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Fujii R, Ando Y, Yamada H, Tsuboi Y, Munetsuna E, Yamazaki M, Mizuno G, Maeda K, Ohashi K, Ishikawa H, Watanabe M, Imaeda N, Goto C, Wakai K, Hashimoto S, Suzuki K. Integration of methylation quantitative trait loci (mQTL) on dietary intake on DNA methylation levels: an example of n-3 PUFA and ABCA1 gene. Eur J Clin Nutr 2023; 77:881-887. [PMID: 37542202 DOI: 10.1038/s41430-023-01315-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Epigenetic studies have reported relationships between dietary nutrient intake and methylation levels. However, genetic variants that may affect DNA methylation (DNAm) pattern, called methylation quantitative loci (mQTL), are usually overlooked in these analyses. We investigated whether mQTL change the relationship between dietary nutrient intake and leukocyte DNAm levels with an example of estimated fatty acid intake and ATP-binding cassette transporter A1 (ABCA1). METHODS A cross-sectional study on 231 participants (108 men, mean age: 62.7 y) without clinical history of cancer and no prescriptions for dyslipidemia. We measured leukocyte DNAm levels of 8 CpG sites within ABCA1 gene by pyrosequencing method and used mean methylation levels for statistical analysis. TaqMan assay was used for genotyping a genetic variant of ABCA1 (rs1800976). Dietary fatty acid intake was estimated with a validated food frequency questionnaire and adjusted for total energy intake by using residual methods. RESULTS Mean ABCA1 DNAm levels were 5% lower with the number of minor alleles in rs1800976 (CC, 40.6%; CG, 35.9%; GG, 30.6%). Higher dietary n-3 PUFA intake was associated with lower ABCA1 DNAm levels (1st (ref) vs. 4th, β [95% CI]: -2.52 [-4.77, -0.28]). After controlling for rs180076, the association between dietary n-3 PUFA intake and ABCA1 DNAm levels was attenuated, but still showed an independent association (1st (ref) vs. 4th, β [95% CI]: -2.00 [-3.84, -0.18]). The interaction of mQTL and dietary n-3 PUFA intake on DNAm levels was not significant. CONCLUSIONS This result suggested that dietary n-3 PUFA intake would be an independent predictor of DNAm levels in ABCA1 gene after adjusting for individual genetic background. Considering mQTL need to broaden into other genes and nutrients for deeper understanding of DNA methylation, which can contribute to personalized nutritional intervention.
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Affiliation(s)
- Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Via Alessandro Volta 21, Bolzano/Bozen, Italy
| | - Yoshitaka Ando
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, 281-1 Hara, Mure-cho, Takamatsu, Japan
| | - Genki Mizuno
- Department of Medical Technology, Tokyo University of Technology School of Health Sciences, 5-23-22 Nishi-Kamata, Ota-ku, Japan
| | - Keisuke Maeda
- Department of Clinical Physiology, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Koji Ohashi
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Hiroaki Ishikawa
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Mami Watanabe
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Nahomi Imaeda
- Department of Nutrition, Faculty of Wellness, Shigakkan University, 55 Nakoyama, Yokonemachi, Obu, Japan
| | - Chiho Goto
- Department of Health and Nutrition, Nagoya Bunri University, 365 Maeda, Inazawa-city, Inazawa, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan.
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2
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Ramos-Lopez O, Martinez JA, Milagro FI. Holistic Integration of Omics Tools for Precision Nutrition in Health and Disease. Nutrients 2022; 14:nu14194074. [PMID: 36235725 PMCID: PMC9572439 DOI: 10.3390/nu14194074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
The combination of multiple omics approaches has emerged as an innovative holistic scope to provide a more comprehensive view of the molecular and physiological events underlying human diseases (including obesity, dyslipidemias, fatty liver, insulin resistance, and inflammation), as well as for elucidating unique and specific metabolic phenotypes. These omics technologies include genomics (polymorphisms and other structural genetic variants), epigenomics (DNA methylation, histone modifications, long non-coding RNA, telomere length), metagenomics (gut microbiota composition, enterotypes), transcriptomics (RNA expression patterns), proteomics (protein quantities), and metabolomics (metabolite profiles), as well as interactions with dietary/nutritional factors. Although more evidence is still necessary, it is expected that the incorporation of integrative omics could be useful not only for risk prediction and early diagnosis but also for guiding tailored dietary treatments and prognosis schemes. Some challenges include ethical and regulatory issues, the lack of robust and reproducible results due to methodological aspects, the high cost of omics methodologies, and high-dimensional data analyses and interpretation. In this review, we provide examples of system biology studies using multi-omics methodologies to unravel novel insights into the mechanisms and pathways connecting the genotype to clinically relevant traits and therapy outcomes for precision nutrition applications in health and disease.
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Affiliation(s)
- Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Mexico
- Correspondence:
| | - J. Alfredo Martinez
- Precision Nutrition and Cardiometabolic Health, IMDEA Food Institute, CEI UAM+CSIC, 28049 Madrid, Spain
| | - Fermin I. Milagro
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, 31008 Pamplona, Spain
- Center for Nutrition Research, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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3
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Mattes RD, Rowe SB, Ohlhorst SD, Brown AW, Hoffman DJ, Liska DJ, Feskens EJM, Dhillon J, Tucker KL, Epstein LH, Neufeld LM, Kelley M, Fukagawa NK, Sunde RA, Zeisel SH, Basile AJ, Borth LE, Jackson E. Valuing the Diversity of Research Methods to Advance Nutrition Science. Adv Nutr 2022; 13:1324-1393. [PMID: 35802522 PMCID: PMC9340992 DOI: 10.1093/advances/nmac043] [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] [Received: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Leonard H Epstein
- University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | | | - Michael Kelley
- Michael Kelley Nutrition Science Consulting, Wauwatosa, WI, USA
| | - Naomi K Fukagawa
- USDA Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | | | - Steven H Zeisel
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Hao X, Li Y, Bian J, Zhang Y, He S, Yu F, Feng Y, Huang L. Impact of DNA methylation on ADME gene expression, drug disposition and efficacy. Drug Metab Rev 2022; 54:194-206. [PMID: 35412942 DOI: 10.1080/03602532.2022.2064488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Interindividual differences in drug response have always existed in clinical treatment. Genes involved in drug absorption, distribution, metabolism, and excretion (ADME) play an important role in the process of pharmacokinetics. The effects of genetic polymorphism and nuclear receptors on the expression of drug metabolism enzymes and transporters can only explain some individual differences in clinical treatment. Several key ADME genes have been demonstrated to be regulated by epigenetic mechanisms that can potentially affect interindividual variability in medical treatment. Emerging studies have focused on the importance of DNA methylation for ADME gene expression and for drug response. Among them, the most studied is anti-tumor drugs, and followed by anti-tuberculous and anti-platelet drugs. Therefore, we provide an epigenetics perspective on variability in drug response. The review summarizes the correlation between ADME gene expression and DNA methylation, including the exact methylation locations, and focuses on the corresponding drug disposition and effects to illuminate interindividual differences in clinical medication.
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Affiliation(s)
- Xu Hao
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China.,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Yuanyuan Li
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China.,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Jialu Bian
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China
| | - Ying Zhang
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China
| | - Shiyu He
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China
| | - Feng Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Yufei Feng
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China
| | - Lin Huang
- Department of Pharmacy, Peking University People's Hospital, Beijing, 100044 China
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5
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Miroshnikova VV, Panteleeva AA, Pobozheva IA, Razgildina ND, Polyakova EA, Markov AV, Belyaeva OD, Berkovich OA, Baranova EI, Nazarenko MS, Puzyrev VP, Pchelina SN. ABCA1 and ABCG1 DNA methylation in epicardial adipose tissue of patients with coronary artery disease. BMC Cardiovasc Disord 2021; 21:566. [PMID: 34837967 PMCID: PMC8627066 DOI: 10.1186/s12872-021-02379-7] [Citation(s) in RCA: 7] [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: 07/27/2020] [Accepted: 11/10/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Recent studies have focused on the potential role of epicardial adipose tissue (EAT) in the development of coronary artery disease (CAD). ABCA1 and ABCG1 transporters regulate cell cholesterol content and reverse cholesterol transport. We aimed to determine whether DNA methylation and mRNA levels of the ABCA1 and ABCG1 genes in EAT and subcutaneous adipose tissue (SAT) were associated with CAD. METHODS Paired EAT and SAT samples were collected from 82 patients undergoing elective cardiac surgery either for coronary artery bypass grafting (CAD group, N = 66) or valve surgery (NCAD group, N = 16). ABCA1 and ABCG1 mRNA levels in EAT and SAT samples were analyzed using real time polymerase chain reaction, ABCA1 protein levels in EAT samples were assessed by western blotting. ABCA1 and ABCG1 DNA methylation analysis was performed in 24 samples from the CAD group and 9 samples from the NCAD group via pyrosequencing. RESULTS DNA methylation levels in the ABCA1 promoter and ABCG1 cg27243685 and cg06500161 CpG sites were higher in EAT samples from patients with CAD compared with NCAD (21.92% vs 10.81%, p = 0.003; 71.51% vs 68.42%, p = 0.024; 46.11% vs 37.79%, p = 0.016, respectively). In patients with CAD, ABCA1 and ABCG1 DNA methylation levels were higher in EAT than in SAT samples (p < 0.05). ABCA1 mRNA levels in EAT samples were reduced in the subgroup of patients with CAD and concomitant carotid artery disease or peripheral artery disease compared with the NCAD group (p = 0.024). ABCA1 protein levels in EAT samples tended to be lower in CAD patients than in the NCAD group (p = 0.053). DNA methylation levels at the ABCG1 cg27243685 site positively correlated with plasma triglyceride concentration (r = 0.510, p = 0.008), body mass index (r = 0.556, p = 0.013) and waist-to-hip ratio (r = 0.504, p = 0.012) in SAT samples. CONCLUSION CAD is associated with ABCA1 and ABCG1 DNA hypermethylation in EAT. CAD with concomitant carotid artery disease or peripheral artery disease is accompanied by decreased ABCA1 gene expression in EAT. DNA methylation levels at the ABCG1 cg27243685 locus in SAT are associated with hypertriglyceridemia and obesity.
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Affiliation(s)
- Valentina V Miroshnikova
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russian Federation.
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation.
| | - Alexandra A Panteleeva
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russian Federation
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
- National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Irina A Pobozheva
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russian Federation
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
- National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Natalia D Razgildina
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russian Federation
| | - Ekaterina A Polyakova
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
| | - Anton V Markov
- Laboratory of Population Genetics, Research Institute of Medical Genetics, Tomsk, Russian Federation
| | - Olga D Belyaeva
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
| | - Olga A Berkovich
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
| | - Elena I Baranova
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
| | - Maria S Nazarenko
- Laboratory of Population Genetics, Research Institute of Medical Genetics, Tomsk, Russian Federation
| | - Valery P Puzyrev
- Laboratory of Population Genetics, Research Institute of Medical Genetics, Tomsk, Russian Federation
| | - Sofya N Pchelina
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russian Federation
- Pavlov First Saint Petersburg State Medical University, St.-Petersburg, Russian Federation
- National Research Centre "Kurchatov Institute", Moscow, Russia
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6
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Jones AC, Irvin MR, Claas SA, Arnett DK. Lipid Phenotypes and DNA Methylation: a Review of the Literature. Curr Atheroscler Rep 2021; 23:71. [PMID: 34468868 DOI: 10.1007/s11883-021-00965-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Epigenetic modifications via DNA methylation have previously been linked to blood lipid levels, dyslipidemias, and atherosclerosis. The purpose of this review is to discuss current literature on the role of DNA methylation on lipid traits and their associated pathologies. RECENT FINDINGS Candidate gene and epigenome-wide approaches have identified differential methylation of genes associated with lipid traits (particularly CPT1A, ABCG1, SREBF1), and novel approaches are being implemented to further characterize these relationships. Moreover, studies on environmental factors have shown that methylation variations at lipid-related genes are associated with diet and pollution exposure. Further investigation is needed to elucidate the directionality of the associations between the environment, lipid traits, and epigenome. Future studies should also seek to increase the diversity of cohorts, as European and Asian ancestry populations are the predominant study populations in the current literature.
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Affiliation(s)
- Alana C Jones
- Medical Scientist Training Program, University of Alabama-Birmingham, Birmingham, AL, USA.,Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Steven A Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, 111 Washington Ave, Lexington, KY, 40508, USA
| | - Donna K Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, 111 Washington Ave, Lexington, KY, 40508, USA.
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7
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Fujii R, Sato S, Tsuboi Y, Cardenas A, Suzuki K. DNA methylation as a mediator of associations between the environment and chronic diseases: A scoping review on application of mediation analysis. Epigenetics 2021; 17:759-785. [PMID: 34384035 DOI: 10.1080/15592294.2021.1959736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA methylation (DNAm) is one of the most studied epigenetic modifications. DNAm has emerged as a key biological mechanism and biomarkers to test associations between environmental exposure and outcomes in epidemiological studies. Although previous studies have focused on associations between DNAm and either exposure/outcomes, it is useful to test for mediation of the association between exposure and outcome by DNAm. The purpose of this scoping review is to introduce the methodological essence of statistical mediation analysis and to examine emerging epidemiological research applying mediation analyses. We conducted this scoping review for published peer-reviewed journals on this topic using online databases (PubMed, Scopus, Cochrane, and CINAHL) ending in December 2020. We extracted a total of 219 articles by initial screening. After reviewing titles, abstracts, and full texts, a total of 69 articles were eligible for this review. The breakdown of studies assigned to each category was 13 for smoking (18.8%), 8 for dietary intake and famine (11.6%), 6 for other lifestyle factors (8.7%), 8 for clinical endpoints (11.6%), 22 for environmental chemical exposures (31.9%), 2 for socioeconomic status (SES) (2.9%), and 10 for genetic factors and race (14.5%). In this review, we provide an exposure-wide summary for the mediation analysis using DNAm levels. However, we found heterogenous methods and interpretations in mediation analysis with typical issues such as different cell compositions and tissue-specificity. Further accumulation of evidence with diverse exposures, populations and with rigorous methodology will be expected to provide further insight in the role of DNAm in disease susceptibility.
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Affiliation(s)
- Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Shuntaro Sato
- Clinical Research Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, California, US
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
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8
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Barradas S, Lucumi D, Agudelo DM, Mentz G. Socioeconomic position and quality of life among Colombian hypertensive patients: The mediating effect of perceived stress. Health Psychol Open 2021; 8:2055102921996934. [PMID: 33747537 PMCID: PMC7905733 DOI: 10.1177/2055102921996934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This study aimed to assess the relationships between socioeconomic position, perceived stress and Health Related Quality of Life (HRQoL) of patients with hypertension. Data were obtained using the baseline survey of 258 patients from the Social Determinants and Inequities in the Control of Blood Hypertension Program (ProDSICHA). HRQoL was measured with SF-8 Health Survey. Socioeconomic position was measured using education, and the MacArthur Scale. Stress was measured with Perceived Stress Scale. A higher educational level was associated with a higher perception of stress (Coeff = 0.78, p = 0.019). Also, a lower position in the community was associated with a higher perception of stress (Coeff = −0.56, p = 0.027). A higher level of perceived stress was associated with a higher level of mental health (Coeff = 0.64, p = 0.000). No statistical differences were found in the relations between socioeconomic position and physical HRQoL. These findings warrant further research to understand the role of socioeconomic position in physical HRQoL.
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Affiliation(s)
- Susana Barradas
- Universidad de los Andes, Colombia.,Universidad Externado de Colombia, Colombia
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9
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Li Y, Zhang Q, Di Zhang, Cai Q, Fan J, Venners SA, Jiang S, Li J, Xu X. The effect of ABCA1 gene DNA methylation on blood pressure levels in a Chinese hyperlipidemic population. J Hum Hypertens 2021; 35:1139-1148. [PMID: 33462393 DOI: 10.1038/s41371-020-00479-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/08/2020] [Accepted: 12/11/2020] [Indexed: 11/09/2022]
Abstract
Hypertension is an important public health challenge worldwide. Epigenetic studies are providing novel insight into the underlying mechanisms of hypertension. We investigated the effect of DNA methylation in ATP-binding cassette transporter 1 (ABCA1) gene on blood pressure levels in a Chinese hyperlipidemic population. We randomly selected 211 individuals with hyperlipidemia who had not received any lipid-lowering treatment at baseline from our previous statin pharmacogenetics study (n = 734). DNA methylation loci at the ABCA1 gene were measured by MethylTarget, a next generation bisulfite sequencing-based multiple targeted cytosine-guanine dinucleotide methylation analysis method. Mean DNA methylation level was used in statistical analysis. In all subjects, higher mean ABCA1_B methylation was positively associated with systolic blood pressure (SBP) (β = 8.27, P = 0.008; β = 8.78, P = 0.005) and explained 2.7% and 5.8% of SBP variation before and after adjustment for lipids, respectively. We further divided all patients into three groups based on the tertile of body mass index (BMI) distribution. In the middle tertile of BMI, there was a significantly positive relationship between mean ABCA1_A methylation and SBP (β = 0.89, P = 0.003) and DBP (β = 0.32, P = 0.030). Mean ABCA1_A methylation explained 11.0% of SBP variation and 5.3% of DBP variation, respectively. Furthermore, mean ABCA1_A methylation (β = 0.79; P = 0.007) together with age and gender explained up to 24.1% of SBP variation. Our study provides new evidence that the ABCA1 DNA methylation profile is associated with blood pressure levels, which highlights that DNA methylation might be a significant molecular mechanism involved in the pathophysiological process of hypertension.
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Affiliation(s)
- Yajie Li
- School of Life Sciences, Anhui University, Hefei, China
| | - Qian Zhang
- School of Life Sciences, Anhui University, Hefei, China
| | - Di Zhang
- School of Life Sciences, Anhui University, Hefei, China
| | - Qianru Cai
- School of Life Sciences, Anhui University, Hefei, China
| | - Juanlin Fan
- School of Life Sciences, Anhui University, Hefei, China
| | - Scott A Venners
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Shanqun Jiang
- School of Life Sciences, Anhui University, Hefei, China. .,Institute of Biomedicine, Anhui Medical University, Hefei, China.
| | - Jianping Li
- Department of Cardiology, Peking University First Hospital, Beijing, China.
| | - Xiping Xu
- Institute of Biomedicine, Anhui Medical University, Hefei, China.,National Clinical Research Study Center for Kidney Disease, State Key Laboratory for Organ Failure Research, Renal Division, Nanfang Hospital, Southern Medical University, Guangzhou, China
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10
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Fujii R, Yamada H, Munetsuna E, Yamazaki M, Mizuno G, Ando Y, Maeda K, Tsuboi Y, Ohashi K, Ishikawa H, Hagiwara C, Wakai K, Hashimoto S, Hamajima N, Suzuki K. Dietary fish and ω-3 polyunsaturated fatty acids are associated with leukocyte ABCA1 DNA methylation levels. Nutrition 2020; 81:110951. [PMID: 33045487 DOI: 10.1016/j.nut.2020.110951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/08/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES A diet rich in fish and ω-3 polyunsaturated fatty acids (PUFAs) has been thought to reduce the risk for cardiovascular disease (CVD). The beneficial effects of fish oil and ω-3 PUFA on CVD can be mediated by epigenetic status of the genes associated with lipid metabolism and inflammation. The aim of this study was to investigate whether dietary fish and fatty acid (FA) intakes are associated with leukocyte ATP-binding cassette transporter A1 (ABCA1) DNA methylation levels in a Japanese population. METHODS This cross-sectional study included 298 adults (137 men and 161 women) without clinical history of CVD or cancer. The pyrosequencing method was used to measure leukocyte ABCA1 DNA methylation levels. Dietary fish and FA intakes were assessed based on the validated food frequency questionnaire. RESULTS Mean ABCA1 DNA methylation levels were significantly lower in the highest fish intake groups (≥5-6/wk) compared with the lowest intake group (≤1-2/wk; P = 0.004). In multivariable linear regression analyses, higher dietary intake of ω-3 PUFAs and ω-3 highly unsaturated fatty acids was significantly associated with decreased levels of ABCA1 DNA methylation (P = 0.001 and 0.005); whereas no significant associations were seen between intake of dietary saturated fatty acid, monounsaturated fatty acid, and ω-6 PUFAs and ABCA1 DNA methylation. CONCLUSION Higher dietary fish and ω-3 PUFA intake were associated with lower ABCA1 DNA levels in a Japanese population. The present results may bring potential insights on biological mechanisms underlying the protective effects of dietary fish and ω-3 PUFA intakes on CVD.
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Affiliation(s)
- Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Japan
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Takamatsu, Japan
| | - Genki Mizuno
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Yoshitaka Ando
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Keisuke Maeda
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Koji Ohashi
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Hiroaki Ishikawa
- Department of Biomedical and Analytical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Chiharu Hagiwara
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nobuyuki Hamajima
- Department of Health Care Administration, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan.
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11
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Zeisel SH. Precision (Personalized) Nutrition: Understanding Metabolic Heterogeneity. Annu Rev Food Sci Technol 2020; 11:71-92. [DOI: 10.1146/annurev-food-032519-051736] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
People differ in their requirements for and responses to nutrients and bioactive molecules in the diet. Many inputs contribute to metabolic heterogeneity (including variations in genetics, epigenetics, microbiome, lifestyle, diet intake, and environmental exposure). Precision nutrition is not about developing unique prescriptions for individual people but rather about stratifying people into different subgroups of the population on the basis of biomarkers of the above-listed sources of metabolic variation and then using this stratification to better estimate the different subgroups’ dietary requirements, thereby enabling better dietary recommendations and interventions. The hope is that we will be able to subcategorize people into ever-smaller groups that can be targeted in terms of recommendations, but we will never achieve this at the individual level, thus, the choice of precision nutrition rather than personalized nutrition to designate this new field. This review focuses mainly on genetically related sources of metabolic heterogeneity and identifies challenges that need to be overcome to achieve a full understanding of the complex interactions between the many sources of metabolic heterogeneity that make people differ from one another in their requirements for and responses to foods. It also discusses the commercial applications of precision nutrition.
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Affiliation(s)
- Steven H. Zeisel
- Nutrition Research Institute, Department of Nutrition, University of North Carolina, Kannapolis, North Carolina 28081, USA
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12
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He Z, Zhang R, Jiang F, Zhang H, Zhao A, Xu B, Jin L, Wang T, Jia W, Jia W, Hu C. FADS1-FADS2 genetic polymorphisms are associated with fatty acid metabolism through changes in DNA methylation and gene expression. Clin Epigenetics 2018; 10:113. [PMID: 30157936 PMCID: PMC6114248 DOI: 10.1186/s13148-018-0545-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background Genome-wide association studies (GWASs) have shown that genetic variants are important determinants of free fatty acid levels. The mechanisms underlying the associations between genetic variants and free fatty acid levels are incompletely understood. Here, we aimed to identify genetic markers that could influence diverse fatty acid levels in a Chinese population and uncover the molecular mechanisms in terms of DNA methylation and gene expression. Results We identified strong associations between single-nucleotide polymorphisms (SNPs) in the fatty acid desaturase (FADS) region and multiple polyunsaturated fatty acids. Expression quantitative trait locus (eQTL) analysis of rs174570 on FADS1 and FADS2 mRNA levels proved that minor allele of rs174570 was associated with decreased FADS1 and FADS2 expression levels (P < 0.05). Methylation quantitative trait locus (mQTL) analysis of rs174570 on DNA methylation levels in three selected regions of FADS region showed that the methylation levels at four CpG sites in FADS1, one CpG site in intragenic region, and three CpG sites in FADS2 were strongly associated with rs174570 (P < 0.05). Then, we demonstrated that methylation levels at three CpG sites in FADS1 were negatively associated with FADS1 and FADS2 expression, while two CpG sites in FADS2 were positively associated with FADS1 and FADS2 expression. Using mediation analysis, we further show that the observed effect of rs174570 on gene expression was tightly correlated with the effect predicted through association with methylation. Conclusions Our findings suggest that genetic variants in the FADS region are major genetic modifiers that can regulate fatty acid metabolism through epigenetic gene regulation. Electronic supplementary material The online version of this article (10.1186/s13148-018-0545-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen He
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China.,Institute for Metabolic Diseases, Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Feng Jiang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Hong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Aihua Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Bo Xu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Li Jin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Tao Wang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China. .,Institute for Metabolic Diseases, Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.
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13
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Abstract
PURPOSE OF REVIEW Postprandial lipemia (PPL), the prolonged increase in plasma triglyceride-rich lipoproteins following food consumption, is an independent risk factor for cardiovascular disease. Genetic variation, environment and the interplay between these direct an individual's postprandial lipid response. From such interplay, inducible and reversible epigenetic changes arise. Increasing evidence suggests epigenetic variation contributes to postprandial response in lipids and risk. RECENT FINDINGS Diet and exercise are central agents affecting postprandial lipemia - triglyceride, but heterogeneity of the findings warrant more and larger studies. Several epigenetic loci identified from a human intervention study account for a substantial proportion of PPL phenotype variation, but the burden to conduct an intervention study of postprandial responses likely limits translation to personalized nutrition. SUMMARY The impact of both DNA methylation patterns and environmental factors such as diet, exercise, sleep and medication on PPL is multifaceted. Discovery of interactions that modify the association between CpG (oligodeoxydinucleotide) methylation and postprandial phenotypes is unfolding.
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Affiliation(s)
| | - Jose M Ordovas
- Jean Mayer-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
- IMDEA Food Institute, CEI UAM + CSIC
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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14
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He Z, Zhang R, Jiang F, Hou W, Hu C. Role of genetic and environmental factors in DNA methylation of lipid metabolism. Genes Dis 2017; 5:9-15. [PMID: 30258929 PMCID: PMC6146210 DOI: 10.1016/j.gendis.2017.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/17/2017] [Indexed: 12/26/2022] Open
Abstract
A number of recent studies revealed that DNA methylation plays a central role in the regulation of lipid metabolism. DNA methylation modifications are important regulators of transcriptional networks that do not affect the DNA sequence and can translate genetic variants and environmental factors into phenotypic traits. Therefore, elucidating the factors that underlie inter-individual DNA methylation variations gives us an opportunity to predict diseases and interfere with the establishment of aberrant DNA methylation early. In this review, we summarize the findings of DNA methylation-related studies focused on unravelling the potential role of genetic and environmental factors in DNA methylation and the regulatory effect of DNA methylation on gene expression in lipid metabolism.
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Affiliation(s)
- Zhen He
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Feng Jiang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wenjing Hou
- Fengxian Central Hospital, Affiliated to Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Institute for Metabolic Diseases, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai, China
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15
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Karimi M, Vedin I, Freund Levi Y, Basun H, Faxén Irving G, Eriksdotter M, Wahlund LO, Schultzberg M, Hjorth E, Cederholm T, Palmblad J. DHA-rich n-3 fatty acid supplementation decreases DNA methylation in blood leukocytes: the OmegAD study. Am J Clin Nutr 2017; 106:1157-1165. [PMID: 28855224 DOI: 10.3945/ajcn.117.155648] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/04/2017] [Indexed: 11/14/2022] Open
Abstract
Background: Dietary fish oils, rich in long-chain n-3 (ω-3) fatty acids (FAs) [e.g., docosahexaenoic acid (DHA, 22:6n-3) and eicosapentaenoic acid (EPA, 20:5n-3)], modulate inflammatory reactions through various mechanisms, including gene expression, which is measured as messenger RNA concentration. However, the effects of long-term treatment of humans with DHA and EPA on various epigenetic factors-such as DNA methylation, which controls messenger RNA generation-are poorly described.Objective: We wanted to determine the effects of 6 mo of dietary supplementation with an n-3 FA preparation rich in DHA on global DNA methylation of peripheral blood leukocytes (PBLs) and the relation to plasma EPA and DHA concentrations in Alzheimer disease (AD) patients.Design: In the present study, DNA methylation in four 5'-cytosine-phosphate-guanine-3' (CpG) sites of long interspersed nuclear element-1 repetitive sequences was assessed in a group of 63 patients (30 given the n-3 FA preparation and 33 given placebo) as an estimation of the global DNA methylation in blood cells. Patients originated from the randomized, double-blind, placebo-controlled OmegAD study, in which 174 AD patients received either 1.7 g DHA and 0.6 g EPA (the n-3 FA group) or placebo daily for 6 mo.Results: At 6 mo, the n-3 FA group displayed marked increases in DHA and EPA plasma concentrations (2.6- and 3.5-fold), as well as decreased methylation in 2 out of 4 CpG sites (P < 0.05 for all), respectively. This hypomethylation in CpG2 and CpG4 sites showed a reverse correlation to changes in plasma EPA concentration (r = -0.25, P = 0.045; and r = -0.26, P = 0.041, respectively), but not to changes in plasma DHA concentration, and were not related to apolipoprotein E-4 allele frequency.Conclusion: Supplementation with n-3 FA for 6 mo was associated with global DNA hypomethylation in PBLs. Our data may be of importance in measuring various effects of marine oils, including gene expression, in patients with AD and in other patients taking n-3 FA supplements. This trial was registered at clinicaltrials.gov as NCT00211159.
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Affiliation(s)
| | - Inger Vedin
- Departments of Medicine and Hematology (HERM) and
| | - Yvonne Freund Levi
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Hans Basun
- Public Health and Caring Sciences, Division of Geriatrics, and
| | - Gerd Faxén Irving
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Maria Eriksdotter
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Lars-Olof Wahlund
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Marianne Schultzberg
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Erik Hjorth
- Neurobiology, Care, Sciences and Society, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; and Departments of
| | - Tommy Cederholm
- Clinical Nutrition and Metabolism, Uppsala University Hospital, Uppsala, Sweden
| | - Jan Palmblad
- Departments of Medicine and Hematology (HERM) and
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16
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Molnos S, Baumbach C, Wahl S, Müller-Nurasyid M, Strauch K, Wang-Sattler R, Waldenberger M, Meitinger T, Adamski J, Kastenmüller G, Suhre K, Peters A, Grallert H, Theis FJ, Gieger C. pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. BMC Bioinformatics 2017; 18:429. [PMID: 28962546 PMCID: PMC5622569 DOI: 10.1186/s12859-017-1838-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associations between genetic variants and metabolite levels. However, only considering genetic variants and their effects on one trait ignores the possible interplay between different “omics” layers. Existing tools only consider single-nucleotide polymorphism (SNP)–SNP interactions, and no practical tool is available for large-scale investigations of the interactions between pairs of arbitrary quantitative variables. Results We developed an R package called pulver to compute p-values for the interaction term in a very large number of linear regression models. Comparisons based on simulated data showed that pulver is much faster than the existing tools. This is achieved by using the correlation coefficient to test the null-hypothesis, which avoids the costly computation of inversions. Additional tricks are a rearrangement of the order, when iterating through the different “omics” layers, and implementing this algorithm in the fast programming language C++. Furthermore, we applied our algorithm to data from the German KORA study to investigate a real-world problem involving the interplay among DNA methylation, genetic variants, and metabolite levels. Conclusions The pulver package is a convenient and rapid tool for screening huge numbers of linear regression models for significant interaction terms in arbitrary pairs of quantitative variables. pulver is written in R and C++, and can be downloaded freely from CRAN at https://cran.r-project.org/web/packages/pulver/. Electronic supplementary material The online version of this article (10.1186/s12859-017-1838-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Molnos
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany. .,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Experimental Genetics, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Twins Research and Genetic Epidemiology, Kings College, London, UK
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Biophysics and Physiology, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Mathematics, Technische Universitat München, Garching, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
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17
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Haerian BS, Haerian MS, Roohi A, Mehrad-Majd H. ABCA1 genetic polymorphisms and type 2 diabetes mellitus and its complications. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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18
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Fairchild AJ, McDaniel HL. Best (but oft-forgotten) practices: mediation analysis. Am J Clin Nutr 2017; 105:1259-1271. [PMID: 28446497 PMCID: PMC5445681 DOI: 10.3945/ajcn.117.152546] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/23/2017] [Indexed: 12/22/2022] Open
Abstract
This contribution in the "Best (but Oft-Forgotten) Practices" series considers mediation analysis. A mediator (sometimes referred to as an intermediate variable, surrogate endpoint, or intermediate endpoint) is a third variable that explains how or why ≥2 other variables relate in a putative causal pathway. The current article discusses mediation analysis with the ultimate intention of helping nutrition researchers to clarify the rationale for examining mediation, avoid common pitfalls when using the model, and conduct well-informed analyses that can contribute to improving causal inference in evaluations of underlying mechanisms of effects on nutrition-related behavioral and health outcomes. We give specific attention to underevaluated limitations inherent in common approaches to mediation. In addition, we discuss how to conduct a power analysis for mediation models and offer an applied example to demonstrate mediation analysis. Finally, we provide an example write-up of mediation analysis results as a model for applied researchers.
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19
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Epigenetic changes in blood leukocytes following an omega-3 fatty acid supplementation. Clin Epigenetics 2017; 9:43. [PMID: 28450971 PMCID: PMC5405524 DOI: 10.1186/s13148-017-0345-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Omega-3 polyunsaturated fatty acids (n-3 FAs) have several beneficial effects on cardiovascular (CV) disease risk factors. These effects on CV risk profile may be mediated by several factors, including epigenetic modifications. Our objective is to investigate, using genome-wide DNA methylation analyses, methylation changes following an n-3 FA supplementation in overweight and obese subjects and to identify specific biological pathways potentially altered by the supplementation. Results Blood leukocytes genome-wide DNA methylation profiles of 36 overweight and obese subjects before and after a 6-week supplementation with 3 g of n-3 FAs were compared using GenomeStudio software. After supplementation, 308 CpG sites, assigned to 231 genes, were differentially methylated (FDR-corrected Diffscore ≥│13│~ P ≤ 0.05). Using Ingenuity Pathway Analysis system, a total of 55 pathways were significantly overrepresented following supplementation. Among these pathways, 16 were related to inflammatory and immune response, lipid metabolism, type 2 diabetes, and cardiovascular signaling. Changes in methylation levels of CpG sites within AKT3, ATF1, HDAC4, and IGFBP5 were correlated with changes in plasma triglyceride and glucose levels as well as with changes in the ratio of total cholesterol/HDL-cholesterol following the supplementation. Conclusions These data provide key differences in blood leukocytes DNA methylation profiles of subjects following an n-3 FA supplementation, which brings new, potential insights on metabolic pathways underlying the effects of n-3 FAs on CV health. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0345-3) contains supplementary material, which is available to authorized users.
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20
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Vineis P, Chatziioannou A, Cunliffe VT, Flanagan JM, Hanson M, Kirsch-Volders M, Kyrtopoulos S. Epigenetic memory in response to environmental stressors. FASEB J 2017; 31:2241-2251. [PMID: 28280003 DOI: 10.1096/fj.201601059rr] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022]
Abstract
Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors.
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Affiliation(s)
- Paolo Vineis
- Medical Research Council-Public Health England Center for Environment and Health, Imperial College London, London, United Kingdom;
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vincent T Cunliffe
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - James M Flanagan
- Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Hanson
- Institute of Developmental Sciences, University Hospital Southampton, University of Southampton, United Kingdom
| | | | - Soterios Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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21
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The integration of epigenetics and genetics in nutrition research for CVD risk factors. Proc Nutr Soc 2016; 76:333-346. [DOI: 10.1017/s0029665116000823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is increasing evidence documenting gene-by-environment (G × E) interactions for CVD related traits. However, the underlying mechanisms are still unclear. DNA methylation may represent one of such potential mechanisms. The objective of this review paper is to summarise the current evidence supporting the interplay among DNA methylation, genetic variants, and environmental factors, specifically (1) the association between SNP and DNA methylation; (2) the role that DNA methylation plays in G × E interactions. The current evidence supports the notion that genotype-dependent methylation may account, in part, for the mechanisms underlying observed G × E interactions in loci such asAPOE, IL6and ATP-binding cassette A1. However, these findings should be validated using intervention studies with high level of scientific evidence. The ultimate goal is to apply the knowledge and the technology generated by this research towards genetically based strategies for the development of personalised nutrition and medicine.
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