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Franco-O'Byrne D, Santamaría-García H, Migeot J, Ibáñez A. Emerging Theories of Allostatic-Interoceptive Overload in Neurodegeneration. Curr Top Behav Neurosci 2024. [PMID: 38637414 DOI: 10.1007/7854_2024_471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Recent integrative multilevel models offer novel insights into the etiology and course of neurodegenerative conditions. The predictive coding of allostatic-interoception theory posits that the brain adapts to environmental demands by modulating internal bodily signals through the allostatic-interoceptive system. Specifically, a domain-general allostatic-interoceptive network exerts adaptive physiological control by fine-tuning initial top-down predictions and bottom-up peripheral signaling. In this context, adequate adaptation implies the minimization of prediction errors thereby optimizing energy expenditure. Abnormalities in top-down interoceptive predictions or peripheral signaling can trigger allostatic overload states, ultimately leading to dysregulated interoceptive and bodily systems (endocrine, immunological, circulatory, etc.). In this context, environmental stress, social determinants of health, and harmful exposomes (i.e., the cumulative life-course exposition to different environmental stressors) may interact with physiological and genetic factors, dysregulating allostatic interoception and precipitating neurodegenerative processes. We review the allostatic-interoceptive overload framework across different neurodegenerative diseases, particularly in the behavioral variant frontotemporal dementia (bvFTD). We describe how concepts of allostasis and interoception could be integrated with principles of predictive coding to explain how the brain optimizes adaptive responses, while maintaining physiological stability through feedback loops with multiple organismic systems. Then, we introduce the model of allostatic-interoceptive overload of bvFTD and discuss its implications for the understanding of pathophysiological and neurocognitive abnormalities in multiple neurodegenerative conditions.
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Affiliation(s)
- Daniel Franco-O'Byrne
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Hernando Santamaría-García
- Global Brain Health Institute, University of California-San Francisco, San Francisco, CA, USA
- Trinity College Dublin, Dublin, Ireland
- Department of Psychiatry, Pontificia Universidad Javeriana, Bogotá, Colombia
- Center of Memory and Cognition Intellectus, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Joaquín Migeot
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Agustín Ibáñez
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile.
- Global Brain Health Institute, University of California-San Francisco, San Francisco, CA, USA.
- Trinity College Dublin, Dublin, Ireland.
- Cognitive Neuroscience Center (CNC), Universidad de San Andrés, Buenos Aires, Argentina.
- Trinity College Institute of Neuroscience (TCIN), Trinity College Dublin, Dublin, Ireland.
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Venkataraghavan S, Pankow JS, Boerwinkle E, Fornage M, Selvin E, Ray D. Epigenome-wide association study of incident type 2 diabetes in Black and White participants from the Atherosclerosis Risk in Communities Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.09.23293896. [PMID: 37609313 PMCID: PMC10441493 DOI: 10.1101/2023.08.09.23293896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
DNA methylation studies of incident type 2 diabetes in US populations are limited, and to our knowledge none included individuals of African descent living in the US. We performed an epigenome-wide association analysis of blood-based methylation levels at CpG sites with incident type 2 diabetes using Cox regression in 2,091 Black and 1,029 White individuals from the Atherosclerosis Risk in Communities study. At an epigenome-wide significance threshold of 10-7, we detected 7 novel diabetes-associated CpG sites in C1orf151 (cg05380846: HR= 0.89, p = 8.4 × 10-12), ZNF2 (cg01585592: HR= 0.88, p = 1.6 × 10-9), JPH3 (cg16696007: HR= 0.87, p = 7.8 × 10-9), GPX6 (cg02793507: HR= 0.85, p = 2.7 × 10-8 and cg00647063: HR= 1.20, p = 2.5 × 10-8), chr17q25 (cg16865890: HR= 0.8, p = 6.9 × 10-8), and chr11p15 (cg13738793: HR= 1.11, p = 7.7 × 10-8). The CpG sites at C1orf151, ZNF2, JPH3 and GPX6, were identified in Black adults, chr17q25 was identified in White adults, and chr11p15 was identified upon meta-analyzing the two groups. The CpG sites at JPH3 and GPX6 were likely associated with incident type 2 diabetes independent of BMI. All the CpG sites, except at JPH3, were likely consequences of elevated glucose at baseline. We additionally replicated known type 2 diabetes-associated CpG sites including cg19693031 at TXNIP, cg00574958 at CPT1A, cg16567056 at PLBC2, cg11024682 at SREBF1, cg08857797 at VPS25, and cg06500161 at ABCG1, 3 of which were replicated in Black adults at the epigenome-wide threshold. We observed modest increase in type 2 diabetes variance explained upon addition of the significantly associated CpG sites to a Cox model that included traditional type 2 diabetes risk factors and fasting glucose (increase from 26.2% to 30.5% in Black adults; increase from 36.9% to 39.4% in White adults). We examined if groups of proximal CpG sites were associated with incident type 2 diabetes using a gene-region specific and a gene-region agnostic differentially methylated region (DMR) analysis. Our DMR analyses revealed several clusters of significant CpG sites, including a DMR consisting of a previously discovered CpG site at ADCY7 and promoter regions of TP63 which were differentially methylated across all race groups. This study illustrates improved discovery of CpG sites/regions by leveraging both individual CpG site and DMR analyses in an unexplored population. Our findings include genes linked to diabetes in experimental studies (e.g., GPX6, JPH3, and TP63), and future gene-specific methylation studies could elucidate the link between genes, environment, and methylation in the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of American
| | - Eric Boerwinkle
- The UTHealth School of Public Health, Houston, Texas, United States of America
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Elizabeth Selvin
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology, & Clinical Research, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
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Huang JY. Complexity Epidemiology in Practice: A Tale of Two Simplicities. Epidemiology 2023; 34:515-519. [PMID: 37042975 DOI: 10.1097/ede.0000000000001623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Affiliation(s)
- Jonathan Yinhao Huang
- From the Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Center for Quantitative Medicine (CQM), Duke-NUS Medical School, Singapore, Singapore
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Abstract
Epigenetics has transformed our understanding of the molecular basis of complex diseases, including cardiovascular and metabolic disorders. This review offers a comprehensive overview of the current state of knowledge on epigenetic processes implicated in cardiovascular and metabolic diseases, highlighting the potential of DNA methylation as a precision medicine biomarker and examining the impact of social determinants of health, gut bacterial epigenomics, noncoding RNA, and epitranscriptomics on disease development and progression. We discuss challenges and barriers to advancing cardiometabolic epigenetics research, along with the opportunities for novel preventive strategies, targeted therapies, and personalized medicine approaches that may arise from a better understanding of epigenetic processes. Emerging technologies, such as single-cell sequencing and epigenetic editing, hold the potential to further enhance our ability to dissect the complex interplay between genetic, environmental, and lifestyle factors. To translate research findings into clinical practice, interdisciplinary collaborations, technical and ethical considerations, and accessibility of resources and knowledge are crucial. Ultimately, the field of epigenetics has the potential to revolutionize the way we approach cardiovascular and metabolic diseases, paving the way for precision medicine and personalized health care, and improving the lives of millions of individuals worldwide affected by these conditions.
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Affiliation(s)
- Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, New York (A.A.B.)
| | - José Ordovás
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, at Tufts University, Boston, MA (J.O.)
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain (J.O.)
- Consortium CIBERObn, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (J.O.)
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Rajaprakash M, Dean LT, Palmore M, Johnson SB, Kaufman J, Fallin DM, Ladd-Acosta C. DNA methylation signatures as biomarkers of socioeconomic position. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac027. [PMID: 36694711 PMCID: PMC9869656 DOI: 10.1093/eep/dvac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 11/22/2022] [Accepted: 12/13/2022] [Indexed: 06/12/2023]
Abstract
This review article provides a framework for the use of deoxyribonucleic acid (DNA) methylation (DNAm) biomarkers to study the biological embedding of socioeconomic position (SEP) and summarizes the latest developments in the area. It presents the emerging literature showing associations between individual- and neighborhood-level SEP exposures and DNAm across the life course. In contrast to questionnaire-based methods of assessing SEP, we suggest that DNAm biomarkers may offer an accessible metric to study questions about SEP and health outcomes, acting as a personal dosimeter of exposure. However, further work remains in standardizing SEP measures across studies and evaluating consistency across domains, tissue types, and time periods. Meta-analyses of epigenetic associations with SEP are offered as one approach to confirm the replication of DNAm loci across studies. The development of DNAm biomarkers of SEP would provide a method for examining its impact on health outcomes in a more robust way, increasing the rigor of epidemiological studies.
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Affiliation(s)
- Meghna Rajaprakash
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lorraine T Dean
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Meredith Palmore
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sara B Johnson
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Joan Kaufman
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniele M Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Zhang W, Li Y, Li Y, Zheng K, Zou S, Jia X, Yang H. Genetically predicted higher educational attainment decreases the risk of stroke: a multivariable Mendelian randomization study. BMC Cardiovasc Disord 2022; 22:269. [PMID: 35710362 PMCID: PMC9205080 DOI: 10.1186/s12872-022-02713-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background The causal association between educational attainment (EA) and stroke remains unclear. Hence, a novel multivariable Mendelian randomization (MVMR) approach was applied to solve this issue. Methods The single nucleotide polymorphisms (SNPs) from a recent genome-wide association study (GWAS) on years of schooling served as instruments. Univariable mendelian randomization (MR) and MVMR analyses were performed to detect the relationship between genetically predicted EA and the stroke risk. In the MVMR, cigarette consumption, alcohol consumption, body mass index (BMI), intelligence, and hypertension were adjusted. The summary statistics for stroke from the MEGASTROKE consortium included 446,696 participants (40,585 cases of stroke and 34,217 cases of ischemic stroke), most of whom were of European descent. Results In the univariable MR, genetically predicated EA could decrease the risks of total stroke (OR = 0.66, 95% CI 0.61–0.72, P = 2.70 × 10–23), ischemic stroke (OR = 0.67, 95% CI 0.61–0.73, P = 2.58 × 10–18), large artery atherosclerosis (OR = 0.51, 95% CI 0.40–0.64, P = 1.80 × 10–8), small vessel stroke (OR = 0.60, 95% CI 0.49–0.73, P = 5.59 × 10–7), and cardioembolic stroke (OR = 0.81, 95% CI 0.68–0.96, P = 1.46 × 10–2) using the inverse-variance weighted (IVW) estimator. Higher EA might be negatively correlated with the odds of total stroke (OR = 0.62, 95% CI 0.50–0.77, P = 1.44 × 10–5), ischemic stroke (OR = 0.63, 95% CI 0.50–0.80, P = 1.41 × 10–4), and cardioembolic stroke (OR = 0.59, 95% CI 0.39–0.90, P = 0.01), but was not significant in large artery atherosclerosis (OR = 0.65, 95% CI 0.37–1.15, P = 0.14) and small vessel stroke (OR = 0.68, 95% CI 0.41–1.13, P = 0.14) after controlling other exposures. Conclusions We found that genetically predicated higher EA decreased the risks of total stroke, ischemic stroke, and cardioembolic stroke, independent of smoking, alcohol consumption, BMI, intelligence, and hypertension.
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Affiliation(s)
- Weihao Zhang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guizhou, 610041, China
| | - Yuanjin Li
- Department of Plastic Surgery, The Third People's Hospital of Guizhou Province, Guizhou, 610041, China
| | - Yuming Li
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guizhou, 610041, China
| | - Kai Zheng
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guizhou, 610041, China
| | - Shenghui Zou
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guizhou, 610041, China
| | - Xing Jia
- Department of Neurosurgery, People's Hospital of Jiajiang County, Leshan, 614000, Sichuan, China
| | - Hua Yang
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guizhou, 610041, China.
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Martin CL, Ghastine L, Lodge EK, Dhingra R, Ward-Caviness CK. Understanding Health Inequalities Through the Lens of Social Epigenetics. Annu Rev Public Health 2022; 43:235-254. [PMID: 35380065 PMCID: PMC9584166 DOI: 10.1146/annurev-publhealth-052020-105613] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Longstanding racial/ethnic inequalities in morbidity and mortality persist in the United States. Although the determinants of health inequalities are complex, social and structural factors produced by inequitable and racialized systems are recognized as contributing sources. Social epigenetics is an emerging area of research that aims to uncover biological pathways through which social experiences affect health outcomes. A growing body of literature links adverse social exposures to epigenetic mechanisms, namely DNA methylation, offering a plausible pathway through which health inequalities may arise. This review provides an overview of social epigenetics and highlights existing literature linking social exposures—i.e., psychosocial stressors, racism, discrimination, socioeconomic position, and neighborhood social environment—to DNA methylation in humans.We conclude with a discussion of social epigenetics as a mechanistic link to health inequalities and provide suggestions for future social epigenetics research on health inequalities.
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Affiliation(s)
- Chantel L Martin
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; .,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lea Ghastine
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;
| | - Evans K Lodge
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; .,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Radhika Dhingra
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Institute of Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cavin K Ward-Caviness
- Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Chapel Hill, North Carolina, USA
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Cerutti J, Lussier AA, Zhu Y, Liu J, Dunn EC. Associations between indicators of socioeconomic position and DNA methylation: a scoping review. Clin Epigenetics 2021; 13:221. [PMID: 34906220 PMCID: PMC8672601 DOI: 10.1186/s13148-021-01189-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Socioeconomic position (SEP) is a major determinant of health across the life course. Yet, little is known about the biological mechanisms explaining this relationship. One possibility widely pursued in the scientific literature is that SEP becomes biologically embedded through epigenetic processes such as DNA methylation (DNAm), wherein the socioeconomic environment causes no alteration in the DNA sequence but modifies gene activity in ways that shape health. METHODS To understand the evidence supporting a potential SEP-DNAm link, we performed a scoping review of published empirical findings on the association between SEP assessed from prenatal development to adulthood and DNAm measured across the life course, with an emphasis on exploring how the developmental timing, duration, and type of SEP exposure influenced DNAm. RESULTS Across the 37 identified studies, we found that: (1) SEP-related DNAm signatures varied across the timing, duration, and type of SEP indicator; (2) however, longitudinal studies examining repeated SEP and DNAm measures are generally lacking; and (3) prior studies are conceptually and methodologically diverse, limiting the interpretability of findings across studies with respect to these three SEP features. CONCLUSIONS Given the complex relationship between SEP and DNAm across the lifespan, these findings underscore the importance of analyzing SEP features, including timing, duration, and type. To guide future research, we highlight additional research gaps and propose four recommendations to further unravel the relationship between SEP and DNAm.
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Affiliation(s)
- Janine Cerutti
- Department of Pscyhology, University of Vermont, 2 Colchester Ave, Burlington, VT, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
| | - Alexandre A Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiwen Zhu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiaxuan Liu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Erin C Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Simches Research Building 6th Floor, Boston, MA, 02114, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Huang JY, Cai S, Huang Z, Tint MT, Yuan WL, Aris IM, Godfrey KM, Karnani N, Lee YS, Chan JKY, Chong YS, Eriksson JG, Chan SY. Analyses of child cardiometabolic phenotype following assisted reproductive technologies using a pragmatic trial emulation approach. Nat Commun 2021; 12:5613. [PMID: 34556649 PMCID: PMC8460697 DOI: 10.1038/s41467-021-25899-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/06/2021] [Indexed: 11/08/2022] Open
Abstract
Assisted reproductive technologies (ART) are increasingly used, however little is known about the long-term health of ART-conceived offspring. Weak selection of comparison groups and poorly characterized mechanisms impede current understanding. In a prospective cohort (Growing Up in Singapore Towards healthy Outcomes; GUSTO; Clinical Trials ID: NCT01174875) including 83 ART-conceived and 1095 spontaneously-conceived singletons, we estimate effects of ART on anthropometry, blood pressure, serum metabolic biomarkers, and cord tissue DNA methylation by emulating a pragmatic trial supported by machine learning-based estimators. We find ART-conceived children to be shorter (-0.5 SD [95% CI: -0.7, -0.2]), lighter (-0.6 SD [-0.9, -0.3]) and have lower skinfold thicknesses (e.g. -14% [-24%, -3%] suprailiac), and blood pressure (-3 mmHg [-6, -0.5] systolic) at 6-6.5 years, with no strong differences in metabolic biomarkers. Differences are not explained by parental anthropometry or comorbidities, polygenic risk score, breastfeeding, or illnesses. Our simulations demonstrate ART is strongly associated with lower NECAB3 DNA methylation, with negative control analyses suggesting these estimates are unbiased. However, methylation changes do not appear to mediate observed differences in child phenotype.
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Affiliation(s)
- Jonathan Yinhao Huang
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.
| | - Shirong Cai
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhongwei Huang
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Mya Thway Tint
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wen Lun Yuan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Université de Paris, CRESS, Inserm, Paris, France
| | - Izzuddin M Aris
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Centre and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton, Southampton, UK
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
- Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Johan Gunnar Eriksson
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- University of Helsinki, Department of General Practise and Primary Health Care, Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Potente C, Harris KM, Chumbley J, Cole SW, Gaydosh L, Xu W, Levitt B, Shanahan MJ. The Early Life Course of Body Weight and Gene Expression Signatures for Disease. Am J Epidemiol 2021; 190:1533-1540. [PMID: 33675221 PMCID: PMC8489427 DOI: 10.1093/aje/kwab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/01/2022] Open
Abstract
We examined the way body-weight patterns through the first 4 decades of life relate to gene expression signatures of common forms of morbidity, including cardiovascular disease (CVD), type 2 diabetes (T2D), and inflammation. As part of wave V of the nationally representative National Longitudinal Study of Adolescent to Adult Health (1997–2018) in the United States, mRNA abundance data were collected from peripheral blood (n = 1,132). We used a Bayesian modeling strategy to examine the relative associations between body size at 5 life stages—birth, adolescence, early adulthood, young adulthood, and adulthood—and gene expression–based disease signatures. We compared life-course models that consider critical or sensitive periods, as well as accumulation over the entire period. Our results are consistent with a sensitive-period model when examining CVD and T2D gene expression signatures: Birth weight has a prominent role for the CVD and T2D signatures (explaining 33.1% and 22.1%, respectively, of the total association accounted for by body size), while the most recent adult obesity status (ages 33–39) is important for both of these gene expression signatures (24.3% and 35.1%, respectively). Body size in all life stages was associated with inflammation, consistent with the accumulation model.
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Affiliation(s)
- Cecilia Potente
- Correspondence to Dr. Cecilia Potente, Jacobs Center for Productive Youth Development, University of Zürich, Andreasstrasse 15, 8050 Zürich, Switzerland (e-mail: ); or Prof. Dr. Michael J. Shanahan, Jacobs Center for Productive Youth Development, University of Zürich, Andreasstrasse 15, 8050 Zürich, Switzerland (e-mail: )
| | | | | | | | | | | | | | - Michael J Shanahan
- Correspondence to Dr. Cecilia Potente, Jacobs Center for Productive Youth Development, University of Zürich, Andreasstrasse 15, 8050 Zürich, Switzerland (e-mail: ); or Prof. Dr. Michael J. Shanahan, Jacobs Center for Productive Youth Development, University of Zürich, Andreasstrasse 15, 8050 Zürich, Switzerland (e-mail: )
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Zhu Y, Simpkin AJ, Suderman MJ, Lussier AA, Walton E, Dunn EC, Smith ADAC. A Structured Approach to Evaluating Life-Course Hypotheses: Moving Beyond Analyses of Exposed Versus Unexposed in the -Omics Context. Am J Epidemiol 2021; 190:1101-1112. [PMID: 33125040 DOI: 10.1093/aje/kwaa246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The structured life-course modeling approach (SLCMA) is a theory-driven analytical method that empirically compares multiple prespecified life-course hypotheses characterizing time-dependent exposure-outcome relationships to determine which theory best fits the observed data. In this study, we performed simulations and empirical analyses to evaluate the performance of the SLCMA when applied to genomewide DNA methylation (DNAm). Using simulations (n = 700), we compared 5 statistical inference tests used with SLCMA, assessing the familywise error rate, statistical power, and confidence interval coverage to determine whether inference based on these tests was valid in the presence of substantial multiple testing and small effects-2 hallmark challenges of inference from -omics data. In the empirical analyses (n = 703), we evaluated the time-dependent relationship between childhood abuse and genomewide DNAm. In simulations, selective inference and the max-|t|-test performed best: Both controlled the familywise error rate and yielded moderate statistical power. Empirical analyses using SLCMA revealed time-dependent effects of childhood abuse on DNAm. Our findings show that SLCMA, applied and interpreted appropriately, can be used in high-throughput settings to examine time-dependent effects underlying exposure-outcome relationships over the life course. We provide recommendations for applying the SLCMA in -omics settings and encourage researchers to move beyond analyses of exposed versus unexposed individuals.
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12
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Zeng P, Shao Z, Zhou X. Statistical methods for mediation analysis in the era of high-throughput genomics: Current successes and future challenges. Comput Struct Biotechnol J 2021; 19:3209-3224. [PMID: 34141140 PMCID: PMC8187160 DOI: 10.1016/j.csbj.2021.05.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mediation analysis investigates the intermediate mechanism through which an exposure exerts its influence on the outcome of interest. Mediation analysis is becoming increasingly popular in high-throughput genomics studies where a common goal is to identify molecular-level traits, such as gene expression or methylation, which actively mediate the genetic or environmental effects on the outcome. Mediation analysis in genomics studies is particularly challenging, however, thanks to the large number of potential mediators measured in these studies as well as the composite null nature of the mediation effect hypothesis. Indeed, while the standard univariate and multivariate mediation methods have been well-established for analyzing one or multiple mediators, they are not well-suited for genomics studies with a large number of mediators and often yield conservative p-values and limited power. Consequently, over the past few years many new high-dimensional mediation methods have been developed for analyzing the large number of potential mediators collected in high-throughput genomics studies. In this work, we present a thorough review of these important recent methodological advances in high-dimensional mediation analysis. Specifically, we describe in detail more than ten high-dimensional mediation methods, focusing on their motivations, basic modeling ideas, specific modeling assumptions, practical successes, methodological limitations, as well as future directions. We hope our review will serve as a useful guidance for statisticians and computational biologists who develop methods of high-dimensional mediation analysis as well as for analysts who apply mediation methods to high-throughput genomics studies.
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Affiliation(s)
- Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
- Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Zhonghe Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor 48109, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor 48109, MI, USA
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13
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Evans L, Engelman M, Mikulas A, Malecki K. How are social determinants of health integrated into epigenetic research? A systematic review. Soc Sci Med 2021; 273:113738. [PMID: 33610974 PMCID: PMC8034414 DOI: 10.1016/j.socscimed.2021.113738] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/26/2020] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE We systematically review the literature on social epigenetics, examining how empirical research to date has conceptualized and operationalized social determinants of health (SDOH). METHODS Using comprehensive search procedures, we identified studies that consider the impact of SDOH on DNA methylation (DNAm), the most common measure of epigenetic change in research on human adult populations. We analyzed the studies to determine: 1) which populations and environments have been investigated in the literature; 2) how SDOH are defined and operationalized; 3) which SDOH have been linked to DNAm; and 4) what lessons from the SDOH literature can be better integrated into future studies exploring the social determinants of health and epigenetic outcomes. RESULTS We identified 67 studies, with 39 to 8397 participants. The SDOH most commonly considered were early life socioeconomic exposures and early life trauma or mental health. Our review highlights four broad challenges: a) high dependence on convenience sampling, b) limited racial/ethnic, and geographic diversity in sampling frames, c) overreliance on individual sociodemographic characteristics as proxies for broader stratification processes, and d) a focus on downstream social determinants of health and individualized experiences with social stressors. CONCLUSIONS Future social epigenetics research should prioritize larger, more diverse and representative population-based samples and employ the SDOH framework to better inform the conceptualization of research questions and interpretation of findings. In particular, the simplified depiction of race/ethnicity, gender, and socioeconomic status as individual-level characteristics should be updated with an explicit acknowledgement that these characteristics are more accurately interpreted as cues used by society to differentiate subpopulations. Social epigenetics research can then more clearly elucidate the biological consequences of these social exposures for patterns of gene expression, subsequent disease etiology, and health inequities.
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Affiliation(s)
- Linnea Evans
- Center for Health Equity Research, Northern Arizona University, USA.
| | - Michal Engelman
- Department of Sociology, University of Wisconsin-Madison, USA
| | - Alex Mikulas
- Department of Sociology, University of Wisconsin-Madison, USA
| | - Kristen Malecki
- Department of Population Health Sciences, University of Wisconsin-Madison, USA
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14
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Yuan S, Xiong Y, Michaëlsson M, Michaëlsson K, Larsson SC. Genetically predicted education attainment in relation to somatic and mental health. Sci Rep 2021; 11:4296. [PMID: 33619316 PMCID: PMC7900220 DOI: 10.1038/s41598-021-83801-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/08/2021] [Indexed: 01/02/2023] Open
Abstract
A deeper understanding of the causal links from education level to health outcomes may shed a light for disease prevention. In the present Mendelian randomization study, we found that genetically higher education level was associated with lower risk of major mental disorders and most somatic diseases, independent of intelligence. Higher education level adjusted for intelligence was associated with lower risk of suicide attempts, insomnia, major depressive disorder, heart failure, stroke, coronary artery disease, lung cancer, breast cancer, type 2 diabetes and rheumatoid arthritis but with higher risk of obsessive-compulsive disorder, anorexia nervosa, anxiety, bipolar disorder and prostate cancer. Higher education level was associated with reduced obesity and smoking, which mediated quite an extent of the associations between education level and health outcomes. These findings emphasize the importance of education to reduce the burden of common diseases.
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Affiliation(s)
- Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Nobelsväg 13, 17177, Stockholm, Sweden
| | - Ying Xiong
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Madeleine Michaëlsson
- Department of Education, Health and Social Studies, Dalarna University, Falun, Sweden
| | - Karl Michaëlsson
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Dag Hammarskjölds Väg 14B, 75185, Uppsala, Sweden
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Nobelsväg 13, 17177, Stockholm, Sweden.
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Dag Hammarskjölds Väg 14B, 75185, Uppsala, Sweden.
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15
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Wood NM, Trebilco T, Cohen-Woods S. Scars of childhood socioeconomic stress: A systematic review. Neurosci Biobehav Rev 2020; 118:397-410. [PMID: 32795493 DOI: 10.1016/j.neubiorev.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 12/17/2022]
Abstract
Childhood socioeconomic position (SEP) is associated with the development of adult psychological outcomes, with DNA methylation (DNAm) as a mechanism to potentially explain these changes. We present the first systematic review synthesising the literature investigating childhood SEP and DNAm. Thirty-two publications were included. Seventeen studies focused on candidate genes, typically focusing on genes implicated with the stress response and/or development of psychiatric conditions. These studies typically investigated different regions of the genes, which revealed inconsistent results. Six studies calculated epigenetic age, with a small number revealing an elevated significant association with childhood SEP. Epigenome-wide studies revealed altered patterns of DNAm which varied between the nine studies. This research area is emerging and demonstrated great variance in findings with no clear patterns identified across studies. Multiple methodological shortcomings are identified, including at the phenotypic level where construct validity of childhood SEP is highly inconsistent, with studies using a wide range of measures. Larger cohorts will be required with international collaborations to strengthen this research area.
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Affiliation(s)
- Natasha M Wood
- Discipline of Psychology, College of Education, Psychology, and Social Work, Flinders University, Adelaide, SA, Australia
| | - Thomas Trebilco
- Discipline of Psychology, College of Education, Psychology, and Social Work, Flinders University, Adelaide, SA, Australia
| | - Sarah Cohen-Woods
- Discipline of Psychology, College of Education, Psychology, and Social Work, Flinders University, Adelaide, SA, Australia; Órama Institute, Flinders University, Adelaide, SA, Australia; Flinders Centre for Innovation in Cancer, Adelaide, SA, Australia.
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16
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Socio-Economic Position Under the Microscope: Getting ‘Under the Skin’ and into the Cells. CURR EPIDEMIOL REP 2019. [DOI: 10.1007/s40471-019-00217-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Hughes A, Smart M, Gorrie-Stone T, Hannon E, Mill J, Bao Y, Burrage J, Schalkwyk L, Kumari M. Socioeconomic Position and DNA Methylation Age Acceleration Across the Life Course. Am J Epidemiol 2018; 187:2346-2354. [PMID: 30060108 PMCID: PMC6211240 DOI: 10.1093/aje/kwy155] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
Accelerated DNA methylation age is linked to all-cause mortality and environmental factors, but studies of associations with socioeconomic position are limited. Researchers generally use small selected samples, and it is unclear how findings obtained with 2 commonly used methods for calculating methylation age (the Horvath method and the Hannum method) translate to general population samples including younger and older adults. Among 1,099 United Kingdom adults aged 28-98 years in 2011-2012, we assessed the relationship of Horvath and Hannum DNA methylation age acceleration with a range of social position measures: current income and employment, education, income and unemployment across a 12-year period, and childhood social class. Accounting for confounders, participants who had been less advantaged in childhood were epigenetically "older" as adults: In comparison with participants who had professional/managerial parents, Hannum age was 1.07 years higher (95% confidence interval: 0.20, 1.94) for participants with parents in semiskilled/unskilled occupations and 1.85 years higher (95% confidence interval: 0.67, 3.02) for those without a working parent at age 14 years. No other robust associations were seen. Results accord with research implicating early life circumstances as critical for DNA methylation age in adulthood. Since methylation age acceleration as measured by the Horvath and Hannum estimators appears strongly linked to chronological age, researchers examining associations with the social environment must take steps to avoid age-related confounding.
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Affiliation(s)
- Amanda Hughes
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
| | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
| | - Tyler Gorrie-Stone
- Department of Biological Sciences, Faculty of Science and Health, University of Essex, Colchester, United Kingdom
| | | | | | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
| | | | - Leo Schalkwyk
- Department of Biological Sciences, Faculty of Science and Health, University of Essex, Colchester, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
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18
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He Z, Zhang R, Jiang F, Zhang H, Zhao A, Xu B, Jin L, Wang T, Jia W, Jia W, Hu C. FADS1-FADS2 genetic polymorphisms are associated with fatty acid metabolism through changes in DNA methylation and gene expression. Clin Epigenetics 2018; 10:113. [PMID: 30157936 PMCID: PMC6114248 DOI: 10.1186/s13148-018-0545-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background Genome-wide association studies (GWASs) have shown that genetic variants are important determinants of free fatty acid levels. The mechanisms underlying the associations between genetic variants and free fatty acid levels are incompletely understood. Here, we aimed to identify genetic markers that could influence diverse fatty acid levels in a Chinese population and uncover the molecular mechanisms in terms of DNA methylation and gene expression. Results We identified strong associations between single-nucleotide polymorphisms (SNPs) in the fatty acid desaturase (FADS) region and multiple polyunsaturated fatty acids. Expression quantitative trait locus (eQTL) analysis of rs174570 on FADS1 and FADS2 mRNA levels proved that minor allele of rs174570 was associated with decreased FADS1 and FADS2 expression levels (P < 0.05). Methylation quantitative trait locus (mQTL) analysis of rs174570 on DNA methylation levels in three selected regions of FADS region showed that the methylation levels at four CpG sites in FADS1, one CpG site in intragenic region, and three CpG sites in FADS2 were strongly associated with rs174570 (P < 0.05). Then, we demonstrated that methylation levels at three CpG sites in FADS1 were negatively associated with FADS1 and FADS2 expression, while two CpG sites in FADS2 were positively associated with FADS1 and FADS2 expression. Using mediation analysis, we further show that the observed effect of rs174570 on gene expression was tightly correlated with the effect predicted through association with methylation. Conclusions Our findings suggest that genetic variants in the FADS region are major genetic modifiers that can regulate fatty acid metabolism through epigenetic gene regulation. Electronic supplementary material The online version of this article (10.1186/s13148-018-0545-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen He
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China.,Institute for Metabolic Diseases, Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Feng Jiang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Hong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Aihua Zhao
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Bo Xu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Li Jin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Tao Wang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China. .,Institute for Metabolic Diseases, Fengxian Central Hospital, The Third School of Clinical Medicine, Southern Medical University, Shanghai, China.
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19
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Huang JY, Kaufman JS. GETTING SERIOUS ABOUT EMBODIMENT: CAUTIONS ABOUT INTERPRETING NOVEL FINDINGS OF SOCIOECONOMIC PATTERNS IN BIOLOGICAL FUNCTION. Am J Epidemiol 2018; 187:1336-1337. [PMID: 29659674 DOI: 10.1093/aje/kwx389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/29/2017] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jonathan Y Huang
- Department of Epidemiology, Biostatistics, and Occupational Health, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Jay S Kaufman
- Department of Epidemiology, Biostatistics, and Occupational Health, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
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20
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van Dongen J, Bonder MJ, Dekkers KF, Nivard MG, van Iterson M, Willemsen G, Beekman M, van der Spek A, van Meurs JBJ, Franke L, Heijmans BT, van Duijn CM, Slagboom PE, Boomsma DI. DNA methylation signatures of educational attainment. NPJ SCIENCE OF LEARNING 2018; 3:7. [PMID: 30631468 PMCID: PMC6220239 DOI: 10.1038/s41539-018-0020-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/18/2017] [Accepted: 02/09/2018] [Indexed: 05/09/2023]
Abstract
Educational attainment is a key behavioural measure in studies of cognitive and physical health, and socioeconomic status. We measured DNA methylation at 410,746 CpGs (N = 4152) and identified 58 CpGs associated with educational attainment at loci characterized by pleiotropic functions shared with neuronal, immune and developmental processes. Associations overlapped with those for smoking behaviour, but remained after accounting for smoking at many CpGs: Effect sizes were on average 28% smaller and genome-wide significant at 11 CpGs after adjusting for smoking and were 62% smaller in never smokers. We examined sources and biological implications of education-related methylation differences, demonstrating correlations with maternal prenatal folate, smoking and air pollution signatures, and associations with gene expression in cis, dynamic methylation in foetal brain, and correlations between blood and brain. Our findings show that the methylome of lower-educated people resembles that of smokers beyond effects of their own smoking behaviour and shows traces of various other exposures.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Koen F. Dekkers
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. Nivard
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Ashley van der Spek
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology section, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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21
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Lawrence GM, Friedlander Y, Calderon-Margalit R, Enquobahrie DA, Huang JY, Tracy RP, Manor O, Siscovick DS, Hochner H. Associations of social environment, socioeconomic position and social mobility with immune response in young adults: the Jerusalem Perinatal Family Follow-Up Study. BMJ Open 2017; 7:e016949. [PMID: 29273651 PMCID: PMC5778288 DOI: 10.1136/bmjopen-2017-016949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Immune response to cytomegalovirus (CMV) impacts adult chronic disease. This study investigates associations of childhood and adulthood social environment, socioeconomic position (SEP) and social mobility with CMV response in young adults. DESIGN Historical prospective study design. SETTING Subcohort of all 17 003 births to residents of Jerusalem between 1974 and 1976. PARTICIPANTS Participants included 1319 young adults born in Jerusalem with extensive archival and follow-up data, including childhood and adulthood SEP-related factors and anti-CMV IgG titre levels and seroprevalence measured at age 32. MAIN EXPOSURE AND OUTCOME MEASURES Principal component analysis was used to transform correlated social environment and SEP-related variables at two time points (childhood and adulthood) into two major scores reflecting household (eg, number of siblings/children, religiosity) and socioeconomic (eg, occupation, education) components. Based on these components, social mobility variables were created. Linear and Poisson regression models were used to investigate associations of components and mobility with anti-CMV IgG titre level and seroprevalence, adjusted for confounders. RESULTS Lower levels of household and socioeconomic components in either childhood or adulthood were associated with higher anti-CMV IgG titre level and seropositivity at age 32. Compared with individuals with stable favourable components, anti-CMV IgG titre level and risk for seropositivity were higher in stable unfavourable household and socioeconomic components (household: β=3.23, P<0.001; relative risk (RR)=1.21, P<0.001; socioeconomic: β=2.20, P=0.001; RR=1.14, P=0.01), downward household mobility (β=4.32, P<0.001; RR=1.26, P<0.001) and upward socioeconomic mobility (β=1.37, P=0.04; RR=1.19, P<0.001). Among seropositive individuals, associations between household components and mobility with anti-CMV IgG titre level were maintained and associations between socioeconomic components and mobility with anti-CMV IgG titre level were attenuated. CONCLUSIONS Our study provides evidence that accumulating low SEP from childhood through adulthood and social mobility may compromise immune response in young adulthood.
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Affiliation(s)
- Gabriella M Lawrence
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Yehiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | | | - Daniel A Enquobahrie
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Jonathan Yinhao Huang
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Institute for Health and Social Policy, McGill University, Montreal, Canada
| | - Russell P Tracy
- Departments of Pathology and Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Orly Manor
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - David S Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York City, New York, USA
| | - Hagit Hochner
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
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22
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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23
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Huang JY, Siscovick DS, Hochner H, Friedlander Y, Enquobahrie DA. Maternal gestational weight gain and DNA methylation in young women: application of life course mediation methods. Epigenomics 2017; 9:1559-1571. [PMID: 29106309 PMCID: PMC5704089 DOI: 10.2217/epi-2017-0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 12/30/2022] Open
Abstract
AIM To investigate the role of maternal gestational weight gain (GWG) and prepregnancy BMI on programming offspring DNA methylation. METHODS Among 589 adult (age = 32) women participants of the Jerusalem Perinatal Study, we quantified DNA methylation in five candidate genes. We used inverse probability-weighting and parametric g-formula to estimate direct effects of maternal prepregnancy BMI and GWG on methylation. RESULTS Higher maternal GWG, but not prepregnancy BMI, was inversely related to offspring ABCA1 methylation (β = -1.1% per quartile; 95% CI: -2.0, -0.3) after accounting for ancestry, parental and offspring exposures. Total and controlled direct effects were nearly identical suggesting included offspring exposures did not mediate this relationship. Results were robust to sensitivity analyses for missing data and model specification. CONCLUSION We find some support for epigenetic programming and highlight strengths and limitations of these methods relative to other prevailing approaches.
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Affiliation(s)
- Jonathan Y Huang
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, Biostatistics and Occupational Health; Institute for Health & Social Policy; McGill University, Montreal, QC, Canada
| | | | - Hagit Hochner
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
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