.2013.301696] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We isolated physical activity attributable to transit use to examine issues of substitution between types of physical activity and potential confounding of transit-related walking with other walking. METHODS Physical activity and transit use data were collected in 2008 to 2009 from 693 Travel Assessment and Community study participants from King County, Washington, equipped with an accelerometer, a portable Global Positioning System, and a 7-day travel log. Physical activity was classified into transit- and non-transit-related walking and nonwalking time. Analyses compared physical activity by type between transit users and nonusers, between less and more frequent transit users, and between transit and nontransit days for transit users. RESULTS Transit users had more daily overall physical activity and more total walking than did nontransit users but did not differ on either non-transit-related walking or nonwalking physical activity. Most frequent transit users had more walking time than least frequent transit users. Higher physical activity levels for transit users were observed only on transit days, with 14.6 minutes (12.4 minutes when adjusted for demographics) of daily physical activity directly linked with transit use. CONCLUSIONS Because transit use was directly related to higher physical activity, future research should examine whether substantive increases in transit access and use lead to more physical activity and related health improvements.
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Affiliation(s)
- Brian E Saelens
- Brian E. Saelens and Chuan Zhou are with Seattle Children's Research Institute and University of Washington School of Medicine Department of Pediatrics, Seattle. Anne Vernez Moudon, Bumjoon Kang, and Philip M. Hurvitz are with the Urban Form Lab and the College of Built Environments Department of Urban Design and Planning, University of Washington
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Humphreys DK, Goodman A, Ogilvie D. Associations between active commuting and physical and mental wellbeing. Prev Med 2013; 57:135-9. [PMID: 23618913 PMCID: PMC3722482 DOI: 10.1016/j.ypmed.2013.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 12/03/2022]
Abstract
OBJECTIVE To examine whether a relationship exists between active commuting and physical and mental wellbeing. METHOD In 2009, cross-sectional postal questionnaire data were collected from a sample of working adults (aged 16 and over) in the Commuting and Health in Cambridge study. Travel behaviour and physical activity were ascertained using the Recent Physical Activity Questionnaire (RPAQ) and a seven-day travel-to-work recall instrument from which weekly time spent in active commuting (walking and cycling) was derived. Physical and mental wellbeing were assessed using the Medical Outcomes Study Short Form survey (SF-8). Associations were tested using multivariable linear regression. RESULTS An association was observed between physical wellbeing (PCS-8) score and time spent in active commuting after adjustment for other physical activity (adjusted regression coefficients 0.48, 0.79 and 1.21 for 30-149 min/week, 150-224 min/week and ≥ 225 min/week respectively versus < 30 min/week, p=0.01 for trend; n=989). No such relationship was found for mental wellbeing (MCS-8) (p=0.52). CONCLUSION Greater time spent actively commuting is associated with higher levels of physical wellbeing. Longitudinal studies should examine the contribution of changing levels of active commuting and other forms of physical activity to overall health and wellbeing.
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Affiliation(s)
- David K Humphreys
- UKCRC Centre for Diet and Activity Research (CEDAR), Institute of Public Health, University of Cambridge, UK.
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Zhang FF, Santella RM, Wolff M, Kappil MA, Markowitz SB, Morabia A. White blood cell global methylation and IL-6 promoter methylation in association with diet and lifestyle risk factors in a cancer-free population. Epigenetics 2012; 7:606-14. [PMID: 22531363 DOI: 10.4161/epi.20236] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Altered levels of global DNA methylation and gene silencing through methylation of promoter regions can impact cancer risk, but little is known about their environmental determinants. We examined the association between lifestyle factors and levels of global genomic methylation and IL-6 promoter methylation in white blood cell DNA of 165 cancer-free subjects, 18-78 years old, enrolled in the COMIR (Commuting Mode and Inflammatory Response) study, New York, 2009-2010. Besides self-administrated questionnaires on diet and physical activity, we measured weight and height, white blood cell (WBC) counts, plasma levels of high sensitivity C-reactive protein (hs-CRP), and genomic (LINE-1) and gene-specific methylation (IL-6) by pyrosequencing in peripheral blood WBC. Mean levels of LINE-1 and IL-6 promoter methylation were 78.2% and 57.1%, respectively. In multivariate linear regression models adjusting for age, gender, race/ethnicity, body mass index, diet, physical activity, WBC counts and CRP, only dietary folate intake from fortified foods was positively associated with LINE-1 methylation. Levels of IL-6 promoter methylation were not significantly correlated with age, gender, race/ethnicity, body mass index, physical activity or diet, including overall dietary patterns and individual food groups and nutrients. There were no apparent associations between levels of methylation and inflammation markers such as WBC counts and hs-CRP. Overall, among several lifestyle factors examined in association with DNA methylation, only dietary folate intake from fortification was associated with LINE-1 methylation. The long-term consequence of folate fortification on DNA methylation needs to be further evaluated in longitudinal settings.
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Affiliation(s)
- Fang Fang Zhang
- Department of Nutrition Science; Friedman School of Nutrition Science and Policy; Tufts University; Boston, MA, USA.
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Morabia A, Costanza MC. Obesity, TV commercials, passive commuting, and smoking. Prev Med 2012; 54:181-2. [PMID: 22464709 DOI: 10.1016/j.ypmed.2012.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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