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Zhou H, Gelernter J. Human genetics and epigenetics of alcohol use disorder. J Clin Invest 2024; 134:e172885. [PMID: 39145449 PMCID: PMC11324314 DOI: 10.1172/jci172885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Alcohol use disorder (AUD) is a prominent contributor to global morbidity and mortality. Its complex etiology involves genetics, epigenetics, and environmental factors. We review progress in understanding the genetics and epigenetics of AUD, summarizing the key findings. Advancements in technology over the decades have elevated research from early candidate gene studies to present-day genome-wide scans, unveiling numerous genetic and epigenetic risk factors for AUD. The latest GWAS on more than one million participants identified more than 100 genetic variants, and the largest epigenome-wide association studies (EWAS) in blood and brain samples have revealed tissue-specific epigenetic changes. Downstream analyses revealed enriched pathways, genetic correlations with other traits, transcriptome-wide association in brain tissues, and drug-gene interactions for AUD. We also discuss limitations and future directions, including increasing the power of GWAS and EWAS studies as well as expanding the diversity of populations included in these analyses. Larger samples, novel technologies, and analytic approaches are essential; these include whole-genome sequencing, multiomics, single-cell sequencing, spatial transcriptomics, deep-learning prediction of variant function, and integrated methods for disease risk prediction.
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Affiliation(s)
- Hang Zhou
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Biomedical Informatics and Data Science
- Center for Brain and Mind Health
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Genetics, and
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
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2
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Crisóstomo L, Oliveira PF, Alves MG. A systematic scientometric review of paternal inheritance of acquired metabolic traits. BMC Biol 2023; 21:255. [PMID: 37953286 PMCID: PMC10641967 DOI: 10.1186/s12915-023-01744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND The concept of the inheritance of acquired traits, a foundational principle of Lamarck's evolutionary theory, has garnered renewed attention in recent years. Evidence for this phenomenon remained limited for decades but gained prominence with the Överkalix cohort study in 2002. This study revealed a link between cardiovascular disease incidence and the food availability experienced by individuals' grandparents during their slow growth periods, reigniting interest in the inheritance of acquired traits, particularly in the context of non-communicable diseases. This scientometric analysis and systematic review comprehensively explores the current landscape of paternally transmitted acquired metabolic traits. RESULTS Utilizing Scopus Advanced search and meticulous screening, we included mammalian studies that document the inheritance or modification of metabolic traits in subsequent generations of unexposed descendants. Our inclusive criteria encompass intergenerational and transgenerational studies, as well as multigenerational exposures. Predominantly, this field has been driven by a select group of researchers, potentially shaping the design and focus of existing studies. Consequently, the literature primarily comprises transgenerational rodent investigations into the effects of ancestral exposure to environmental pollutants on sperm DNA methylation. The complexity and volume of data often lead to multiple or redundant publications. This practice, while understandable, may obscure the true extent of the impact of ancestral exposures on the health of non-exposed descendants. In addition to DNA methylation, studies have illuminated the role of sperm RNAs and histone marks in paternally acquired metabolic disorders, expanding our understanding of the mechanisms underlying epigenetic inheritance. CONCLUSIONS This review serves as a comprehensive resource, shedding light on the current state of research in this critical area of science, and underscores the need for continued exploration to uncover the full spectrum of paternally mediated metabolic inheritance.
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Affiliation(s)
- Luís Crisóstomo
- Departmento de Anatomia, UMIB - Unidade Multidisciplinar de Investigação Biomédica, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade Do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, Porto, Portugal
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Pedro F Oliveira
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Marco G Alves
- Departmento de Anatomia, UMIB - Unidade Multidisciplinar de Investigação Biomédica, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade Do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, Porto, Portugal.
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona, Spain.
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona, Spain.
- Institute of Biomedicine - iBiMED and Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
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3
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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Lv J, Jia H, Mo M, Yuan J, Wu Z, Zhang S, Zhe F, Gu B, Fan B, Li C, Zhang T, Zhu J. Changes of serum metabolites levels during neoadjuvant chemoradiation and prediction of the pathological response in locally advanced rectal cancer. Metabolomics 2022; 18:99. [PMID: 36441416 DOI: 10.1007/s11306-022-01959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Previous studies have explored prediction value of serum metabolites in neoadjuvant chemoradiation therapy (NCRT) response for rectal cancer. To date, limited literature is available for serum metabolome changes dynamically through NCRT. OBJECTIVES This study aimed to explore temporal change pattern of serum metabolites during NCRT, and potential metabolic biomarkers to predict the pathological response to NCRT in locally advanced rectal cancer (LARC) patients. METHODS Based on dynamic UHPLC-QTOF-MS untargeted metabolomics design, this study included 106 LARC patients treated with NCRT. Biological samples of the enrolled patients were collected in five consecutive time-points. Untargeted metabolomics was used to profile serum metabolic signatures from LARC patients. Then, we used fuzzy C-means clustering (FCM) to explore temporal change patterns in metabolites cluster and identify monotonously changing metabolites during NCRT. Repeated measure analysis of variance (RM-ANOVA) and multilevel partial least-squares discriminant analysis (ML-PLS-DA) were performed to select metabolic biomarkers. Finally, a panel of dynamic differential metabolites was used to build logistic regression prediction models. RESULTS Metabolite profiles showed a clearly tendency of separation between different follow-up panels. We identified two clusters of 155 serum metabolites with monotonously changing patterns during NCRT (74 decreased metabolites and 81 increased metabolites). Using RM-ANOVA and ML-PLS-DA, 8 metabolites (L-Norleucine, Betaine, Hypoxanthine, Acetylcholine, 1-Hexadecanoyl-sn-glycero-3-phosphocholine, Glycerophosphocholine, Alpha-ketoisovaleric acid, N-Acetyl-L-alanine) were further identified as dynamic differential biomarkers for predicting NCRT sensitivity. The area under the ROC curve (AUC) of prediction model combined with the baseline measurement was 0.54 (95%CI = 0.43 ~ 0.65). By incorporating the variability indexes of 8 dynamic differential metabolites, the prediction model showed better discrimination performance than baseline measurement, with AUC = 0.67 (95%CI 0.57 ~ 0.77), 0.64 (0.53 ~ 0.75), 0.60 (0.50 ~ 0.71), and 0.56 (0.45 ~ 0.67) for the variability index of difference, linear slope, ratio, and standard deviation, respectively. CONCLUSION This study identified eight metabolites as dynamic differential biomarkers to discriminate NCRT-sensitive and resistant patients. The changes of metabolite level during NCRT show better performance in predicting NCRT sensitivity. These findings highlight the clinical significance of metabolites variabilities in metabolomics analysis.
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Affiliation(s)
- Jiali Lv
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huixun Jia
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Clinical Statistics Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Miao Mo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Clinical Statistics Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jing Yuan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Clinical Statistics Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhenyu Wu
- Department of Biostatistics, School of Public Health, Key Laboratory of Public Health Safety and Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Shuai Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fan Zhe
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bingbing Gu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bingbing Fan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chunxia Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Ji Zhu
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.
- Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, China.
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Abstract
Advances in high-throughput technologies and the generation of multiomics, such as genomic, epigenomic, transcriptomic, and metabolomic data, are paving the way for the biological risk stratification and prediction of oral diseases. When integrated with electronic health records, survey, census, and/or epidemiologic data, multiomics are anticipated to facilitate data-driven precision oral health, or the delivery of the right oral health intervention to the right individuals/populations at the right time. Meanwhile, multiomics may be modified by a multitude of social exposures, cumulatively along the life course and at various time points from conception onward, also referred to as the socio-exposome. For example, adverse exposures, such as precarious social and living conditions and related psychosocial stress among others, have been linked to specific genes being switched "on and off" through epigenetic mechanisms. These in turn are associated with various health conditions in different age groups and populations. This article argues that considering the impact of the socio-exposome in the biological profiling for precision oral health applications is necessary to ensure that definitions of biological risk do not override social ones. To facilitate the uptake of the socio-exposome in multiomics oral health studies and subsequent interventions, 3 pertinent facets are discussed. First, a summary of the epigenetic landscape of oral health is presented. Next, findings from the nondental literature are drawn on to elaborate the pathways and mechanisms that link the socio-exposome with gene expression-or the biological embedding of social experiences through epigenetics. Then, methodological considerations for implementing social epigenomics into oral health research are highlighted, with emphasis on the implications for study design and interpretation. The article concludes by shedding light on some of the current and prospective opportunities for social epigenomics research applied to the study of life course oral epidemiology.
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Affiliation(s)
- N Gomaa
- Schulich School of Medicine and Dentistry, Western University, London, Canada.,Children's Health Research Institute, London, Canada
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6
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de Castilhos JK, Campagnolo PDB, de Almeida S, Vitolo MR, Mattevi VS. Impact of maternal dietary counseling in the first year of life on DNA methylation in a cohort of children. Genet Mol Biol 2021; 44:e20200330. [PMID: 34874049 PMCID: PMC8670011 DOI: 10.1590/1678-4685-gmb-2020-0330] [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] [Received: 09/16/2020] [Accepted: 09/28/2021] [Indexed: 01/16/2023] Open
Abstract
Epigenetic modifications established during prenatal and early life, including DNA methylation, have been suggested as potential mediators of the interaction between environmental exposures during the perinatal period and adult metabolic health adverse outcomes, especially cardiometabolic complications and overweight. The effect of a dietary intervention in the first year of life on global methylation levels in leukocyte samples from a cohort of children born between 2001 and 2002 in southern Brazil was examined. Overall methylation measurements were performed using enzyme-linked immunosorbent assays on DNA samples from 237 children at 4 years old. Mean methylation values were higher in the intervention group (mean: 2.20 ± 1.31%) than in the control group (mean: 1.65 ± 1.11%; P = 0.001). It was observed that nutritional counseling in the first year increased breastfeeding duration and stimulated the development of healthier eating habits. Therefore, these factors might have contributed to increase global DNA methylation. The findings of the present study reinforce the notion that performing nutritional interventions in the early stages of life is important and provide further evidence of the interaction between the environment and epigenetic traits.
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Affiliation(s)
| | | | - Silvana de Almeida
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Márcia Regina Vitolo
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Vanessa Suñé Mattevi
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
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7
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Arumugam T, Chuturgoon AA. Toxicoepigenetic consequences of fumonisin B 1 exposure: current knowledge and future perspective. Epigenomics 2021; 13:1849-1852. [PMID: 34647484 DOI: 10.2217/epi-2021-0329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Thilona Arumugam
- Discipline of Medical Biochemistry, School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Anil A Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
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8
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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9
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Fischer MA, Vondriska TM. Clinical epigenomics for cardiovascular disease: Diagnostics and therapies. J Mol Cell Cardiol 2021; 154:97-105. [PMID: 33561434 PMCID: PMC8330446 DOI: 10.1016/j.yjmcc.2021.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/05/2021] [Accepted: 01/10/2021] [Indexed: 12/28/2022]
Abstract
The study of epigenomics has advanced in recent years to span the regulation of a single genetic locus to the structure and orientation of entire chromosomes within the nucleus. In this review, we focus on the challenges and opportunities of clinical epigenomics in cardiovascular disease. As an integrator of genetic and environmental inputs, and because of advances in measurement techniques that are highly reproducible and provide sequence information, the epigenome is a rich source of potential biosignatures of cardiovascular health and disease. Most of the studies to date have focused on the latter, and herein we discuss observations on epigenomic changes in human cardiovascular disease, examining the role of protein modifiers of chromatin, noncoding RNAs and DNA modification. We provide an overview of cardiovascular epigenomics, discussing the challenges of data sovereignty, data analysis, doctor-patient ethics and innovations necessary to implement precision health.
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Affiliation(s)
- Matthew A Fischer
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, USA.
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, USA
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10
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Abstract
Aim: Social scientists have placed particularly high expectations on the study of epigenomics to explain how exposure to adverse social factors like poverty, child maltreatment and racism - particularly early in childhood - might contribute to complex diseases. However, progress has stalled, reflecting many of the same challenges faced in genomics, including overhype, lack of diversity in samples, limited replication and difficulty interpreting significance of findings. Materials & methods: This review focuses on the future of social epigenomics by discussing progress made, ongoing methodological and analytical challenges and suggestions for improvement. Results & conclusion: Recommendations include more diverse sample types, cross-cultural, longitudinal and multi-generational studies. True integration of social and epigenomic data will require increased access to both data types in publicly available databases, enhanced data integration frameworks, and more collaborative efforts between social scientists and geneticists.
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Affiliation(s)
- Amy L Non
- Department of Anthropology at the University of California, San Diego, 92093 CA, USA
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11
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Mulder RH, Neumann A, Cecil CAM, Walton E, Houtepen LC, Simpkin AJ, Rijlaarsdam J, Heijmans BT, Gaunt TR, Felix JF, Jaddoe VWV, Bakermans-Kranenburg MJ, Tiemeier H, Relton CL, van IJzendoorn MH, Suderman M. Epigenome-wide change and variation in DNA methylation in childhood: trajectories from birth to late adolescence. Hum Mol Genet 2021; 30:119-134. [PMID: 33450751 PMCID: PMC8033147 DOI: 10.1093/hmg/ddaa280] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation (DNAm) is known to play a pivotal role in childhood health and development, but a comprehensive characterization of genome-wide DNAm trajectories across this age period is currently lacking. We have therefore performed a series of epigenome-wide association studies in 5019 blood samples collected at multiple time-points from birth to late adolescence from 2348 participants of two large independent cohorts. DNAm profiles of autosomal CpG sites (CpGs) were generated using the Illumina Infinium HumanMethylation450 BeadChip. Change over time was widespread, observed at over one-half (53%) of CpGs. In most cases, DNAm was decreasing (36% of CpGs). Inter-individual variation in linear trajectories was similarly widespread (27% of CpGs). Evidence for non-linear change and inter-individual variation in non-linear trajectories was somewhat less common (11 and 8% of CpGs, respectively). Very little inter-individual variation in change was explained by sex differences (0.4% of CpGs) even though sex-specific DNAm was observed at 5% of CpGs. DNAm trajectories were distributed non-randomly across the genome. For example, CpGs with decreasing DNAm were enriched in gene bodies and enhancers and were annotated to genes enriched in immune-developmental functions. In contrast, CpGs with increasing DNAm were enriched in promoter regions and annotated to genes enriched in neurodevelopmental functions. These findings depict a methylome undergoing widespread and often non-linear change throughout childhood. They support a developmental role for DNA methylation that extends beyond birth into late adolescence and has implications for understanding life-long health and disease. DNAm trajectories can be visualized at http://epidelta.mrcieu.ac.uk.
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Affiliation(s)
- Rosa H Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Institute of Education and Child Studies, Leiden University, Leiden, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Psychology, Institute of Psychology, Psychiatry and Neuroscience, King's College London, London, UK
| | - Esther Walton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Department of Psychology, University of Bath, Bath, UK
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew J Simpkin
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Jolien Rijlaarsdam
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands.,School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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12
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Kandaswamy R, Hannon E, Arseneault L, Mansell G, Sugden K, Williams B, Burrage J, Staley JR, Pishva E, Dahir A, Roberts S, Danese A, Mill J, Fisher HL, Wong CCY. DNA methylation signatures of adolescent victimization: analysis of a longitudinal monozygotic twin sample. Epigenetics 2020; 16:1169-1186. [PMID: 33371772 PMCID: PMC8813077 DOI: 10.1080/15592294.2020.1853317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence suggests that individuals exposed to victimization at key developmental stages may have different epigenetic fingerprints compared to those exposed to no/minimal stressful events, however results are inconclusive. This study aimed to strengthen causal inference regarding the impact of adolescent victimization on the epigenome by controlling for genetic variation, age, gender, and shared environmental exposures. We conducted longitudinal epigenome-wide association analyses (EWAS) on DNA methylation (DNAm) profiles of 118 monozygotic (MZ) twin pairs from the Environmental Risk study with and without severe adolescent victimization generated using buccal DNA collected at ages 5, 10 and 18, and the Illumina EPIC array. Additionally, we performed cross-sectional EWAS on age-18 blood and buccal DNA from the same individuals to elucidate tissue-specific signatures of severe adolescent victimization. Our analyses identified 20 suggestive differentially methylated positions (DMPs) (P < 5e-05), with altered DNAm trajectories between ages 10–18 associated with severe adolescent victimization (∆Beta range = −5.5%−5.3%). Age-18 cross-sectional analyses revealed 72 blood (∆Beta range = −2.2%−3.4%) and 42 buccal (∆Beta range = −3.6%−4.6%) suggestive severe adolescent victimization-associated DMPs, with some evidence of convergent signals between these two tissue types. Downstream regional analysis identified significant differentially methylated regions (DMRs) in LGR6 and ANK3 (Šidák P = 5e-09 and 4.07e-06), and one upstream of CCL27 (Šidák P = 2.80e-06) in age-18 blood and buccal EWAS, respectively. Our study represents the first longitudinal MZ twin analysis of DNAm and severe adolescent victimization, providing initial evidence for altered DNA methylomic signatures in individuals exposed to adolescent victimization.
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Affiliation(s)
- Radhika Kandaswamy
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Louise Arseneault
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,ESRC Centre for Society & Mental Health, King's College London, London, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Benjamin Williams
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - James R Staley
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ehsan Pishva
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Aisha Dahir
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Susanna Roberts
- King's College London, Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, London UK
| | - Andrea Danese
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,King's College London, Department of Child & Adolescent Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, London UK.,National & Specialist CAMHS Clinic for Trauma, Anxiety and Depression, South London & Maudsley NHS Foundation Trust, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Helen L Fisher
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,ESRC Centre for Society & Mental Health, King's College London, London, UK
| | - Chloe C Y Wong
- King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
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13
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Fogle BM, Tsai J, Mota N, Harpaz-Rotem I, Krystal JH, Southwick SM, Pietrzak RH. The National Health and Resilience in Veterans Study: A Narrative Review and Future Directions. Front Psychiatry 2020; 11:538218. [PMID: 33362593 PMCID: PMC7755975 DOI: 10.3389/fpsyt.2020.538218] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/27/2020] [Indexed: 12/26/2022] Open
Abstract
United States (U.S.) veterans are substantially older than their non-veteran counterparts. However, nationally representative, population-based data on the unique health needs of this population are lacking. Such data are critical to informing the design of large-scale outreach initiatives, and to ensure the effectiveness of service care delivery both within and outside of the Veterans Affairs healthcare system. The National Health and Resilience in Veterans Study (NHRVS) is a contemporary, nationally representative, prospective study of two independent cohorts (n = 3,157 and n = 1,484) of U.S. veterans, which is examining longitudinal changes, and key risk and protective factors for several health outcomes. In this narrative review, we summarize the main findings of all NHRVS studies (n = 82) published as of June 2020, and discuss the clinical implications, limitations, and future directions of this study. Review of these articles was organized into six major topic areas: post-traumatic stress disorder, suicidality, aging, resilience and post-traumatic growth, special topics relevant to veterans, and genetics and epigenetics. Collectively, results of these studies suggest that while a significant minority of veterans screen positive for mental disorders, the majority are psychologically resilient. They further suggest that prevention and treatment efforts designed to promote protective psychosocial characteristics (i.e., resilience, gratitude, purpose in life), and social connectedness (i.e., secure attachment, community integration, social engagement) help mitigate risk for mental disorders, and promote psychological resilience and post-traumatic growth in this population.
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Affiliation(s)
- Brienna M. Fogle
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Jack Tsai
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Natalie Mota
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Ilan Harpaz-Rotem
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - John H. Krystal
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Steven M. Southwick
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
| | - Robert H. Pietrzak
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, VA Connecticut Healthcare System, West Haven, CT, United States
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, United States
- Department of Social and Behavioral Sciences, Yale School of Public Health, New Haven, CT, United States
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14
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Branje S, Geeraerts S, de Zeeuw EL, Oerlemans AM, Koopman-Verhoeff ME, Schulz S, Nelemans S, Meeus W, Hartman CA, Hillegers MHJ, Oldehinkel AJ, Boomsma DI. Intergenerational transmission: Theoretical and methodological issues and an introduction to four Dutch cohorts. Dev Cogn Neurosci 2020; 45:100835. [PMID: 32823179 PMCID: PMC7451818 DOI: 10.1016/j.dcn.2020.100835] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/27/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023] Open
Abstract
Behaviors, traits and characteristics are transmitted from parents to offspring because of complex genetic and non-genetic processes. We review genetic and non-genetic mechanisms of intergenerational transmission of psychopathology and parenting and focus on recent methodological advances in disentangling genetic and non-genetic factors. In light of this review, we propose that future studies on intergenerational transmission should aim to disentangle genetic and non-genetic transmission, take a long-term longitudinal perspective, and focus on paternal and maternal intergenerational transmission. We present four large longitudinal cohort studies within the Consortium on Individual Development, which together address many of these methodological challenges. These four cohort studies aim to examine the extent to which genetic and non-genetic transmission from the parental generation shapes parenting behavior and psychopathology in the next generation, as well as the extent to which self-regulation and social competence mediate this transmission. Conjointly, these four cohorts provide a comprehensive approach to the study of intergenerational transmission.
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Affiliation(s)
- Susan Branje
- Youth and Family, Department of Educational and Pedagogical Sciences, Utrecht University, Utrecht, the Netherlands.
| | - Sanne Geeraerts
- Youth and Family, Department of Educational and Pedagogical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Eveline L de Zeeuw
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Anoek M Oerlemans
- Department of Psychiatry, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - M Elisabeth Koopman-Verhoeff
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Susanne Schulz
- Youth and Family, Department of Educational and Pedagogical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Stefanie Nelemans
- Youth and Family, Department of Educational and Pedagogical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wim Meeus
- Youth and Family, Department of Educational and Pedagogical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Catharina A Hartman
- Department of Psychiatry, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Manon H J Hillegers
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albertine J Oldehinkel
- Department of Psychiatry, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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15
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Jaddoe VWV, Felix JF, Andersen AMN, Charles MA, Chatzi L, Corpeleijn E, Donner N, Elhakeem A, Eriksson JG, Foong R, Grote V, Haakma S, Hanson M, Harris JR, Heude B, Huang RC, Inskip H, Järvelin MR, Koletzko B, Lawlor DA, Lindeboom M, McEachan RRC, Mikkola TM, Nader JLT, de Moira AP, Pizzi C, Richiardi L, Sebert S, Schwalber A, Sunyer J, Swertz MA, Vafeiadi M, Vrijheid M, Wright J, Duijts L. The LifeCycle Project-EU Child Cohort Network: a federated analysis infrastructure and harmonized data of more than 250,000 children and parents. Eur J Epidemiol 2020; 35:709-724. [PMID: 32705500 PMCID: PMC7387322 DOI: 10.1007/s10654-020-00662-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022]
Abstract
Early life is an important window of opportunity to improve health across the full lifecycle. An accumulating body of evidence suggests that exposure to adverse stressors during early life leads to developmental adaptations, which subsequently affect disease risk in later life. Also, geographical, socio-economic, and ethnic differences are related to health inequalities from early life onwards. To address these important public health challenges, many European pregnancy and childhood cohorts have been established over the last 30 years. The enormous wealth of data of these cohorts has led to important new biological insights and important impact for health from early life onwards. The impact of these cohorts and their data could be further increased by combining data from different cohorts. Combining data will lead to the possibility of identifying smaller effect estimates, and the opportunity to better identify risk groups and risk factors leading to disease across the lifecycle across countries. Also, it enables research on better causal understanding and modelling of life course health trajectories. The EU Child Cohort Network, established by the Horizon2020-funded LifeCycle Project, brings together nineteen pregnancy and childhood cohorts, together including more than 250,000 children and their parents. A large set of variables has been harmonised and standardized across these cohorts. The harmonized data are kept within each institution and can be accessed by external researchers through a shared federated data analysis platform using the R-based platform DataSHIELD, which takes relevant national and international data regulations into account. The EU Child Cohort Network has an open character. All protocols for data harmonization and setting up the data analysis platform are available online. The EU Child Cohort Network creates great opportunities for researchers to use data from different cohorts, during and beyond the LifeCycle Project duration. It also provides a novel model for collaborative research in large research infrastructures with individual-level data. The LifeCycle Project will translate results from research using the EU Child Cohort Network into recommendations for targeted prevention strategies to improve health trajectories for current and future generations by optimizing their earliest phases of life.
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Affiliation(s)
- Vincent W V Jaddoe
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands. .,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Janine F Felix
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne-Marie Nybo Andersen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France.,ELFE Joint Unit, French Institute for Demographic Studies (Ined), French Institute for Medical Research and Health (INSERM), French Blood Agency, Aubervilliers, France
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nina Donner
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore.,Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology (A*STAR), Singapore, Singapore
| | - Rachel Foong
- Telethon Kids Institute, Perth, WA, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, WA, Australia
| | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Sido Haakma
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Mark Hanson
- Institute of Developmental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jennifer R Harris
- Centre for Fertility and Health, The Norwegian Institute of Public Health, Oslo, Norway.,Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | | | - Hazel Inskip
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Marjo-Riitta Järvelin
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK.,Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Berthold Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Maarten Lindeboom
- Department of Economics, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosemary R C McEachan
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | - Johanna L T Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Angela Pinot de Moira
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Costanza Pizzi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sylvain Sebert
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ameli Schwalber
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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16
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Walsh NM, O’Brien EC, Geraghty AA, Byrne DF, Whelan A, Reilly S, Murray S, Reilly C, Adams E, Farnan PM, McAuliffe FM. Taking guidance from parents involved in a longitudinal birth cohort - the ROLO family advisory committee. RESEARCH INVOLVEMENT AND ENGAGEMENT 2020; 6:16. [PMID: 32368350 PMCID: PMC7189585 DOI: 10.1186/s40900-020-00200-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The ROLO Study (Randomised cOntrol trial of a Low glycaemic index diet in pregnancy to prevent macrosomia) was a randomised control trial conducted between 2007 and 2011 to examine if a low glycaemic index (GI) diet could reduce the incidence of macrosomia. The ROLO Family Advisory Committee is a self-selected group of parents who are involved in the longitudinal follow-up of the ROLO Study. The committee was established in 2017 and the goal is to achieve a partnership between ROLO families and researchers, leading to improved research quality, relevance, and outcomes. This research method is termed "Public and patient involvement (PPI)" and describes how researchers collaborate and engage with the public in order to make research more relevant to them. METHODS The ROLO study mothers and children have been prospectively followed-up at multiple time points post-pregnancy. In October 2017, all women were invited to join the ROLO Family Advisory Committee via email or via advertisement on the ROLO Study Facebook page. Fathers and other guardians of the study children were also invited to join. Two annual meetings with the research team and parents were held in 2018 and 2019. The meetings were recorded, transcribed verbatim by researchers, and thematically analysed. RESULTS Parents provided opinions on the areas they felt should be explored within the ROLO study using information that was collected up to the current follow-up point. They also shared views on research interests which were of importance to them. These topics included; child mental health, fussy eating in childhood and healthy eating policies in schools. Mothers were much more concerned about factors which influenced their child's health rather than their own. Incorporating an element of PPI to this study was found to be a positive learning experience for participants and researchers. CONCLUSION The involvement of parents has enriched the research agenda at the UCD Perinatal Research Centre. We will continue to engage with the parents of the ROLO Study and plan to involve the children to explore their opinions at the next opportunity.
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Affiliation(s)
- N. M. Walsh
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - E. C. O’Brien
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - A. A. Geraghty
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - D. F. Byrne
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - A. Whelan
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - S. Reilly
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - S. Murray
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - C. Reilly
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - E. Adams
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - P. M. Farnan
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - F. M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
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17
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M. Nilsen F, Frank J, S. Tulve N. A Systematic Review and Meta-Analysis Investigating the Relationship between Exposures to Chemical and Non-Chemical Stressors during Prenatal Development and Childhood Externalizing Behaviors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17072361. [PMID: 32244397 PMCID: PMC7177257 DOI: 10.3390/ijerph17072361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
Childhood behavioral outcomes have been linked to low quality intrauterine environments caused by prenatal exposures to both chemical and non-chemical stressors. The effect(s) from the many stressors a child can be prenatally exposed to may be influenced by complex interactive relationships that are just beginning to be understood. Chemical stressors influence behavioral outcomes by affecting the monoamine oxidase A (MAOA) enzyme, which is involved in serotonin metabolism and the neuroendocrine response to stress. Non-chemical stressors, particularly those associated with violence, have been shown to influence and exacerbate the externalizing behavioral outcomes associated with low MAOA activity and slowed serotonin metabolism. The adverse developmental effects associated with high stress and maternal drug use during pregnancy are well documented. However, research examining the combined effects of other non-chemical and chemical stressors on development and childhood outcomes as a result of gestational exposures is scarce but is an expanding field. In this systematic review, we examined the extant literature to explore the interrelationships between exposures to chemical and non-chemical stressors (specifically stressful/traumatic experiences), MAOA characteristics, and childhood externalizing behaviors. We observed that exposures to chemical stressors (recreational drugs and environmental chemicals) are significantly related to externalizing behavioral outcomes in children. We also observed that existing literature examining the interactions between MAOA characteristics, exposures to chemical stressors, and traumatic experiences and their effects on behavioral outcomes is sparse. We propose that maternal stress and cortisol fluctuations during pregnancy may be an avenue to link these concepts. We recommend that future studies investigating childhood behaviors include chemical and non-chemical stressors as well as children’s inherent genetic characteristics to gain a holistic understanding of the relationship between prenatal exposures and childhood behavioral outcomes.
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Affiliation(s)
- Frances M. Nilsen
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Office of Research and Development, 109 TW Alexander Dr., Research Triangle Park, NC 27709, USA;
- Correspondence:
| | - Jessica Frank
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Office of Research and Development, 109 TW Alexander Dr., Research Triangle Park, NC 27709, USA;
| | - Nicolle S. Tulve
- U.S. Environmental Protection Agency, Office of Research and Development, 109 TW Alexander Dr., Research Triangle Park, NC 27709, USA;
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18
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McKenzie KA, Hunt SL, Hulshof G, Mudaranthakam DP, Meyer K, Vidoni ED, Burns JM, Mahnken JD. A semi-automated pipeline for fulfillment of resource requests from a longitudinal Alzheimer's disease registry. JAMIA Open 2019; 2:516-520. [PMID: 32025648 PMCID: PMC6993996 DOI: 10.1093/jamiaopen/ooz032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022] Open
Abstract
Objective Managing registries with continual data collection poses challenges, such as following reproducible research protocols and guaranteeing data accessibility. The University of Kansas (KU) Alzheimer’s Disease Center (ADC) maintains one such registry: Curated Clinical Cohort Phenotypes and Observations (C3PO). We created an automated and reproducible process by which investigators have access to C3PO data. Materials and Methods Data was input into Research Electronic Data Capture. Monthly, data part of the Uniform Data Set (UDS), that is data also collected at other ADCs, was uploaded to the National Alzheimer’s Coordinating Center (NACC). Quarterly, NACC cleaned, curated, and returned the UDS to the KU Data Management and Statistics (DMS) Core, where it was stored in C3PO with other quarterly curated site-specific data. Investigators seeking to utilize C3PO submitted a research proposal and requested variables via the publicly accessible and searchable data dictionary. The DMS Core used this variable list and an automated SAS program to create a subset of C3PO. Results C3PO contained 1913 variables stored in 15 datasets. From 2017 to 2018, 38 data requests were completed for several KU departments and other research institutions. Completing data requests became more efficient; C3PO subsets were produced in under 10 seconds. Discussion The data management strategy outlined above facilitated reproducible research practices, which is fundamental to the future of research as it allows replication and verification to occur. Conclusion We created a transparent, automated, and efficient process of extracting subsets of data from a registry where data was changing daily.
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Affiliation(s)
- Katelyn A McKenzie
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Suzanne L Hunt
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA.,University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA
| | - Genevieve Hulshof
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dinesh Pal Mudaranthakam
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA.,University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA
| | - Kayla Meyer
- University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA
| | - Eric D Vidoni
- University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA.,Department of Neurology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jeffrey M Burns
- University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA.,Department of Neurology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jonathan D Mahnken
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA.,University of Kansas Alzheimer's Disease Center, Fairway, Kansas, USA
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19
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Chidambaran V, Zhang X, Geisler K, Stubbeman BL, Chen X, Weirauch MT, Meller J, Ji H. Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study. THE JOURNAL OF PAIN 2019; 20:771-785. [PMID: 30639570 PMCID: PMC6616015 DOI: 10.1016/j.jpain.2018.12.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
We have reported child anxiety sensitivity (Child Anxiety Sensitivity Index [CASI]) predicts chronic postsurgical pain (CPSP). Herein, we evaluated DNA methylation profiles to understand the gene-environment interactions underlying CPSP and CASI, to identify shared, enriched, genomic pathways. In 73 prospectively recruited adolescents undergoing spine fusion, preoperative CASI and pain data over 12 months after surgery were collected. DNA from the peripheral blood of evaluable subjects with (n = 16) and without CPSP (n = 40) were analyzed using MethylationEPIC arrays. We identified 637 and 2,445 differentially DNA methylated positions (DMPs) associated with CPSP and CASI, respectively (P ≤ .05). Ingenuity pathway analysis of 39 genes with DMPs for both CPSP and CASI revealed enrichment of several canonical pathways, including GABA receptor (P = .00016 for CPSP; P =.0008 for CASI) and dopamine-DARPP32 feedback in cyclic adenosine monophosphate (P = .004 for CPSP and P =.00003 for CASI) signaling. Gene-gene interaction network enrichment analysis revealed participation of pathways in cell signaling, molecular transport, metabolism, and neurologic diseases (P < 10-8). Bioinformatic approaches to identify histone marks and transcription factor (TF) binding events underlying DMPs, showed their location in active regulatory regions in pain pathway relevant brain cells. Using Enrichr/Pinet enrichment and Library of Integrated Network-Based Cellular Signatures knockdown signatures, we identified TFs regulating genes with DMPs in association with CPSP and CASI. In conclusion, we identified epigenetically enriched pathways associated with CPSP and anxiety sensitivity in children undergoing surgery. Our findings support GABA hypofunction and the roles of the dopamine-DARPP32 pathway in emotion/reward and pain. This pilot study provides new epigenetic insights into the pathophysiology of CPSP and a basis for future studies in biomarker development and targetable interventions. PERSPECTIVE: Differential DNA methylation in regulatory genomic regions enriching shared neural pathways were associated with CPSP and CASI in adolescents undergoing spine surgery. Our findings support GABA hypofunction and the roles of the dopamine-DARPP32 pathway in emotion/reward contributing to behavioral maintenance of pain 10 to 12 months after surgery.
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Affiliation(s)
- Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children's Hospital, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio.
| | - Xue Zhang
- Pyrosequencing core for genomic and epigenomic research, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Kristie Geisler
- Department of Anesthesiology, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Bobbie L Stubbeman
- Department of Anesthesiology, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jarek Meller
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hong Ji
- Department of Environmental Health, University of Cincinnati; Division of Asthma Research, Cincinnati Children's Hospital, Cincinnati, Ohio
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20
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Liu J, Zhao W, Ammous F, Turner ST, Mosley TH, Zhou X, Smith JA. Longitudinal analysis of epigenome-wide DNA methylation reveals novel smoking-related loci in African Americans. Epigenetics 2019; 14:171-184. [PMID: 30764717 PMCID: PMC6557606 DOI: 10.1080/15592294.2019.1581589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/26/2019] [Accepted: 02/03/2019] [Indexed: 10/27/2022] Open
Abstract
Changes in DNA methylation may be a potential mechanism that mediates the effects of smoking on physiological function and subsequent disease risk. Given the dynamic nature of the epigenome, longitudinal studies are indispensable for investigating smoking-induced methylation changes over time. Using blood samples collected approximately five years apart in 380 African Americans (mean age 60.7 years) from the Genetic Epidemiology Network of Arteriopathy (GENOA) study, we measured DNA methylation levels using Illumina HumanMethylation BeadChips. We evaluated the association between Phase 1 smoking status and rate of methylation change, using generalized estimating equation models. Among the 6958 CpG sites examined, smoking status was associated with methylation change for 22 CpGs (false discovery rate q < 0.1), with the majority (91%) becoming less methylated over time. Methylation change was greater in ever smokers than never smokers, and the absolute differences in rates of change ranged from 0.18 to 0.77 per decade in M value, equivalent to a β value change of 0.013 to 0.047 per decade. Significant enrichment was observed for CpG islands, enhancers, and DNAse hypersensitivity sites (p < 0.05). Although biological pathway analyses were not significant, most of the 22 CpGs were within genes known to be associated with cardiovascular disease, cancers, and aging. In conclusion, we identified epigenetic signatures for cigarette smoking that may have been missed in cross-sectional analyses, providing insight into the epigenetic effect of smoking and highlighting the importance of longitudinal analysis in understanding the dynamic human epigenome.
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Affiliation(s)
- Jiaxuan Liu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Thomas H. Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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21
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Alfano R, Guida F, Galobardes B, Chadeau-Hyam M, Delpierre C, Ghantous A, Henderson J, Herceg Z, Jain P, Nawrot TS, Relton C, Vineis P, Castagné R, Plusquin M. Socioeconomic position during pregnancy and DNA methylation signatures at three stages across early life: epigenome-wide association studies in the ALSPAC birth cohort. Int J Epidemiol 2019; 48:30-44. [PMID: 30590607 PMCID: PMC6443021 DOI: 10.1093/ije/dyy259] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Socioeconomic experiences are recognized determinants of health, and recent work has shown that social disadvantages in early life may induce sustained biological changes at molecular level that are detectable later in life. However, the dynamics and persistence of biological embedding of socioeconomic position (SEP) remains vastly unexplored. METHODS Using the data from the ALSPAC birth cohort, we performed epigenome-wide association studies of DNA methylation changes at three life stages (birth, n = 914; childhood at mean age 7.5 years, n = 973; and adolescence at mean age 15.5 years, n = 974), measured using the Illumina HumanMethylation450 Beadchip, in relation to pregnancy SEP indicators (maternal and paternal education and occupation). RESULTS Across the four early life SEP metrics investigated, only maternal education was associated with methylation levels at birth, and four CpGs mapped to SULF1, GLB1L2 and RPUSD1 genes were identified [false discovery rate (FDR)-corrected P-value <0.05]. No epigenetic signature was found associated with maternal education in child samples, but methylation levels at 20 CpG loci were found significantly associated with maternal education in adolescence. Although no overlap was found between the differentially methylated CpG sites at different ages, we identified two CpG sites at birth and during adolescence which are 219 bp apart in the SULF1 gene that encodes an heparan sulphatase involved in modulation of signalling pathways. Using data from an independent birth cohort, the ENVIRONAGE cohort, we were not able to replicate these findings. CONCLUSIONS Taken together, our results suggest that parental SEP, and particularly maternal education, may influence the offspring's methylome at birth and adolescence.
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Affiliation(s)
- Rossella Alfano
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Florence Guida
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
| | - Bruna Galobardes
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Cyrille Delpierre
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - John Henderson
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Pooja Jain
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- IIGM, Italian Institute for Genomic Medicine, Turin, Italy
| | - Raphaële Castagné
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Michelle Plusquin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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22
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Hamilton OKL, Zhang Q, McRae AF, Walker RM, Morris SW, Redmond P, Campbell A, Murray AD, Porteous DJ, Evans KL, McIntosh AM, Deary IJ, Marioni RE. An epigenetic score for BMI based on DNA methylation correlates with poor physical health and major disease in the Lothian Birth Cohort. Int J Obes (Lond) 2019; 43:1795-1802. [PMID: 30842548 PMCID: PMC6760607 DOI: 10.1038/s41366-018-0262-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/09/2018] [Accepted: 10/14/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND The relationship between obesity and adverse health is well established, but little is known about the contribution of DNA methylation to obesity-related health outcomes. This study tests associations between an epigenetic score for body mass index (BMI) and health-related, cognitive, psychosocial and lifestyle outcomes in the Lothian Birth Cohort 1936. This study also tests whether these associations are independent of phenotypic BMI. METHOD Analyses were conducted using data from the Lothian Birth Cohort 1936 (n = 892). Weights for the epigenetic BMI score were derived using penalised regression on methylation data from unrelated Generation Scotland participants (n = 2562). Associations were tested for replication in an independent sample: the Lothian Birth Cohort 1921 (n = 433). RESULTS A higher epigenetic BMI score was associated with higher BMI (R2 = 0.1), greater body weight (R2 = 0.06), greater time taken to walk 6 m, poorer lung function and poorer general physical health (all R2 = 0.02), greater levels of triglycerides (R2 = 0.09), greater %total HbA1c (R2 = 0.06), lower levels of high-density lipoprotein cholesterol (HDL; R2 = 0.08), higher HDL ratio (HDL/total cholesterol; R2 = 0.03), lower health-related quality of life, physical inactivity, and greater social deprivation (all R2 = 0.02). The epigenetic BMI score (per SD) was also associated with type 2 diabetes (OR 2.17, 95% CI 1.67, 2.84), cardiovascular disease (OR 1.45, 95% CI 1.24, 1.71) and high blood pressure (OR 1.30, 95% CI 1.13, 1.49; all p < 0.00026 after Bonferroni correction). Associations were replicated for BMI (R2 = 0.06), body weight (R2 = 0.04), health-related quality of life (R2 = 0.02), HbA1c (R2 = 0.07) and triglycerides (R2 = 0.07; all p < 0.0045 after Bonferroni correction). CONCLUSIONS We observed and replicated associations between an epigenetic score for BMI and variables related to poor physical health and metabolic syndrome. Regression models with both epigenetic and phenotypic BMI scores as predictors accounted for a greater proportion of variance in all outcome variables than either predictor alone, demonstrating independent and additive effects of epigenetic and phenotypic BMI scores.
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Affiliation(s)
- Olivia K. L. Hamilton
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK
| | - Qian Zhang
- 0000 0000 9320 7537grid.1003.2Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD Australia
| | - Allan F. McRae
- 0000 0000 9320 7537grid.1003.2Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD Australia ,0000 0000 9320 7537grid.1003.2Queensland Brain Institute, University of Queensland, Brisbane, QLD Australia
| | - Rosie M. Walker
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Stewart W. Morris
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Paul Redmond
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Archie Campbell
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alison D. Murray
- 0000 0004 1936 7291grid.7107.1Aberdeen Biomedical Imaging Centre, Lilian Sutton Building, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD UK
| | - David J. Porteous
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Kathryn L. Evans
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Andrew M. McIntosh
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK ,0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF UK
| | - Ian J. Deary
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, Edinburgh, Scotland UK
| | - Riccardo E. Marioni
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
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23
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Esposito G, Azhari A, Borelli JL. Gene × Environment Interaction in Developmental Disorders: Where Do We Stand and What's Next? Front Psychol 2018; 9:2036. [PMID: 30416467 PMCID: PMC6212589 DOI: 10.3389/fpsyg.2018.02036] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/03/2018] [Indexed: 02/01/2023] Open
Abstract
Although the field of psychiatry has witnessed the proliferation of studies on Gene × Environment (G×E) interactions, still limited is the knowledge we possess of G×E interactions regarding developmental disorders. In this perspective paper, we discuss why G×E interaction studies are needed to broaden our knowledge of developmental disorders. We also discuss the different roles of hazardous versus self-generated environmental factors and how these types of factors may differentially engage with an individual's genetic background in predicting a resulting phenotype. Then, we present examplar studies that highlight the role of G×E in predicting atypical developmental trajectories as well as provide insight regarding treatment outcomes. Supported by these examples, we explore the need to move beyond merely examining statistical interactions between genes and the environment, and the motivation to investigate specific genetic susceptibility and environmental contexts that drive developmental disorders. We propose that further parsing of genetic and environmental components is required to fully understand the unique contribution of each factor to the etiology of developmental disorders. Finally, with a greater appreciation of the complexities of G×E interaction, this discussion will converge upon the potential implications for clinical and translational research.
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Affiliation(s)
- Gianluca Esposito
- Psychology Program, Nanyang Technological University, Singapore, Singapore
- Department of Psychology and Cognitive Science, University of Trento, Trento, Italy
| | - Atiqah Azhari
- Psychology Program, Nanyang Technological University, Singapore, Singapore
| | - Jessica L. Borelli
- Department of Psychological Science, University of California, Irvine, Irvine, CA, United States
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24
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Goodman SJ, Roubinov DS, Bush NR, Park M, Farré P, Emberly E, Hertzman C, Essex MJ, Kobor MS, Boyce WT. Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood. Dev Sci 2018; 22:e12739. [PMID: 30176105 PMCID: PMC6433477 DOI: 10.1111/desc.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
Abstract
A growing body of research has documented associations between adverse childhood environments and DNA methylation, highlighting epigenetic processes as potential mechanisms through which early external contexts influence health across the life course. The present study tested a complementary hypothesis: indicators of children's early internal, biological, and behavioral responses to stressful challenges may also be linked to stable patterns of DNA methylation later in life. Children's autonomic nervous system reactivity, temperament, and mental health symptoms were prospectively assessed from infancy through early childhood, and principal components analysis (PCA) was applied to derive composites of biological and behavioral reactivity. Buccal epithelial cells were collected from participants at 15 and 18 years of age. Findings revealed an association between early life biobehavioral inhibition/disinhibition and DNA methylation across many genes. Notably, reactive, inhibited children were found to have decreased DNA methylation of the DLX5 and IGF2 genes at both time points, as compared to non‐reactive, disinhibited children. Results of the present study are provisional but suggest that the gene's profile of DNA methylation may constitute a biomarker of normative or potentially pathological differences in reactivity. Overall, findings provide a foundation for future research to explore relations among epigenetic processes and differences in both individual‐level biobehavioral risk and qualities of the early, external childhood environment.
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Affiliation(s)
- Sarah J Goodman
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Nicole R Bush
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California
| | - Mina Park
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Pau Farré
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Eldon Emberly
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Clyde Hertzman
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Marilyn J Essex
- Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - W Thomas Boyce
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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25
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Abstract
BACKGROUND Longitudinal data and repeated measurements in epigenome-wide association studies (EWAS) provide a rich resource for understanding epigenetics. We summarize 7 analytical approaches to the GAW20 data sets that addressed challenges and potential applications of phenotypic and epigenetic data. All contributions used the GAW20 real data set and employed either linear mixed effect (LME) models or marginal models through generalized estimating equations (GEE). These contributions were subdivided into 3 categories: (a) quality control (QC) methods for DNA methylation data; (b) heritability estimates pretreatment and posttreatment with fenofibrate; and (c) impact of drug response pretreatment and posttreatment with fenofibrate on DNA methylation and blood lipids. RESULTS Two contributions addressed QC and identified large statistical differences with pretreatment and posttreatment DNA methylation, possibly a result of batch effects. Two contributions compared epigenome-wide heritability estimates pretreatment and posttreatment, with one employing a Bayesian LME and the other using a variance-component LME. Density curves comparing these studies indicated these heritability estimates were similar. Another contribution used a variance-component LME to depict the proportion of heritability resulting from a genetic and shared environment. By including environmental exposures as random effects, the authors found heritability estimates became more stable but not significantly different. Two contributions investigated treatment response. One estimated drug-associated methylation effects on triglyceride levels as the response, and identified 11 significant cytosine-phosphate-guanine (CpG) sites with or without adjusting for high-density lipoprotein. The second contribution performed weighted gene coexpression network analysis and identified 6 significant modules of at least 30 CpG sites, including 3 modules with topological differences pretreatment and posttreatment. CONCLUSIONS Four conclusions from this GAW20 working group are: (a) QC measures are an important consideration for EWAS studies that are investigating multiple time points or repeated measurements; (b) application of heritability estimates between time points for individual CpG sites is a useful QC measure for DNA methylation studies; (c) drug intervention demonstrated strong epigenome-wide DNA methylation patterns across the 2 time points; and (d) new statistical methods are required to account for the environmental contributions of DNA methylation across time. These contributions demonstrate numerous opportunities exist for the analysis of longitudinal data in future epigenetic studies.
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Affiliation(s)
- Haakon E. Nustad
- Department of Medical Genetics, Oslo University Hospital, Kirkeveien 166, 0450 Oslo, Norway
- Faculty of Medicine, University of Oslo, Klaus Torgårds vei 3, 0372 Oslo, Norway
- PharmaTox Strategic Research Initiative, University of Oslo, Sem Sælands vei 3, 0371 Oslo, Norway
| | - Marcio Almeida
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, One West University Blvd., STDOI Modular Building #100, Brownsville, TX 78520 USA
| | - Angelo J. Canty
- Department of Mathematics and Statistics, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4K1 Canada
| | - Marissa LeBlanc
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Klaus Torgårds vei 3, 0372 Oslo, Norway
| | - Christian M. Page
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Klaus Torgårds vei 3, 0372 Oslo, Norway
- Department of Non-communicable disease, Norwegian Institute of Public Health, Marcus Thranes Gate 6, 0473 Oslo, Norway
| | - Phillip E. Melton
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Pharmacy and Biomedical Sciences, Curtin University and the University of Western Australia, 35 Stirling Hwy. (M409), Crawley, WA 6009 Australia
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26
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Radwan H, Hashim M, Shaker Obaid R, Hasan H, Naja F, Al Ghazal H, Jan Jan Mohamed H, Rizk R, Al Hilali M, Rayess R, Izzaldin G. The Mother-Infant Study Cohort (MISC): Methodology, challenges, and baseline characteristics. PLoS One 2018; 13:e0198278. [PMID: 29851999 PMCID: PMC5978878 DOI: 10.1371/journal.pone.0198278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/16/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The United Arab Emirates (UAE) exhibits alarming high prevalence of Non-Communicable Diseases (NCDs) and their risk factors. Emerging evidence highlighted the role of maternal and early child nutrition in preventing later-onset NCDs. The objectives of this article are to describe the design and methodology of the first Mother and Infant Study Cohort (MISC) in UAE; present the baseline demographic characteristics of the study participants; and discuss the challenges of the cohort and their respective responding strategies. METHODS The MISC is an ongoing two-year prospective cohort study which recruited Arab pregnant women in their third trimester from prenatal clinics in Dubai, Sharjah and Ajman. Participants will be interviewed six times (once during pregnancy, at delivery, and at 2, 6, 12 and 24months postpartum). Perinatal information is obtained from hospital records. Collected data include socio-demographic characteristics, lifestyle, dietary intake and anthropometry; infant feeding practices, cognitive development; along with maternal and infant blood profile and breast milk profile. RESULTS The preliminary results reported that 256 completed baseline assessment (mean age: 30.5±6.0 years; 76.6% multiparous; about 60% were either overweight or obese before pregnancy). The prevalence of gestational diabetes was 19.2%. Upon delivery, 208 women-infant pairs were retained (mean gestational age: 38.5±1.5 weeks; 33.3% caesarean section delivery; 5.3% low birthweight; 5.7% macrosomic deliveries). Besides participant retention, the main encountered challenges pertained to cultural complexity, underestimation the necessary start-up time, staff, and costs, and biochemical data collection. CONCLUSIONS Despite numerous methodological, logistical and sociocultural challenges, satisfactory follow-up rates are recorded. Strategies addressing challenges are documented, providing information for planning and implementing future birth cohort studies locally and internationally.
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Affiliation(s)
- Hadia Radwan
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Mona Hashim
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Reyad Shaker Obaid
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Hayder Hasan
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Farah Naja
- Department of Nutrition and Food Sciences, American University of Beirut, Beirut, Lebanon
| | - Hessa Al Ghazal
- Family Health Promotion Center, Sharjah, United Arab Emirates
| | | | - Rana Rizk
- Department of Health Services Research, Maastricht University, Maastricht, The Netherlands
- Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie (INSPECT-LB), The Lebanese University, Beirut, Lebanon
| | - Marwa Al Hilali
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Rana Rayess
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
| | - Ghamra Izzaldin
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, Research Institute of Medical and Health Sciences(RIMHS), University of Sharjah, Sharjah, United Arab Emirates
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Maud C, Ryan J, McIntosh JE, Olsson CA. The role of oxytocin receptor gene (OXTR) DNA methylation (DNAm) in human social and emotional functioning: a systematic narrative review. BMC Psychiatry 2018; 18:154. [PMID: 29843655 PMCID: PMC5975530 DOI: 10.1186/s12888-018-1740-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/11/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The neuropeptide Oxytocin (OXT) plays a central role in birthing, mother-infant bonding and a broad range of related social behaviours in mammals. More recently, interest has extended to epigenetic programming of genes involved in oxytocinergic neurotransmission. This review brings together early findings in a rapidly developing field of research, examining relationships between DNA methylation (DNAm) of the Oxytocin Receptor Gene (OXTR) and social and emotional behaviour in human populations. METHOD A systematic search across Web of Knowledge/Science, Scopus, Medline and EMBASE captured all published studies prior to June 2017 examining the association between OXTR DNAm and human social and emotional outcomes. Search terms included 'oxytocin gene' or 'oxytocin receptor gene' and 'epigenetics' or 'DNA methylation'. Any article with a focus on social and emotional functioning was then identified from this set by manual review. RESULTS Nineteen studies met eligibility criteria. There was considerable heterogeneity of study populations, tissue samples, instrumentation, measurement, and OXTR site foci. Only three studies examined functional consequences of OXTR DNAm on gene expression and protein synthesis. Increases in OXTR DNAm were associated with callous-unemotional traits in youth, social cognitive deficits in Autistic Spectrum Disorder (ASD), rigid thinking in anorexia nervosa, affect regulation problems, and problems with facial and emotional recognition. In contrast, reductions in DNAm were associated with perinatal stress, postnatal depression, social anxiety and autism in children. CONCLUSIONS Consistent with an emerging field of inquiry, there is not yet sufficient evidence to draw conclusions about the role of OXTR DNAm in human social and emotional behaviour. However, taken together, findings point to increased OXTR DNAm in general impairments in social, cognitive and emotional functioning, and decreased OXTR DNAm in specific patterns of impairment related to mood and anxiety disorders (but not in all). Future progress in this field would be enhanced by adequately powered designs, greater phenotypic precision, and methodological improvements including longitudinal studies with multiple time-points to facilitate causal inference.
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Affiliation(s)
- Catherine Maud
- Deakin University Geelong, Centre for Social and Early Emotional Development, Faculty of Health, School of Psychology, 221 Burwood Highway, Burwood, VIC, 3125, Australia.
| | - Joanne Ryan
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia.,Department of Epidemiology and Preventative Medicine, School of Public Health and Preventative Medicine, Monash University, Prahran, VIC, 3004, Australia
| | - Jennifer E McIntosh
- Deakin University Geelong, Centre for Social and Early Emotional Development, Faculty of Health, School of Psychology, 221 Burwood Highway, Burwood, VIC, 3125, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia
| | - Craig A Olsson
- Deakin University Geelong, Centre for Social and Early Emotional Development, Faculty of Health, School of Psychology, 221 Burwood Highway, Burwood, VIC, 3125, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, 3052, Australia
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28
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Bae JM. Interpretation of the hygiene and microflora hypothesis for allergic diseases through epigenetic epidemiology. Epidemiol Health 2018; 40:e2018006. [PMID: 29587338 PMCID: PMC5968202 DOI: 10.4178/epih.e2018006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/10/2018] [Indexed: 01/08/2023] Open
Abstract
The hygiene hypothesis (HH) proposed by Strachan in 1989 was expanded to explain the inverse association between the occurrence of allergy disorders and the risk of infectious diseases and parasite infestation. The microflora hypothesis (MH) suggests that gut microbial dysbiosis in early life might trigger hypersensitivity disorders. The sharing concept of both HH and MH is gene-environment interaction, which is also a key concept in epigenetics. The amalgamation of epidemiology and epigenetics has created a scientific discipline termed epigenetic epidemiology. To accomplish an era of gene-environment-wide interaction studies, it is necessary to launch a national human epigenome project.
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Affiliation(s)
- Jong-Myon Bae
- Department of Preventive Medicine, Jeju National University School of Medicine, Jeju, Korea
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29
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Herceg Z, Ghantous A, Wild CP, Sklias A, Casati L, Duthie SJ, Fry R, Issa JP, Kellermayer R, Koturbash I, Kondo Y, Lepeule J, Lima SC, Marsit CJ, Rakyan V, Saffery R, Taylor JA, Teschendorff AE, Ushijima T, Vineis P, Walker CL, Waterland RA, Wiemels J, Ambatipudi S, Esposti DD, Hernandez-Vargas H. Roadmap for investigating epigenome deregulation and environmental origins of cancer. Int J Cancer 2018; 142:874-882. [PMID: 28836271 PMCID: PMC6027626 DOI: 10.1002/ijc.31014] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/25/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022]
Abstract
The interaction between the (epi)genetic makeup of an individual and his/her environmental exposure record (exposome) is accepted as a determinant factor for a significant proportion of human malignancies. Recent evidence has highlighted the key role of epigenetic mechanisms in mediating gene-environment interactions and translating exposures into tumorigenesis. There is also growing evidence that epigenetic changes may be risk factor-specific ("fingerprints") that should prove instrumental in the discovery of new biomarkers in cancer. Here, we review the state of the science of epigenetics associated with environmental stimuli and cancer risk, highlighting key developments in the field. Critical knowledge gaps and research needs are discussed and advances in epigenomics that may help in understanding the functional relevance of epigenetic alterations. Key elements required for causality inferences linking epigenetic changes to exposure and cancer are discussed and how these alterations can be incorporated in carcinogen evaluation and in understanding mechanisms underlying epigenome deregulation by the environment.
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Affiliation(s)
- Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Christopher P. Wild
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Athena Sklias
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Lavinia Casati
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Susan J. Duthie
- School of Pharmacy and Life Sciences, The Robert Gordon University, Aberdeen, United Kingdom
| | - Rebecca Fry
- Gillings School of Global Public Health, UNC, Chapel Hill, NC
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research & Molecular Biology, Philadelphia, PA
| | | | | | - Yukata Kondo
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | | | | | - Vardhman Rakyan
- Centre for Genomics and Child Health, Blizard Institute, London, United Kingdom
| | | | | | - Andrew E. Teschendorff
- Statistical Cancer Genomics, UCL Cancer Institute & Dept. of Woman’s Cancer, University College London, United Kingdom
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China
| | | | - Paolo Vineis
- MRC/PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Cheryl Lyn Walker
- Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX
| | - Robert A. Waterland
- Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX
| | - Joe Wiemels
- UCSF School of Medicine, Epidemiology & Biostatistics, San Francisco, CA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Davide Degli Esposti
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, Lyon 69008, France
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30
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Lea AJ, Tung J, Archie EA, Alberts SC. Developmental plasticity: Bridging research in evolution and human health. Evol Med Public Health 2018; 2017:162-175. [PMID: 29424834 PMCID: PMC5798083 DOI: 10.1093/emph/eox019] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023] Open
Abstract
Early life experiences can have profound and persistent effects on traits expressed throughout the life course, with consequences for later life behavior, disease risk, and mortality rates. The shaping of later life traits by early life environments, known as 'developmental plasticity', has been well-documented in humans and non-human animals, and has consequently captured the attention of both evolutionary biologists and researchers studying human health. Importantly, the parallel significance of developmental plasticity across multiple fields presents a timely opportunity to build a comprehensive understanding of this phenomenon. We aim to facilitate this goal by highlighting key outstanding questions shared by both evolutionary and health researchers, and by identifying theory and empirical work from both research traditions that is designed to address these questions. Specifically, we focus on: (i) evolutionary explanations for developmental plasticity, (ii) the genetics of developmental plasticity and (iii) the molecular mechanisms that mediate developmental plasticity. In each section, we emphasize the conceptual gains in human health and evolutionary biology that would follow from filling current knowledge gaps using interdisciplinary approaches. We encourage researchers interested in developmental plasticity to evaluate their own work in light of research from diverse fields, with the ultimate goal of establishing a cross-disciplinary understanding of developmental plasticity.
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Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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31
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A pilot study to understand feasibility and acceptability of stool and cord blood sample collection for a large-scale longitudinal birth cohort. BMC Pregnancy Childbirth 2017; 17:439. [PMID: 29282072 PMCID: PMC5745976 DOI: 10.1186/s12884-017-1627-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 12/13/2017] [Indexed: 12/24/2022] Open
Abstract
Background Few data are available to guide biological sample collection around the time of birth for large-scale birth cohorts. We are designing a large UK birth cohort to investigate the role of infection and the developing immune system in determining future health and disease. We undertook a pilot to develop methodology for the main study, gain practical experience of collecting samples, and understand the acceptability of sample collection to women in late pregnancy. Methods Between February–July 2014, we piloted the feasibility and acceptability of collecting maternal stool, baby stool and cord blood samples from participants recruited at prolonged pregnancy and planned pre-labour caesarean section clinics at University College London Hospital. Participating women were asked to complete acceptability questionnaires. Results Overall, 265 women were approached and 171 (65%) participated, with ≥1 sample collected from 113 women or their baby (66%). Women had a mean age of 34 years, were primarily of white ethnicity (130/166, 78%), and half were nulliparous (86/169, 51%). Women undergoing planned pre-labour caesarean section were more likely than those who delivered vaginally to provide ≥1 sample (98% vs 54%), but less likely to provide maternal stool (10% vs 43%). Pre-sample questionnaires were completed by 110/171 women (64%). Most women reported feeling comfortable with samples being collected from their baby (<10% uncomfortable), but were less comfortable about their own stool (19% uncomfortable) or a vaginal swab (24% uncomfortable). Conclusions It is possible to collect a range of biological samples from women around the time of delivery, and this was acceptable for most women. These data inform study design and protocol development for large-scale birth cohorts. Electronic supplementary material The online version of this article (10.1186/s12884-017-1627-7) contains supplementary material, which is available to authorized users.
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Wilson R, Wahl S, Pfeiffer L, Ward-Caviness CK, Kunze S, Kretschmer A, Reischl E, Peters A, Gieger C, Waldenberger M. The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers. BMC Genomics 2017; 18:805. [PMID: 29047347 PMCID: PMC6389045 DOI: 10.1186/s12864-017-4198-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking. Results Our results indicate that after quitting smoking the most rapid reversion of altered methylation occurs within the first two decades, with reversion rates related to the initial differences in methylation. For 52 CpG sites, the change in methylation from baseline to follow-up is significantly different for former smokers relative to the change for never smokers (lowest p-value 3.61 x 10-39 for cg26703534, gene AHRR). Most of these sites’ respective regions have been previously implicated in smoking-associated diseases. Despite the early rapid change, dynamism of methylation appears greater in former smokers vs never smokers even four decades after cessation. Furthermore, our study reveals the heterogeneous effect of continued smoking: the methylation levels of some loci further diverge between smokers and non-smokers, while others re-approach. Though intensity of smoking habit appears more significant than duration, results remain inconclusive. Conclusions This study improves the understanding of the dynamic link between cigarette smoking and methylation, revealing the continued fluctuation of methylation levels decades after smoking cessation and demonstrating that continuing smoking can have an array of effects. The results can facilitate insights into the molecular mechanisms behind smoking-induced disturbed methylation, improving the possibility for development of biomarkers of past smoking behavior and increasing the understanding of the molecular path from exposure to disease. Electronic supplementary material The online version of this article (10.1186/s12864-017-4198-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany. .,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany. .,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit Molecular Epidemiology (AME), Ingolstädter Landstr. 1, D-85764, Neuherberg, Germany.
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,German Center for Diabetes Research (DZD e.V.), München-Neuherberg, Bavaria, Germany
| | - Liliane Pfeiffer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Cavin K Ward-Caviness
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Environmental Public Health Division, US Environmental Protection Agency, Chapel Hill, NC, 27514, USA
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Bavaria, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,German Center for Diabetes Research (DZD e.V.), München-Neuherberg, Bavaria, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany
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Sweatt JD, Tamminga CA. An epigenomics approach to individual differences and its translation to neuropsychiatric conditions. DIALOGUES IN CLINICAL NEUROSCIENCE 2017. [PMID: 27757063 PMCID: PMC5067146 DOI: 10.31887/dcns.2016.18.3/dsweatt] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review concerns epigenetic mechanisms and their roles in conferring interindividual differences, especially as related to experientially acquired and genetically driven changes in central nervous system (CNS) function. In addition, the review contains commentary regarding the possible ways in which epigenomic changes may contribute to neuropsychiatric conditions and disorders and ways in which epigenotyping might be cross-correlated with clinical phenotyping in the context of precision medicine. The review begins with a basic description of epigenetic marking in the CNS and how these changes are powerful regulators of gene readout. Means for characterizing the individual epigenotype are briefly described, with a focus on DNA cytosine methylation as a readily measurable, stable epigenetic mark. This background enables a discussion of how “epigenotyping” might be integrated along with genotyping and deep phenotyping as a means of implementing advanced precision medicine. Finally, the commentary addresses two exemplars when considering how epigenotype may correlate with and modulate cognitive and behavioral phenotype: schizophrenia and Rett syndrome. These two disorders provide an interesting compare-and-contrast example regarding possible epigenotypic regulation of behavior: whereas Rett syndrome is clearly established as being caused by disruption of the function of an epigenetic “reader” of the DNA cytosine methylome—methyl-CpG-binding protein 2 (MeCP2)—the case for a role for epigenetic mechanisms in schizophrenia is still quite speculative.
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Affiliation(s)
- J David Sweatt
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Hartwig FP, Loret de Mola C, Davies NM, Victora CG, Relton CL. Breastfeeding effects on DNA methylation in the offspring: A systematic literature review. PLoS One 2017; 12:e0173070. [PMID: 28257446 PMCID: PMC5336253 DOI: 10.1371/journal.pone.0173070] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/14/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breastfeeding benefits both infants and mothers. Recent research shows long-term health and human capital benefits among individuals who were breastfed. Epigenetic mechanisms have been suggested as potential mediators of the effects of early-life exposures on later health outcomes. We reviewed the literature on the potential effects of breastfeeding on DNA methylation. METHODS Studies reporting original results and evaluating DNA methylation differences according to breastfeeding/breast milk groups (e.g., ever vs. never comparisons, different categories of breastfeeding duration, etc) were eligible. Six databases were searched simultaneously using Ovid, and the resulting studies were evaluated independently by two reviewers. RESULTS Seven eligible studies were identified. Five were conducted in humans. Studies were heterogeneous regarding sample selection, age, target methylation regions, methylation measurement and breastfeeding categorisation. Collectively, the studies suggest that breastfeeding might be negatively associated with promoter methylation of LEP (which encodes an anorexigenic hormone), CDKN2A (involved in tumour suppression) and Slc2a4 genes (which encodes an insulin-related glucose transporter) and positively with promoter methylation of the Nyp (which encodes an orexigenic neuropeptide) gene, as well as influence global methylation patterns and modulate epigenetic effects of some genetic variants. CONCLUSIONS The findings from our systematic review are far from conclusive due to the small number of studies and their inherent limitations. Further studies are required to understand the actual potential role of epigenetics in the associations of breastfeeding with later health outcomes. Suggestions for future investigations, focusing on epigenome-wide association studies, are provided.
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Affiliation(s)
- Fernando Pires Hartwig
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | | | - Neil Martin Davies
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
| | - Cesar Gomes Victora
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
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Mode of delivery affected questionnaire response rates in a birth cohort study. J Clin Epidemiol 2016; 81:64-71. [PMID: 27663611 PMCID: PMC5323059 DOI: 10.1016/j.jclinepi.2016.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/30/2016] [Accepted: 09/09/2016] [Indexed: 11/26/2022]
Abstract
Objectives Cohort studies must collect data from their participants as economically as possible, while maintaining response rates. This randomized controlled trial investigated whether offering a choice of online or paper questionnaires resulted in improved response rates compared with offering online first. Study Design and Setting Eligible participants were young people in the Avon Longitudinal Study of Parents and Children (ALSPAC) study (born April 1, 1991, to December 31, 1992, in the Avon area). After exclusions, 8,795 participants were randomized. The “online first” group were invited to complete the questionnaire online. The “choice” group were also sent a paper questionnaire and offered a choice of completion method. The trial was embedded within routine data collection. The main outcome measure was the number of questionnaires returned. Data on costs were also collected. Results Those in the “online first” arm of the trial were less likely to return a questionnaire [adjusted odds ratio: 0.90; 95% confidence interval (CI): 0.82, 0.99]. The “choice” arm was more expensive (mean difference per participant £0.71; 95% CI: £0.65, £0.76). It cost an extra £47 to have one extra person to complete the questionnaire in the “choice” arm. Conclusion Offering a choice of completion methods (paper or online) for questionnaires in ALSPAC increased response rates but was more expensive than offering online first.
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Ferrucci L, Cooper R, Shardell M, Simonsick EM, Schrack JA, Kuh D. Age-Related Change in Mobility: Perspectives From Life Course Epidemiology and Geroscience. J Gerontol A Biol Sci Med Sci 2016; 71:1184-94. [PMID: 26975983 PMCID: PMC4978365 DOI: 10.1093/gerona/glw043] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/19/2016] [Indexed: 12/18/2022] Open
Abstract
Mobility is the most studied and most relevant physical ability affecting quality of life with strong prognostic value for disability and survival. Natural selection has built the "engine" of mobility with great robustness, redundancy, and functional reserve. Efficient patterns of mobility can be acquired during development even by children affected by severe impairments. Analogously, age-associated impairments in mobility-related physiological systems are compensated and overt limitations of mobility only occur when the severity can no longer be compensated. Mobility loss in older persons usually results from multiple impairments in the central nervous system, muscles, joints, and energetic and sensory physiological systems. Early preclinical changes in these physiological systems that precede mobility loss have been poorly studied. Peak performance, rate of decline, compensatory behaviors, or subclinical deterioration of physiological resources may cumulatively influence both timing of mobility loss and chances of recovery, but their role as risk factors has not been adequately characterized. Understanding the natural history of these early changes and intervening on them would likely be the most effective strategy to reduce the burden of disability in the population. For example, young women with low bone peak mass could be counseled to start strength resistance exercise to reduce their high risk of developing osteoporosis and fracture later in life. Expanding this approach to other physiological domains requires collecting and interpreting data from life course epidemiological studies, establishing normative measures of mobility, physical function, and physical activity, and connecting them with life course trajectories of the mobility-relevant physiological domains.
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Affiliation(s)
| | - Rachel Cooper
- Medical Research Council Unit for Lifelong Health and Ageing at UCL, London, UK
| | | | | | - Jennifer A Schrack
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Diana Kuh
- Medical Research Council Unit for Lifelong Health and Ageing at UCL, London, UK
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Pan H, Holbrook JD, Karnani N, Kwoh CK. Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment. BMC Bioinformatics 2016; 17:299. [PMID: 27480116 PMCID: PMC4970299 DOI: 10.1186/s12859-016-1161-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/21/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The interplay among genetic, environment and epigenetic variation is not fully understood. Advances in high-throughput genotyping methods, high-density DNA methylation detection and well-characterized sample collections, enable epigenetic association studies at the genomic and population levels (EWAS). The field has extended to interrogate the interaction of environmental and genetic (GxE) influences on epigenetic variation. Also, the detection of methylation quantitative trait loci (methQTLs) and their association with health status has enhanced our knowledge of epigenetic mechanisms in disease trajectory. However analysis of this type of data brings computational challenges and there are few practical solutions to enable large scale studies in standard computational environments. RESULTS GEM is a highly efficient R tool suite for performing epigenome wide association studies (EWAS). GEM provides three major functions named GEM_Emodel, GEM_Gmodel and GEM_GxEmodel to study the interplay of Gene, Environment and Methylation (GEM). Within GEM, the pre-existing "Matrix eQTL" package is utilized and extended to study methylation quantitative trait loci (methQTL) and the interaction of genotype and environment (GxE) to determine DNA methylation variation, using matrix based iterative correlation and memory-efficient data analysis. Benchmarking presented here on a publicly available dataset, demonstrated that GEM can facilitate reliable genome-wide methQTL and GxE analysis on a standard laptop computer within minutes. CONCLUSIONS The GEM package facilitates efficient EWAS study in large cohorts. It is written in R code and can be freely downloaded from Bioconductor at https://www.bioconductor.org/packages/GEM/ .
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Affiliation(s)
- Hong Pan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), Singapore, 117609, Singapore.,School of Computer Science and Engineering, Nanyang Technological University (NTU), Singapore, 639798, Singapore
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), Singapore, 117609, Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), Singapore, 117609, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 119228, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University (NTU), Singapore, 639798, Singapore.
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Lin X, Barton S, Holbrook JD. How to make DNA methylome wide association studies more powerful. Epigenomics 2016; 8:1117-29. [PMID: 27052998 PMCID: PMC5066141 DOI: 10.2217/epi-2016-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/23/2016] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies had a troublesome adolescence, while researchers increased statistical power, in part by increasing subject numbers. Interrogating the interaction of genetic and environmental influences raised new challenges of statistical power, which were not easily bested by the addition of subjects. Screening the DNA methylome offers an attractive alternative as methylation can be thought of as a proxy for the combined influences of genetics and environment. There are statistical challenges unique to DNA methylome data and also multiple features, which can be exploited to increase power. We anticipate the development of DNA methylome association study designs and new analytical methods, together with integration of data from other molecular species and other studies, which will boost statistical power and tackle causality. In this way, the molecular trajectories that underlie disease development will be uncovered.
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Affiliation(s)
- Xinyi Lin
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences (SICS), Agency for Science & Technology Research (A*STAR), Brenner Centre for Molecular Medicine, 30 Medical Drive, 117609, Singapore
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Ben-Shlomo Y, Cooper R, Kuh D. The last two decades of life course epidemiology, and its relevance for research on ageing. Int J Epidemiol 2016; 45:973-988. [PMID: 27880685 PMCID: PMC5841628 DOI: 10.1093/ije/dyw096] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2016] [Indexed: 12/11/2022] Open
Affiliation(s)
- Yoav Ben-Shlomo
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Rachel Cooper
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
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40
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Doan SN, Tardif T, Miller A, Olson S, Kessler D, Felt B, Wang L. Consequences of 'tiger' parenting: a cross-cultural study of maternal psychological control and children's cortisol stress response. Dev Sci 2016; 20. [PMID: 27146549 DOI: 10.1111/desc.12404] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/22/2015] [Indexed: 11/28/2022]
Abstract
Parenting strategies involving psychological control are associated with increased adjustment problems in children. However, no research has examined the extent to which culture and psychological control predict children's stress physiology. We examine cultural differences in maternal psychological control and its associations with children's cortisol. Chinese (N = 59) and American (N = 45) mother-child dyads participated in the study. Mothers reported on psychological control. Children's cortisol was collected during a stressor and two indices of Area Under the Curve (AUC) were computed: AUCg which accounts for total output, and AUCi, which captures reactivity. Results indicate that Chinese mothers reported higher levels of psychological control and Chinese children had higher levels of AUCg than their American counterparts. Across both cultures, psychological control was significantly associated with increased cortisol levels as indexed by AUCg. There were no associations for AUCi. Finally, mediation analyses demonstrated that psychological control fully explained cultural differences in children's cortisol stress response as indexed by AUCg.
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Affiliation(s)
- Stacey N Doan
- Department of Psychology, Claremont McKenna College, USA
| | - Twila Tardif
- School of Public Health, University of Michigan, USA
| | - Alison Miller
- Department of Psychology, University of Michigan, USA
| | - Sheryl Olson
- School of Public Health, University of Michigan, USA
| | - Daniel Kessler
- Departments of Psychiatry and Philosophy, University of Michigan, USA
| | - Barbara Felt
- Department of Pediatrics and Communicable Diseases, University of Michigan, USA
| | - Li Wang
- Department of Psychology and Beijing Key Laboratory of Behavior and Mental Health, Peking University, China
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Richmond RC, Sharp GC, Ward ME, Fraser A, Lyttleton O, McArdle WL, Ring SM, Gaunt TR, Lawlor DA, Davey Smith G, Relton CL. DNA Methylation and BMI: Investigating Identified Methylation Sites at HIF3A in a Causal Framework. Diabetes 2016; 65:1231-44. [PMID: 26861784 PMCID: PMC4839211 DOI: 10.2337/db15-0996] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 02/01/2016] [Indexed: 12/18/2022]
Abstract
Multiple differentially methylated sites and regions associated with adiposity have now been identified in large-scale cross-sectional studies. We tested for replication of associations between previously identified CpG sites at HIF3A and adiposity in ∼1,000 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC). Availability of methylation and adiposity measures at multiple time points, as well as genetic data, allowed us to assess the temporal associations between adiposity and methylation and to make inferences regarding causality and directionality. Overall, our results were discordant with those expected if HIF3A methylation has a causal effect on BMI and provided more evidence for causality in the reverse direction (i.e., an effect of BMI on HIF3A methylation). These results are based on robust evidence from longitudinal analyses and were also partially supported by Mendelian randomization analysis, although this latter analysis was underpowered to detect a causal effect of BMI on HIF3A methylation. Our results also highlight an apparent long-lasting intergenerational influence of maternal BMI on offspring methylation at this locus, which may confound associations between own adiposity and HIF3A methylation. Further work is required to replicate and uncover the mechanisms underlying the direct and intergenerational effect of adiposity on DNA methylation.
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Affiliation(s)
- Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K.
| | - Mary E Ward
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Abigail Fraser
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Oliver Lyttleton
- School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Susan M Ring
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Tom R Gaunt
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Debbie A Lawlor
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, U.K. School of Social and Community Medicine, University of Bristol, Bristol, U.K. Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, U.K
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Zhong J, Agha G, Baccarelli AA. The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies. Circ Res 2016; 118:119-131. [PMID: 26837743 DOI: 10.1161/circresaha.115.305206] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/01/2015] [Indexed: 01/14/2023]
Abstract
Epidemiological studies have demonstrated that genetic, environmental, behavioral, and clinical factors contribute to cardiovascular disease development. How these risk factors interact at the cellular level to cause cardiovascular disease is not well known. Epigenetic epidemiology enables researchers to explore critical links between genomic coding, modifiable exposures, and manifestation of disease phenotype. One epigenetic link, DNA methylation, is potentially an important mechanism underlying these associations. In the past decade, there has been a significant increase in the number of epidemiological studies investigating cardiovascular risk factors and outcomes in relation to DNA methylation, but many gaps remain in our understanding of the underlying cause and biological implications. In this review, we provide a brief overview of the biology and mechanisms of DNA methylation and its role in cardiovascular disease. In addition, we summarize the current evidence base in epigenetic epidemiology studies relevant to cardiovascular health and disease and discuss the limitations, challenges, and future directions of the field. Finally, we provide guidelines for well-designed epigenetic epidemiology studies, with particular focus on methodological aspects, study design, and analytical challenges.
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Affiliation(s)
- Jia Zhong
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Golareh Agha
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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43
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Assessment of Offspring DNA Methylation across the Lifecourse Associated with Prenatal Maternal Smoking Using Bayesian Mixture Modelling. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:14461-76. [PMID: 26580635 PMCID: PMC4661660 DOI: 10.3390/ijerph121114461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/02/2022]
Abstract
A growing body of research has implicated DNA methylation as a potential mediator of the effects of maternal smoking in pregnancy on offspring ill-health. Data were available from a UK birth cohort of children with DNA methylation measured at birth, age 7 and 17. One issue when analysing genome-wide DNA methylation data is the correlation of methylation levels between CpG sites, though this can be crudely bypassed using a data reduction method. In this manuscript we investigate the effect of sustained maternal smoking in pregnancy on longitudinal DNA methylation in their offspring using a Bayesian hierarchical mixture model. This model avoids the data reduction used in previous analyses. Four of the 28 previously identified, smoking related CpG sites were shown to have offspring methylation related to maternal smoking using this method, replicating findings in well-known smoking related genes MYO1G and GFI1. Further weak associations were found at the AHRR and CYP1A1 loci. In conclusion, we have demonstrated the utility of the Bayesian mixture model method for investigation of longitudinal DNA methylation data and this method should be considered for use in whole genome applications.
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44
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Klijn SL, Weijenberg MP, Lemmens P, van den Brandt PA, Lima Passos V. Introducing the fit-criteria assessment plot - A visualisation tool to assist class enumeration in group-based trajectory modelling. Stat Methods Med Res 2015; 26:2424-2436. [PMID: 26265768 DOI: 10.1177/0962280215598665] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background and objective Group-based trajectory modelling is a model-based clustering technique applied for the identification of latent patterns of temporal changes. Despite its manifold applications in clinical and health sciences, potential problems of the model selection procedure are often overlooked. The choice of the number of latent trajectories (class-enumeration), for instance, is to a large degree based on statistical criteria that are not fail-safe. Moreover, the process as a whole is not transparent. To facilitate class enumeration, we introduce a graphical summary display of several fit and model adequacy criteria, the fit-criteria assessment plot. Methods An R-code that accepts universal data input is presented. The programme condenses relevant group-based trajectory modelling output information of model fit indices in automated graphical displays. Examples based on real and simulated data are provided to illustrate, assess and validate fit-criteria assessment plot's utility. Results Fit-criteria assessment plot provides an overview of fit criteria on a single page, placing users in an informed position to make a decision. Fit-criteria assessment plot does not automatically select the most appropriate model but eases the model assessment procedure. Conclusions Fit-criteria assessment plot is an exploratory, visualisation tool that can be employed to assist decisions in the initial and decisive phase of group-based trajectory modelling analysis. Considering group-based trajectory modelling's widespread resonance in medical and epidemiological sciences, a more comprehensive, easily interpretable and transparent display of the iterative process of class enumeration may foster group-based trajectory modelling's adequate use.
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Affiliation(s)
- Sven L Klijn
- 1 Department of Methodology and Statistics, Maastricht University, Maastricht, the Netherlands
| | - Matty P Weijenberg
- 2 Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht, the Netherlands
| | - Paul Lemmens
- 3 Department of Health Promotion, Maastricht, the Netherlands
| | - Piet A van den Brandt
- 4 Department of Epidemiology, GROW School for Oncology and Developmental Biology, CAPHRI School for Public Health and Primary Care, Maastricht University, Maastricht, the Netherlands
| | - Valéria Lima Passos
- 1 Department of Methodology and Statistics, Maastricht University, Maastricht, the Netherlands
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45
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Relton CL, Hartwig FP, Davey Smith G. From stem cells to the law courts: DNA methylation, the forensic epigenome and the possibility of a biosocial archive. Int J Epidemiol 2015; 44:1083-93. [PMID: 26424516 PMCID: PMC5279868 DOI: 10.1093/ije/dyv198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The growth in epigenetics continues to attract considerable cross-disciplinary interest, apparently representing an opportunity to move beyond genomics towards the goal of understanding phenotypic variability from molecular through organismal to the societal level. The epigenome may also harbour useful information about life-time exposures (measured or unmeasured) irrespective of their influence on health or disease, creating the potential for a person-specific biosocial archive . Furthermore such data may prove of use in providing identifying information, providing the possibility of a future forensic epigenome . The mechanisms involved in ensuring that environmentally induced epigenetic changes perpetuate across the life course remain unclear. Here we propose a potential role of adult stem cells in maintaining epigenetic states provides a useful basis for formulating such epidemiologically-relevant concepts.
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Affiliation(s)
- Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | | | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
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46
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Affiliation(s)
- Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Room 109, The Mount, 9 Jubilee Road, Parktown, 2050, Gauteng, Johannesburg, South Africa
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47
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Silver MJ, Kessler NJ, Hennig BJ, Dominguez-Salas P, Laritsky E, Baker MS, Coarfa C, Hernandez-Vargas H, Castelino JM, Routledge MN, Gong YY, Herceg Z, Lee YS, Lee K, Moore SE, Fulford AJ, Prentice AM, Waterland RA. Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment. Genome Biol 2015; 16:118. [PMID: 26062908 PMCID: PMC4464629 DOI: 10.1186/s13059-015-0660-y] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interindividual epigenetic variation that occurs systemically must be established prior to gastrulation in the very early embryo and, because it is systemic, can be assessed in easily biopsiable tissues. We employ two independent genome-wide approaches to search for such variants. RESULTS First, we screen for metastable epialleles by performing genomewide bisulfite sequencing in peripheral blood lymphocyte (PBL) and hair follicle DNA from two Caucasian adults. Second, we conduct a genomewide screen for genomic regions at which PBL DNA methylation is affected by season of conception in rural Gambia. Remarkably, both approaches identify the genomically imprinted VTRNA2-1 as a top environmentally responsive epiallele. We demonstrate systemic and stochastic interindividual variation in DNA methylation at the VTRNA2-1 differentially methylated region in healthy Caucasian and Asian adults and show, in rural Gambians, that periconceptional environment affects offspring VTRNA2-1 epigenotype, which is stable over at least 10 years. This unbiased screen also identifies over 100 additional candidate metastable epialleles, and shows that these are associated with cis genomic features including transposable elements. CONCLUSIONS The non-coding VTRNA2-1 transcript (also called nc886) is a putative tumor suppressor and modulator of innate immunity. Thus, these data indicating environmentally induced loss of imprinting at VTRNA2-1 constitute a plausible causal pathway linking early embryonic environment, epigenetic alteration, and human disease. More broadly, the list of candidate metastable epialleles provides a resource for future studies of epigenetic variation and human disease.
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Affiliation(s)
- Matt J Silver
- MRC International Nutrition Group at London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- MRC Keneba, MRC Unit, Atlantic Boulevard, Fajara, P. O. Box 273, Banjul, The Gambia.
| | - Noah J Kessler
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Branwen J Hennig
- MRC International Nutrition Group at London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- MRC Keneba, MRC Unit, Atlantic Boulevard, Fajara, P. O. Box 273, Banjul, The Gambia.
| | - Paula Dominguez-Salas
- Veterinary Epidemiology, Economics and Public Health Group, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, AL9 7TA, UK.
- International Livestock Research Institute, Old Naivasha Rd, Nairobi, 00100, Kenya.
| | - Eleonora Laritsky
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Maria S Baker
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Cristian Coarfa
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon, CEDEX 08, France.
| | | | | | - Yun Yun Gong
- Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon, CEDEX 08, France.
| | - Yong Sun Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA.
| | - Kwanbok Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA.
| | - Sophie E Moore
- MRC International Nutrition Group at London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- MRC Keneba, MRC Unit, Atlantic Boulevard, Fajara, P. O. Box 273, Banjul, The Gambia.
- MRC Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK.
| | - Anthony J Fulford
- MRC International Nutrition Group at London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- MRC Keneba, MRC Unit, Atlantic Boulevard, Fajara, P. O. Box 273, Banjul, The Gambia.
| | - Andrew M Prentice
- MRC International Nutrition Group at London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- MRC Keneba, MRC Unit, Atlantic Boulevard, Fajara, P. O. Box 273, Banjul, The Gambia.
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.
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Relton CL, Gaunt T, McArdle W, Ho K, Duggirala A, Shihab H, Woodward G, Lyttleton O, Evans DM, Reik W, Paul YL, Ficz G, Ozanne SE, Wipat A, Flanagan K, Lister A, Heijmans BT, Ring SM, Davey Smith G. Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES). Int J Epidemiol 2015; 44:1181-90. [PMID: 25991711 DOI: 10.1093/ije/dyv072] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Caroline L Relton
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK,
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Karen Ho
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Aparna Duggirala
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Hashem Shihab
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Geoff Woodward
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Oliver Lyttleton
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - David M Evans
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK, University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia
| | - Wolf Reik
- Babraham Institute, Cambridge, UK, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Gabriella Ficz
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Susan E Ozanne
- University of Cambridge Institute of Metabolic Sciences and MRC Metabolic Diseases Unit, Cambridge, UK
| | - Anil Wipat
- School of Computer Science, Newcastle University, Newcastle upon Tyne, UK and
| | - Keith Flanagan
- School of Computer Science, Newcastle University, Newcastle upon Tyne, UK and
| | - Allyson Lister
- School of Computer Science, Newcastle University, Newcastle upon Tyne, UK and
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, and School of Social and Community Medicine, University of Bristol, Bristol, UK
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49
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Richmond RC, Timpson NJ, Sørensen TIA. Exploring possible epigenetic mediation of early-life environmental exposures on adiposity and obesity development. Int J Epidemiol 2015; 44:1191-8. [PMID: 25953782 DOI: 10.1093/ije/dyv066] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark and Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, Copenhagen, Denmark
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50
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Pazin MJ. Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harb Protoc 2015; 2015:522-36. [PMID: 25762420 DOI: 10.1101/pdb.top084988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
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Affiliation(s)
- Michael J Pazin
- Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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