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Wu N, Zheng W, Zhou Y, Tian Y, Tang M, Feng X, Ashrafizadeh M, Wang Y, Niu X, Tambuwala M, Wang L, Tergaonkar V, Sethi G, Klionsky D, Huang L, Gu M. Autophagy in aging-related diseases and cancer: Principles, regulatory mechanisms and therapeutic potential. Ageing Res Rev 2024; 100:102428. [PMID: 39038742 DOI: 10.1016/j.arr.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Macroautophagy/autophagy is primarily accountable for the degradation of damaged organelles and toxic macromolecules in the cells. Regarding the essential function of autophagy for preserving cellular homeostasis, changes in, or dysfunction of, autophagy flux can lead to disease development. In the current paper, the complicated function of autophagy in aging-associated pathologies and cancer is evaluated, highlighting the underlying molecular mechanisms that can affect longevity and disease pathogenesis. As a natural biological process, a reduction in autophagy is observed with aging, resulting in an accumulation of cell damage and the development of different diseases, including neurological disorders, cardiovascular diseases, and cancer. The MTOR, AMPK, and ATG proteins demonstrate changes during aging, and they are promising therapeutic targets. Insulin/IGF1, TOR, PKA, AKT/PKB, caloric restriction and mitochondrial respiration are vital for lifespan regulation and can modulate or have an interaction with autophagy. The specific types of autophagy, such as mitophagy that degrades mitochondria, can regulate aging by affecting these organelles and eliminating those mitochondria with genomic mutations. Autophagy and its specific types contribute to the regulation of carcinogenesis and they are able to dually enhance or decrease cancer progression. Cancer hallmarks, including proliferation, metastasis, therapy resistance and immune reactions, are tightly regulated by autophagy, supporting the conclusion that autophagy is a promising target in cancer therapy.
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Affiliation(s)
- Na Wu
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Wenhui Zheng
- Department of Anesthesiology, The Shengjing Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Yundong Zhou
- Department of Thoracic Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315040, China
| | - Yu Tian
- School of Public Health, Benedictine University, No.5700 College Road, Lisle, IL 60532, USA; Research Center, the Huizhou Central People's Hospital, Guangdong Medical University, Huizhou, Guangdong, China
| | - Min Tang
- Department of Oncology, Chongqing General Hospital, Chongqing University, Chongqing 401120, China
| | - Xiaoqiang Feng
- Center of Stem Cell and Regenerative Medicine, Gaozhou People's Hospital, Gaozhou, Guangdong 525200, China
| | - Milad Ashrafizadeh
- Department of Radiation Oncology, Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China; Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yuzhuo Wang
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Xiaojia Niu
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Murtaza Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600, Singapore
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A⁎STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore 117600, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.
| | - Daniel Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Li Huang
- Center of Stem Cell and Regenerative Medicine, Gaozhou People's Hospital, Gaozhou, Guangdong 525200, China.
| | - Ming Gu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
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2
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Power GM, Sanderson E, Pagoni P, Fraser A, Morris T, Prince C, Frayling TM, Heron J, Richardson TG, Richmond R, Tyrrell J, Warrington N, Davey Smith G, Howe LD, Tilling KM. Methodological approaches, challenges, and opportunities in the application of Mendelian randomisation to lifecourse epidemiology: A systematic literature review. Eur J Epidemiol 2024; 39:501-520. [PMID: 37938447 PMCID: PMC7616129 DOI: 10.1007/s10654-023-01032-1] [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: 05/16/2023] [Accepted: 07/21/2023] [Indexed: 11/09/2023]
Abstract
Diseases diagnosed in adulthood may have antecedents throughout (including prenatal) life. Gaining a better understanding of how exposures at different stages in the lifecourse influence health outcomes is key to elucidating the potential benefits of disease prevention strategies. Mendelian randomisation (MR) is increasingly used to estimate causal effects of exposures across the lifecourse on later life outcomes. This systematic literature review explores MR methods used to perform lifecourse investigations and reviews previous work that has utilised MR to elucidate the effects of factors acting at different stages of the lifecourse. We conducted searches in PubMed, Embase, Medline and MedRXiv databases. Thirteen methodological studies were identified. Four studies focused on the impact of time-varying exposures in the interpretation of "standard" MR techniques, five presented methods for repeat measures of the same exposure, and four described methodological approaches to handling multigenerational exposures. A further 127 studies presented the results of an applied research question. Over half of these estimated effects in a single generation and were largely confined to the exploration of questions regarding body composition. The remaining mostly estimated maternal effects. There is a growing body of research focused on the development and application of MR methods to address lifecourse research questions. The underlying assumptions require careful consideration and the interpretation of results rely on select conditions. Whilst we do not advocate for a particular strategy, we encourage practitioners to make informed decisions on how to approach a research question in this field with a solid understanding of the limitations present and how these may be affected by the research question, modelling approach, instrument selection, and data availability.
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Affiliation(s)
- Grace M Power
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
| | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Panagiota Pagoni
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Abigail Fraser
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tim Morris
- Centre for Longitudinal Studies, Social Research Institute, University College London, London, UK
| | - Claire Prince
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Jon Heron
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Rebecca Richmond
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Nicole Warrington
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- NIHR Bristol Biomedical Research Centre Bristol, University Hospitals Bristol and Weston NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Laura D Howe
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Kate M Tilling
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
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Yuliyanasari N, Rejeki PS, Hidayati HB, Subsomwong P, Miftahussurur M. The effect of intermittent fasting on preventing obesity-related early aging from a molecular and cellular perspective. J Med Life 2024; 17:261-272. [PMID: 39044934 PMCID: PMC11262604 DOI: 10.25122/jml-2023-0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/30/2023] [Indexed: 07/25/2024] Open
Abstract
Obesity is a global health concern owing to its association with numerous degenerative diseases and the fact that it may lead to early aging. Various markers of aging, including telomere attrition, epigenetic alterations, altered protein homeostasis, mitochondrial dysfunction, cellular senescence, stem cell disorders, and intercellular communication, are influenced by obesity. Consequently, there is a critical need for safe and effective approaches to prevent obesity and mitigate the onset of premature aging. In recent years, intermittent fasting (IF), a dietary strategy that alternates between periods of fasting and feeding, has emerged as a promising dietary strategy that holds potential in counteracting the aging process associated with obesity. This article explores the molecular and cellular mechanisms through which IF affects obesity-related early aging. IF regulates various physiological processes and organ systems, including the liver, brain, muscles, intestines, blood, adipose tissues, endocrine system, and cardiovascular system. Moreover, IF modulates key signaling pathways such as AMP-activated protein kinase (AMPK), sirtuins, phosphatidylinositol 3-kinase (PI3K)/Akt, mammalian target of rapamycin (mTOR), and fork head box O (FOXO). By targeting these pathways, IF has the potential to attenuate aging phenotypes associated with obesity-related early aging. Overall, IF offers promising avenues for promoting healthier lifestyles and mitigating the premature aging process in individuals affected by obesity.
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Key Words
- ADF, alternate-day fasting
- ADMF, alternate-day modified fasting
- AMPK, AMP-activated protein kinase
- BMI, body mass index
- FOXO, fork head box O
- IF, intermittent fasting
- IIS, insulin/insulin-like growth factor signaling
- PF, periodic fasting
- PGC-1α, peroxisome proliferator-activated receptor gamma coactivator 1-alpha
- PI3K, phosphatidylinositol 3-kinase
- TRE, time-restricted eating
- aging
- human health
- intermittent fasting
- mTOR, mammalian target of rapamycin
- obesity
- β-HB, β-hydroxy butyric acid
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Affiliation(s)
- Nurma Yuliyanasari
- Doctoral Program of Medical Science, Faculty Of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Department of Physiology, Faculty of Medicine, Universitas Muhammadiyah Surabaya, Surabaya, Indonesia
| | - Purwo Sri Rejeki
- Physiology Division, Department of Medical Physiology and Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Hanik Badriyah Hidayati
- Department of Neurology, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | - Muhammad Miftahussurur
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Diseases, Universitas Airlangga, Surabaya, Indonesia
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Gorzkiewicz M, Łoś-Rycharska E, Gawryjołek J, Gołębiewski M, Krogulska A, Grzybowski T. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between Polish infants with the food allergy and/or atopic dermatitis and without the disease. Front Immunol 2023; 14:1209190. [PMID: 37520545 PMCID: PMC10373304 DOI: 10.3389/fimmu.2023.1209190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Objectives Epigenetic dynamics has been indicated to play a role in allergy development. The environmental stimuli have been shown to influence the methylation processes. This study investigated the differences in CpGs methylation rate of immune-attached genes between healthy and allergic infants. The research was aimed at finding evidence for the impact of environmental factors on methylation-based regulation of immunological processes in early childhood. Methods The analysis of methylation level of CpGs in the IL4, IL5, IL10, IFNG and FOXP3 genes was performed using high resolution melt real time PCR technology. DNA was isolated from whole blood of Polish healthy and allergic infants, with food allergy and/or atopic dermatitis, aged under six months. Results The significantly lower methylation level of FOXP3 among allergic infants compared to healthy ones was reported. Additional differences in methylation rates were found, when combining with environmental factors. In different studied groups, negative correlations between age and the IL10 and FOXP3 methylation were detected, and positive - in the case of IL4. Among infants with different allergy symptoms, the decrease in methylation level of IFNG, IL10, IL4 and FOXP3 associated with passive smoke exposure was observed. Complications during pregnancy were linked to different pattern of the IFNG, IL5, IL4 and IL10 methylation depending on allergy status. The IFNG and IL5 methylation rates were higher among exclusively breastfed infants with atopic dermatitis compared to the non-breastfed. A decrease in the IFNG methylation was noted among allergic patients fed exclusively with milk formula. In different study groups, a negative correlation between IFNG, IL5 methylation and maternal BMI or IL5 methylation and weight was noted. Some positive correlations between methylation rate of IL10 and child's weight were found. A higher methylation of IL4 was positively correlated with the number of family members with allergy. Conclusion The FOXP3 methylation in allergic infants was lower than in the healthy ones. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between the studied groups. The results offer insights into epigenetic regulation of immunological response in early childhood.
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Affiliation(s)
- Marta Gorzkiewicz
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Ewa Łoś-Rycharska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Julia Gawryjołek
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Aneta Krogulska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
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Lister NB, Baur LA, Felix JF, Hill AJ, Marcus C, Reinehr T, Summerbell C, Wabitsch M. Child and adolescent obesity. Nat Rev Dis Primers 2023; 9:24. [PMID: 37202378 DOI: 10.1038/s41572-023-00435-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
The prevalence of child and adolescent obesity has plateaued at high levels in most high-income countries and is increasing in many low-income and middle-income countries. Obesity arises when a mix of genetic and epigenetic factors, behavioural risk patterns and broader environmental and sociocultural influences affect the two body weight regulation systems: energy homeostasis, including leptin and gastrointestinal tract signals, operating predominantly at an unconscious level, and cognitive-emotional control that is regulated by higher brain centres, operating at a conscious level. Health-related quality of life is reduced in those with obesity. Comorbidities of obesity, including type 2 diabetes mellitus, fatty liver disease and depression, are more likely in adolescents and in those with severe obesity. Treatment incorporates a respectful, stigma-free and family-based approach involving multiple components, and addresses dietary, physical activity, sedentary and sleep behaviours. In adolescents in particular, adjunctive therapies can be valuable, such as more intensive dietary therapies, pharmacotherapy and bariatric surgery. Prevention of obesity requires a whole-system approach and joined-up policy initiatives across government departments. Development and implementation of interventions to prevent paediatric obesity in children should focus on interventions that are feasible, effective and likely to reduce gaps in health inequalities.
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Affiliation(s)
- Natalie B Lister
- Children's Hospital Westmead Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Louise A Baur
- Children's Hospital Westmead Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia.
- Weight Management Services, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Paediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Andrew J Hill
- Institute of Health Sciences, School of Medicine, University of Leeds, Leeds, UK
| | - Claude Marcus
- Division of Paediatrics, Department of Clinical Science Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Reinehr
- Vestische Hospital for Children and Adolescents Datteln, University of Witten/Herdecke, Datteln, Germany
| | - Carolyn Summerbell
- Department of Sport and Exercise Sciences, Durham University, Durham, UK
| | - Martin Wabitsch
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, Ulm University Medical Centre, Ulm, Germany
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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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Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
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Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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8
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Huang R, Melton P, Burton M, Beilin L, Clarke-Harris R, Cook E, Godfrey K, Burdge G, Mori T, Anderson D, Rauschert S, Craig JM, Kobor M, MacIsaac J, Morin A, Oddy W, Pennell C, Holbrook J, Lillycrop K. Adiposity associated DNA methylation signatures in adolescents are related to leptin and perinatal factors. Epigenetics 2022; 17:819-836. [PMID: 33550919 PMCID: PMC9423832 DOI: 10.1080/15592294.2021.1876297] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022] Open
Abstract
Epigenetics links perinatal influences with later obesity. We identifed differentially methylated CpG (dmCpG) loci measured at 17 years associated with concurrent adiposity measures and examined whether these were associated with hsCRP, adipokines, and early life environmental factors. Genome-wide DNA methylation from 1192 Raine Study participants at 17 years, identified 29 dmCpGs (Bonferroni corrected p < 1.06E-07) associated with body mass index (BMI), 10 with waist circumference (WC) and 9 with subcutaneous fat thickness. DmCpGs within Ras Association (RalGDS/AF-6), Pleckstrin Homology Domains 1 (RAPH1), Musashi RNA-Binding Protein 2 (MSI2), and solute carrier family 25 member 10 (SLC25A10) are associated with both BMI and WC. Validation by pyrosequencing confirmed these associations and showed that MSI2 , SLC25A10 , and RAPH1 methylation was positively associated with serum leptin. These were also associated with the early environment; MSI2 methylation (β = 0.81, p = 0.0004) was associated with pregnancy maternal smoking, SLC25A10 (CpG2 β = 0.12, p = 0.002) with pre- and early pregnancy BMI, and RAPH1 (β = -1.49, p = 0.036) with gestational weight gain. Adjusting for perinatal factors, methylation of the dmCpGs within MSI2, RAPH1, and SLC25A10 independently predicted BMI, accounting for 24% of variance. MSI2 methylation was additionally associated with BMI over time (17 years old β = 0.026, p = 0.0025; 20 years old β = 0.027, p = 0.0029) and between generations (mother β = 0.044, p = 7.5e-04). Overall findings suggest that DNA methylation in MSI2, RAPH1, and SLC25A10 in blood may be robust markers, mediating through early life factors.
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Affiliation(s)
- R.C. Huang
- Telethon Kids Institute, University of Western Australia, Australia
| | - P.E. Melton
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
- Menzies Institute for Medical Research, University of Tasmania, Australia
| | - M.A. Burton
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - L.J. Beilin
- Medical School, The University of Western Australia, Australia
| | - R Clarke-Harris
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - E Cook
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - K.M. Godfrey
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - G.C. Burdge
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - T.A. Mori
- Medical School, The University of Western Australia, Australia
| | - D Anderson
- Telethon Kids Institute, University of Western Australia, Australia
| | - S. Rauschert
- Telethon Kids Institute, University of Western Australia, Australia
| | - J. M. Craig
- Centre for Molecular and Medical Research, School of Medicine, Deakin University, Geelong, Victoria, Australia
- Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - M.S. Kobor
- Department of Medical Genetics, University of British Columbia, VancouverCanada
| | - J.L. MacIsaac
- Department of Medical Genetics, University of British Columbia, VancouverCanada
| | - A.M. Morin
- Department of Medical Genetics, University of British Columbia, VancouverCanada
| | - W.H. Oddy
- Menzies Institute for Medical Research, University of Tasmania, Australia
| | - C.E. Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Australia
| | - J.D. Holbrook
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - K.A. Lillycrop
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
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9
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Ling C, Bacos K, Rönn T. Epigenetics of type 2 diabetes mellitus and weight change - a tool for precision medicine? Nat Rev Endocrinol 2022; 18:433-448. [PMID: 35513492 DOI: 10.1038/s41574-022-00671-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Pioneering studies performed over the past few decades demonstrate links between epigenetics and type 2 diabetes mellitus (T2DM), the metabolic disorder with the most rapidly increasing prevalence in the world. Importantly, these studies identified epigenetic modifications, including altered DNA methylation, in pancreatic islets, adipose tissue, skeletal muscle and the liver from individuals with T2DM. As non-genetic factors that affect the risk of T2DM, such as obesity, unhealthy diet, physical inactivity, ageing and the intrauterine environment, have been associated with epigenetic modifications in healthy individuals, epigenetics probably also contributes to T2DM development. In addition, genetic factors associated with T2DM and obesity affect the epigenome in human tissues. Notably, causal mediation analyses found DNA methylation to be a potential mediator of genetic associations with metabolic traits and disease. In the past few years, translational studies have identified blood-based epigenetic markers that might be further developed and used for precision medicine to help patients with T2DM receive optimal therapy and to identify patients at risk of complications. This Review focuses on epigenetic mechanisms in the development of T2DM and the regulation of body weight in humans, with a special focus on precision medicine.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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11
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Etzel L, Hastings WJ, Hall MA, Heim CM, Meaney MJ, Noll JG, O'Donnell KJ, Pokhvisneva I, Rose EJ, Schreier HMC, Shenk CE, Shalev I. Obesity and accelerated epigenetic aging in a high-risk cohort of children. Sci Rep 2022; 12:8328. [PMID: 35585103 PMCID: PMC9117197 DOI: 10.1038/s41598-022-11562-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
New insights into mechanisms linking obesity to poor health outcomes suggest a role for cellular aging pathways, casting obesity as a disease of accelerated biological aging. Although obesity has been linked to accelerated epigenetic aging in middle-aged adults, the impact during childhood remains unclear. We tested the association between body mass index (BMI) and accelerated epigenetic aging in a cohort of high-risk children. Participants were children (N = 273, aged 8 to 14 years, 82% investigated for maltreatment) recruited to the Child Health Study, an ongoing prospective study of youth investigated for maltreatment and a comparison youth. BMI was measured as a continuous variable. Accelerated epigenetic aging of blood leukocytes was defined as the age-adjusted residuals of several established epigenetic aging clocks (Horvath, Hannum, GrimAge, PhenoAge) along with a newer algorithm, the DunedinPoAm, developed to quantify the pace-of-aging. Hypotheses were tested with generalized linear models. Higher age-and sex- adjusted z-scored BMI was significantly correlated with household income, blood cell counts, and three of the accelerated epigenetic aging measures: GrimAge (r = 0.31, P < .0001), PhenoAge (r = 0.24, P < .0001), and DunedinPoAm (r = 0.38, P < .0001). In fully adjusted models, GrimAge (β = 0.07; P = .0009) and DunedinPoAm (β = 0.0017; P < .0001) remained significantly associated with higher age- and sex-adjusted z-scored BMI. Maltreatment-status was not associated with accelerated epigenetic aging. In a high-risk cohort of children, higher BMI predicted epigenetic aging as assessed by two epigenetic aging clocks. These results suggest the association between obesity and accelerated epigenetic aging begins in early life, with implications for future morbidity and mortality risk.
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Affiliation(s)
- Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Molly A Hall
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Christine M Heim
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Institute of Medical Psychology, Humboldt-Universität Zu Berlin, Berlin Institute of Health (BIH), Berlin, Germany
| | - Michael J Meaney
- Departments of Psychiatry and Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Jennie G Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - Kieran J O'Donnell
- Yale Child Study Center, Yale University, New Haven, CT, USA
- Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Irina Pokhvisneva
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Emma J Rose
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, PA, USA
| | - Hannah M C Schreier
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Chad E Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA.
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12
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Alfano R, Robinson O, Handakas E, Nawrot TS, Vineis P, Plusquin M. Perspectives and challenges of epigenetic determinants of childhood obesity: A systematic review. Obes Rev 2022; 23 Suppl 1:e13389. [PMID: 34816569 DOI: 10.1111/obr.13389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/20/2022]
Abstract
The tremendous increase in childhood obesity prevalence over the last few decades cannot merely be explained by genetics and evolutionary changes in the genome, implying that gene-environment interactions, such as epigenetic modifications, likely play a major role. This systematic review aims to summarize the evidence of the association between epigenetics and childhood obesity. A literature search was performed via PubMed and Scopus engines using a combination of terms related to epigenetics and pediatric obesity. Articles studying the association between epigenetic mechanisms (including DNA methylation and hydroxymethylation, non-coding RNAs, and chromatin and histones modification) and obesity and/or overweight (or any related anthropometric parameters) in children (0-18 years) were included. The risk of bias was assessed with a modified Newcastle-Ottawa scale for non-randomized studies. One hundred twenty-one studies explored epigenetic changes related to childhood obesity. DNA methylation was the most widely investigated mechanism (N = 101 studies), followed by non-coding RNAs (N = 19 studies) with evidence suggestive of an association with childhood obesity for DNA methylation of specific genes and microRNAs (miRNAs). One study, focusing on histones modification, was identified. Heterogeneity of findings may have hindered more insights into the epigenetic changes related to childhood obesity. Gaps and challenges that future research should face are herein described.
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Affiliation(s)
- Rossella Alfano
- Department of Epidemiology and Biostatistics, The School of Public Health, 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
| | - Oliver Robinson
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK.,Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
| | - Evangelos Handakas
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK.,Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK.,Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK.,Unit of Molecular and Genetic Epidemiology, Human Genetic Foundation (HuGeF), Turin, Italy
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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Porcu E, Sjaarda J, Lepik K, Carmeli C, Darrous L, Sulc J, Mounier N, Kutalik Z. Causal Inference Methods to Integrate Omics and Complex Traits. Cold Spring Harb Perspect Med 2021; 11:a040493. [PMID: 32816877 PMCID: PMC8091955 DOI: 10.1101/cshperspect.a040493] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Major biotechnological advances have facilitated a tremendous boost to the collection of (gen-/transcript-/prote-/methyl-/metabol-)omics data in very large sample sizes worldwide. Coordinated efforts have yielded a deluge of studies associating diseases with genetic markers (genome-wide association studies) or with molecular phenotypes. Whereas omics-disease associations have led to biologically meaningful and coherent mechanisms, the identified (non-germline) disease biomarkers may simply be correlates or consequences of the explored diseases. To move beyond this realm, Mendelian randomization provides a principled framework to integrate information on omics- and disease-associated genetic variants to pinpoint molecular traits causally driving disease development. In this review, we show the latest advances in this field, flag up key challenges for the future, and propose potential solutions.
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Affiliation(s)
- Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Jennifer Sjaarda
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Kaido Lepik
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
- Institute of Computer Science, University of Tartu, Tartu 50409, Estonia
| | - Cristian Carmeli
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Liza Darrous
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Jonathan Sulc
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Ninon Mounier
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5AX, United Kingdom
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14
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Juvinao-Quintero DL, Marioni RE, Ochoa-Rosales C, Russ TC, Deary IJ, van Meurs JBJ, Voortman T, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA methylation of blood cells is associated with prevalent type 2 diabetes in a meta-analysis of four European cohorts. Clin Epigenetics 2021; 13:40. [PMID: 33622391 PMCID: PMC7903628 DOI: 10.1186/s13148-021-01027-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/11/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a heterogeneous disease with well-known genetic and environmental risk factors contributing to its prevalence. Epigenetic mechanisms related to changes in DNA methylation (DNAm), may also contribute to T2D risk, but larger studies are required to discover novel markers, and to confirm existing ones. RESULTS We performed a large meta-analysis of individual epigenome-wide association studies (EWAS) of prevalent T2D conducted in four European studies using peripheral blood DNAm. Analysis of differentially methylated regions (DMR) was also undertaken, based on the meta-analysis results. We found three novel CpGs associated with prevalent T2D in Europeans at cg00144180 (HDAC4), cg16765088 (near SYNM) and cg24704287 (near MIR23A) and confirmed three CpGs previously identified (mapping to TXNIP, ABCG1 and CPT1A). We also identified 77 T2D associated DMRs, most of them hypomethylated in T2D cases versus controls. In adjusted regressions among diabetic-free participants in ALSPAC, we found that all six CpGs identified in the meta-EWAS were associated with white cell-types. We estimated that these six CpGs captured 11% of the variation in T2D, which was similar to the variation explained by the model including only the common risk factors of BMI, sex, age and smoking (R2 = 10.6%). CONCLUSIONS This study identifies novel loci associated with T2D in Europeans. We also demonstrate associations of the same loci with other traits. Future studies should investigate if our findings are generalizable in non-European populations, and potential roles of these epigenetic markers in T2D etiology or in determining long term consequences of T2D.
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Affiliation(s)
- Diana L. Juvinao-Quintero
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA 02215 USA
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Carolina Ochoa-Rosales
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
- Centro de Vida Saludable de La Universidad de Concepción, Victoria 580, Concepción, Chile
| | - Tom C. Russ
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ UK
- Edinburgh Dementia Prevention Research Group, University of Edinburgh, Edinburgh, EH16 4UX UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Ian J. Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Joyce B. J. van Meurs
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, 3000 CA The Netherlands
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA 02215 USA
| | - Gemma C. Sharp
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
- Bristol NIHR Biomedical Research Centre, Oakfield House, Oakfield Grove, Bristol, BS8 2BN UK
| | - Hannah R. Elliott
- MRC Integrative Epidemiology, Bristol Medical School, Bristol, BS8 2BN UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
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15
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Diemer EW, Labrecque JA, Neumann A, Tiemeier H, Swanson SA. Mendelian randomisation approaches to the study of prenatal exposures: A systematic review. Paediatr Perinat Epidemiol 2021; 35:130-142. [PMID: 32779786 PMCID: PMC7891574 DOI: 10.1111/ppe.12691] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Mendelian randomisation (MR) designs apply instrumental variable techniques using genetic variants to study causal effects. MR is increasingly used to evaluate the role of maternal exposures during pregnancy on offspring health. OBJECTIVES We review the application of MR to prenatal exposures and describe reporting of methodologic challenges in this area. DATA SOURCES We searched PubMed, EMBASE, Medline Ovid, Cochrane Central, Web of Science, and Google Scholar. STUDY SELECTION AND DATA EXTRACTION Eligible studies met the following criteria: (a) a maternal pregnancy exposure; (b) an outcome assessed in offspring of the pregnancy; and (c) a genetic variant or score proposed as an instrument or proxy for an exposure. SYNTHESIS We quantified the frequency of reporting of MR conditions stated, techniques used to examine assumption plausibility, and reported limitations. RESULTS Forty-three eligible studies were identified. When discussing challenges or limitations, the most common issues described were known potential biases in the broader MR literature, including population stratification (n = 29), weak instrument bias (n = 18), and certain types of pleiotropy (n = 30). Of 22 studies presenting point estimates for the effect of exposure, four defined their causal estimand. Twenty-four studies discussed issues unique to prenatal MR, including selection on pregnancy (n = 1) and pleiotropy via postnatal exposure (n = 10) or offspring genotype (n = 20). CONCLUSIONS Prenatal MR studies frequently discuss issues that affect all MR studies, but rarely discuss problems specific to the prenatal context, including selection on pregnancy and effects of postnatal exposure. Future prenatal MR studies should report and attempt to falsify their assumptions, with particular attention to issues specific to prenatal MR. Further research is needed to evaluate the impacts of biases unique to prenatal MR in practice.
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Affiliation(s)
- Elizabeth W. Diemer
- Department of Child and Adolescent PsychiatryErasmus MCRotterdamThe Netherlands
| | | | - Alexander Neumann
- Department of Child and Adolescent PsychiatryErasmus MCRotterdamThe Netherlands,Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Henning Tiemeier
- Department of Child and Adolescent PsychiatryErasmus MCRotterdamThe Netherlands,Department of Social and Behavioral ScienceHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Sonja A. Swanson
- Department of EpidemiologyErasmus MCRotterdamThe Netherlands,Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
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16
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Abstract
The pathophysiology of obesity is complex and includes changes in eating behavior, genetic, epigenetic, environmental factors, and much more. To date, ~40 genetic polymorphisms are associated with obesity and fat distribution. However, since these options do not fully explain the inheritance of obesity, other options, such as epigenetic changes, need to be considered. Epigenetic modifications affect gene expression without changing the deoxyribonucleic acid sequence. In addition, environmental exposure during critical periods of development can affect the epigenetic tags and lead to obesity. A deeper understanding of the epigenetic mechanisms underlying obesity can aid in prevention based on lifestyle changes. This review focuses on the role of epigenetic modifications in the development of obesity and related conditions.
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Affiliation(s)
- O. M. Drapkina
- National Research Center for Therapy and Preventive Medicine
| | - O. T. Kim
- National Research Center for Therapy and Preventive Medicine
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17
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Böttcher Y. Epigenetische Mechanismen bei Adipositas: Finetuning der Genaktivität durch DNA-Methylierung – Bertram-Preis 2020 – eine Kurzübersicht der Preisträgerin Yvonne Böttcher. DIABETOL STOFFWECHS 2020. [DOI: 10.1055/a-1247-1099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yvonne Böttcher
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Medical Division, Akershus University Hospital, Lørenskog, Norway
- Integriertes Forschungs- und Behandlungszentrum (IFB) AdipositasErkrankungen, Universitätsmedizin Leipzig, Leipzig
- Helmholtz-Institut für Metabolismus-, Adipositas- und Gefäßforschung (HI-MAG) des Helmholtz Zentrums München an der Universität Leipzig und dem Universitätsklinikum Leipzig, Leipzig (als Gastwissenschaftlerin)
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18
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Vehmeijer FOL, Küpers LK, Sharp GC, Salas LA, Lent S, Jima DD, Tindula G, Reese S, Qi C, Gruzieva O, Page C, Rezwan FI, Melton PE, Nohr E, Escaramís G, Rzehak P, Heiskala A, Gong T, Tuominen ST, Gao L, Ross JP, Starling AP, Holloway JW, Yousefi P, Aasvang GM, Beilin LJ, Bergström A, Binder E, Chatzi L, Corpeleijn E, Czamara D, Eskenazi B, Ewart S, Ferre N, Grote V, Gruszfeld D, Håberg SE, Hoyo C, Huen K, Karlsson R, Kull I, Langhendries JP, Lepeule J, Magnus MC, Maguire RL, Molloy PL, Monnereau C, Mori TA, Oken E, Räikkönen K, Rifas-Shiman S, Ruiz-Arenas C, Sebert S, Ullemar V, Verduci E, Vonk JM, Xu CJ, Yang IV, Zhang H, Zhang W, Karmaus W, Dabelea D, Muhlhausler BS, Breton CV, Lahti J, Almqvist C, Jarvelin MR, Koletzko B, Vrijheid M, Sørensen TIA, Huang RC, Arshad SH, Nystad W, Melén E, Koppelman GH, London SJ, Holland N, Bustamante M, Murphy SK, Hivert MF, Baccarelli A, Relton CL, Snieder H, Jaddoe VWV, Felix JF. DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies. Genome Med 2020; 12:105. [PMID: 33239103 PMCID: PMC7687793 DOI: 10.1186/s13073-020-00810-w] [Citation(s) in RCA: 33] [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: 03/29/2020] [Accepted: 11/12/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unknown. More insight into this relationship at younger ages may have implications for future prevention of obesity and its related traits. METHODS We examined whether DNA methylation in cord blood and whole blood in childhood and adolescence was associated with BMI in the age range from 2 to 18 years using both cross-sectional and longitudinal models. We performed meta-analyses of epigenome-wide association studies including up to 4133 children from 23 studies. We examined the overlap of findings reported in previous studies in children and adults with those in our analyses and calculated enrichment. RESULTS DNA methylation at three CpGs (cg05937453, cg25212453, and cg10040131), each in a different age range, was associated with BMI at Bonferroni significance, P < 1.06 × 10-7, with a 0.96 standard deviation score (SDS) (standard error (SE) 0.17), 0.32 SDS (SE 0.06), and 0.32 BMI SDS (SE 0.06) higher BMI per 10% increase in methylation, respectively. DNA methylation at nine additional CpGs in the cross-sectional childhood model was associated with BMI at false discovery rate significance. The strength of the associations of DNA methylation at the 187 CpGs previously identified to be associated with adult BMI, increased with advancing age across childhood and adolescence in our analyses. In addition, correlation coefficients between effect estimates for those CpGs in adults and in children and adolescents also increased. Among the top findings for each age range, we observed increasing enrichment for the CpGs that were previously identified in adults (birth Penrichment = 1; childhood Penrichment = 2.00 × 10-4; adolescence Penrichment = 2.10 × 10-7). CONCLUSIONS There were only minimal associations of DNA methylation with childhood and adolescent BMI. With the advancing age of the participants across childhood and adolescence, we observed increasing overlap with altered DNA methylation loci reported in association with adult BMI. These findings may be compatible with the hypothesis that DNA methylation differences are mostly a consequence rather than a cause of obesity.
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Affiliation(s)
- Florianne O L Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Room Na-2918, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Sarah Reese
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Cancan Qi
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, The Netherlands
- University Medical Center Groningen GRIAC Research Institute, University of Groningen, Groningen, the Netherlands
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Christian Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, UK
- Human Development and Health, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Philip E Melton
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, Western Austalia, Australia
| | - Ellen Nohr
- Centre for Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Geòrgia Escaramís
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Research group on Statistics, Econometrics and Health (GRECS), University of Girona, Girona, Spain
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Samuli T Tuominen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jason P Ross
- CSIRO Health and Biosecurity, North Ryde, New South Wales, Australia
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Gunn Marit Aasvang
- Department of Air Pollution and Noise, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Natalia Ferre
- Pediatrics, Nutrition and Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | | | - Johanna Lepeule
- Université Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Raleigh, NC, USA
| | - Peter L Molloy
- CSIRO Health and Biosecurity, North Ryde, New South Wales, Australia
| | - Claire Monnereau
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Room Na-2918, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Trevor A Mori
- Medical School, University of Western Australia, Perth, Australia
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sheryl Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elvira Verduci
- Department of Pediatrics, San Paolo Hospital, University of Milan, Milan, Italy
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University Medical Center Groningen GRIAC Research Institute, University of Groningen, Groningen, the Netherlands
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, The Netherlands
- University Medical Center Groningen GRIAC Research Institute, University of Groningen, Groningen, the Netherlands
- Department of Gastroenterology, Hepatology and Endocrinology, CiiM, Centre for Individualised Infection Medicine, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Public Health, Section of Epidemiology, and The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, Groningen, The Netherlands
- University Medical Center Groningen GRIAC Research Institute, University of Groningen, Groningen, the Netherlands
| | - Stephanie J London
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Raleigh, NC, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Room Na-2918, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Room Na-2918, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, the Netherlands.
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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19
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Berberine improves insulin resistance in adipocyte models by regulating the methylation of hypoxia-inducible factor-3α. Biosci Rep 2020; 39:220717. [PMID: 31652442 PMCID: PMC6822485 DOI: 10.1042/bsr20192059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
Methylation of hypoxia-inducible factor-3α (HIF3A) was previously demonstrated to be highly associated with insulin resistance (IR) in patients with gestational diabetes mellitus (GDM). We aimed to study the therapeutic effects of Berberine (BBR) on GDM and the possible mechanisms. The expressions and methylated states of HIF3A in pregnant women with GDM were compared with that in healthy controls. The IR cell models of 3T3-L1 adipocytes was constructed by 1 μmol/l dexamethasone (Dex) and 1 μmol/l insulin (Ins). To evaluate the effects of BBR on IR adipocyte models, cells were subjected to BBR treatment at different concentrations. Transfection of HIF3A siRNA further confirmed the role of HIF3A in the BBR-induced improving effects. Low expression and high methylation of HIF3A gene were frequent in the GDM pregnancies. BBR treatment noticeably increased the glucose usage rates, adiponectin secretion and cell differentiation of IR 3T3-L1 adipocytes. Increased HIF3A expression and decreased methylated state of HIF3A were also found in IR adipocytes. Furthermore, HIF3A silencing not only reversed the effects of BBR on improving insulin sensibility, but also partially abolished the expression alterations of insulin-related genes in IR adipocytes induced by BBR treatment. Our results suggest that BBR improves insulin sensibility in IR adipocyte models, and the improving effects of BBR are possibly realized through the inhibition of HIF3A methylation.
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20
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Epigenetic signatures associated with maternal body mass index or gestational weight gain: a systematic review. J Dev Orig Health Dis 2020; 12:373-383. [PMID: 32873364 DOI: 10.1017/s2040174420000811] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maternal body mass index (BMI) and gestational weight gain (GWG) impacts both the mother's and the child's health, and epigenetic modifications have been suggested to mediate some of these effects in offspring. This systematic review aimed to summarize the current literature on associations between maternal BMI and GWG and epigenetic marks. We performed systematic searches in PubMed and EMBASE and manual searches of reference lists. We included 49 studies exploring the association between maternal BMI and/or GWG and DNA methylation or miRNA; 7 performed in maternal tissues, 13 in placental tissue and 38 in different offspring tissues. The most consistent findings were reported for the relationship between maternal BMI, in particular pre-pregnant BMI, and expression of miRNA Let-7d in both maternal blood and placental tissue, methylation of the gene HIF3A in umbilical cord blood and umbilical tissue, and with expression in the miR-210 target gene, BDNF in placental tissue and cord blood. Correspondingly, methylation of BDNF was also found in placental tissue and cord blood. The current evidence suggests that maternal BMI is associated with some epigenetic signatures in the mother, the placenta and her offspring, which could indicate that some of the effects proposed by the Developmental Origins of Health and Disease-hypothesis may be mediated by epigenetic marks. In conclusion, there is a need for large, well-designed studies and meta-analyses that can clarify the relationship between BMI, GWG and epigenetic changes.
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21
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Cronjé HT, Elliott HR, Nienaber-Rousseau C, Pieters M. Leveraging the urban-rural divide for epigenetic research. Epigenomics 2020; 12:1071-1081. [PMID: 32657149 DOI: 10.2217/epi-2020-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urbanization coincides with a complex change in environmental exposure and a rapid increase in noncommunicable diseases (NCDs). Epigenetics, including DNA methylation (DNAm), is thought to mediate part of the association between genetic/environmental exposure and NCDs. The urban-rural divide provides a unique opportunity to investigate the effect of the combined presence of multiple forms of environmental exposure on DNAm and the related increase in disease risk. This review evaluates the ability of three epidemiological study designs (migration, income-comparative and urban-rural designs) to investigate the role of DNAm in the association between urbanization and the rise in NCD prevalence. We also discuss the ability of each study design to address the gaps in the current literature, including the complex methylation-mediated risk attributable to the cluster of forms of exposure characterizing urban and rural living, while providing a platform for developing countries to leverage their demographic discrepancies in future research ventures.
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Affiliation(s)
- Héléne T Cronjé
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cornelie Nienaber-Rousseau
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Marlien Pieters
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
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22
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Diels S, Vanden Berghe W, Van Hul W. Insights into the multifactorial causation of obesity by integrated genetic and epigenetic analysis. Obes Rev 2020; 21:e13019. [PMID: 32170999 DOI: 10.1111/obr.13019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022]
Abstract
Obesity is a highly heritable multifactorial disease that places an enormous burden on human health. Its increasing prevalence and the concomitant-reduced life expectancy has intensified the search for new analytical methods that can reduce the knowledge gap between genetic susceptibility and functional consequences of the disease pathology. Although the influence of genetics and epigenetics has been studied independently in the past, there is increasing evidence that genetic variants interact with environmental factors through epigenetic regulation. This suggests that a combined analysis of genetic and epigenetic variation may be more effective in characterizing the obesity phenotype. To date, limited genome-wide integrative analyses have been performed. In this review, we provide an overview of the latest findings, advantages, and challenges and discuss future perspectives.
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Affiliation(s)
- Sara Diels
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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23
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Mansell T, Burgner D, Ponsonby AL, Collier F, Pezic A, Vuillermin P, Juonala M, Ryan J, Saffery R. HIF3A cord blood methylation and systolic blood pressure at 4 years - a population-based cohort study. Epigenetics 2020; 15:1361-1369. [PMID: 32530724 DOI: 10.1080/15592294.2020.1781027] [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] [Indexed: 01/11/2023] Open
Abstract
Methylation levels at the hypoxia-inducible factor 3α gene (HIF3A) in blood have been linked to body mass index (BMI) in adults. Despite evidence implicating HIF3A in angiogenesis and metabolism, no studies have examined links between HIF3A methylation in early life and cardiovascular health. Here, we investigated the relationship between HIF3A methylation in blood at birth and 12 months of age with cardiovascular measures at 4 years. We also examined influences of prenatal exposures, birth outcomes, and genetic variation. Methylation of two HIF3A promoter regions in cord blood was measured using Sequenom EpiTYPER mass-spectrometry. The first promoter region was also measured in 12-month blood. Four-year cardiovascular measures included blood pressure, pulse wave velocity, and aortic and carotid intima-media thickness. Associations were tested using partial correlation tests and linear regression modelling. Methylation of the first HIF3A promoter in cord and 12-month blood was not associated with four-year measures. There was modest evidence of an association between DNA methylation at the second HIF3A promoter in cord blood and four-year systolic blood pressure (n = 353, r = 0.12, p = 0.03). In sex-stratified analysis, methylation of the second promoter was modestly associated with systolic and diastolic blood pressure (r = 0.16, p = 0.03 for both) in males only. In conclusion, HIF3A methylation at birth shows some evidence of an association with later blood pressure in childhood. Further work should determine whether this relationship persists into later childhood, and should assess potential functional links between HIF3A methylation and cardiovascular health more generally.
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Affiliation(s)
- Toby Mansell
- Murdoch Children's Research Institute , Parkville, Australia.,Department of Paediatrics, University of Melbourne , Parkville, Australia
| | - David Burgner
- Murdoch Children's Research Institute , Parkville, Australia.,Department of Paediatrics, University of Melbourne , Parkville, Australia.,Department of Paediatrics, Monash University , Clayton, Australia
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute , Parkville, Australia.,Department of Paediatrics, University of Melbourne , Parkville, Australia.,Neuroepidemiology Research Group, The Florey Institute of Neuroscience and Mental Health , Parkville, Australia
| | - Fiona Collier
- Murdoch Children's Research Institute , Parkville, Australia.,School of Medicine, Deakin University , Geelong, Australia.,Child Health Research Unit, Barwon Health , Geelong, Australia
| | - Angela Pezic
- Murdoch Children's Research Institute , Parkville, Australia
| | - Peter Vuillermin
- Murdoch Children's Research Institute , Parkville, Australia.,School of Medicine, Deakin University , Geelong, Australia.,Child Health Research Unit, Barwon Health , Geelong, Australia
| | - Markus Juonala
- Murdoch Children's Research Institute , Parkville, Australia.,Department of Medicine, University of Turku , Turku, Finland.,Division of Medicine, Turku University Hospital , Turku, Finland
| | - Joanne Ryan
- Murdoch Children's Research Institute , Parkville, Australia.,School of Public Health & Preventive Medicine, Monash University , Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute , Parkville, Australia.,Department of Paediatrics, University of Melbourne , Parkville, Australia
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24
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Lima RS, Assis Silva Gomes J, Moreira PR. An overview about DNA methylation in childhood obesity: Characteristics of the studies and main findings. J Cell Biochem 2020; 121:3042-3057. [DOI: 10.1002/jcb.29544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Rafael Silva Lima
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
| | - Juliana Assis Silva Gomes
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
| | - Paula Rocha Moreira
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
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25
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Hypermethylation of the TSPOAP1-AS1 Promoter May Be Associated with Obesity in Overweight/Obese Korean Subjects. Int J Mol Sci 2020; 21:ijms21093307. [PMID: 32392798 PMCID: PMC7246878 DOI: 10.3390/ijms21093307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 01/18/2023] Open
Abstract
Obesity is a major chronic disease associated with the risk of serious cardiovascular or endocrinal diseases, such as hypertension, diabetes, atherosclerosis and stroke. Considerable interest has been directed towards the potential effects of epigenetic variations in obesity. In this study, we evaluated DNA methylation level at the promoter region of the gene encoding TSPO-associated protein 1 antisense RNA 1 (TSPOAP1-AS1) in 80 overweight/obese subjects (body mass index (BMI) > 25) and 104 non-obese subjects who participated in the SOPI-Stroke study in Korea. DNA methylation was measured using bisulfite amplicon sequencing (BSAS). A general linear model or relative correlation was used to determine the effects of DNA methylation on obesity and obese phenotypes. Notably, the mean level of DNA methylation was significantly higher in the overweight/obese group than in the non-obese group (18.62% vs. 17.18%). Further analyses revealed significant positive correlations of the BMI, the serum total cholesterol and low-density lipoprotein cholesterol levels with the DNA methylation level (p = 0.0493, p = 0.003, and p = 0.0094, respectively). The study findings suggest an association between DNA methylation at the TSPOAP1-AS1 promoter and overweight/obesity. Accordingly, methylation in this promoter region might be a potential predictor of obesity.
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26
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Cadiou S, Bustamante M, Agier L, Andrusaityte S, Basagaña X, Carracedo A, Chatzi L, Grazuleviciene R, Gonzalez JR, Gutzkow KB, Maitre L, Mason D, Millot F, Nieuwenhuijsen M, Papadopoulou E, Santorelli G, Saulnier PJ, Vives M, Wright J, Vrijheid M, Slama R. Using methylome data to inform exposome-health association studies: An application to the identification of environmental drivers of child body mass index. ENVIRONMENT INTERNATIONAL 2020; 138:105622. [PMID: 32179316 PMCID: PMC8713647 DOI: 10.1016/j.envint.2020.105622] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The exposome is defined as encompassing all environmental exposures one undergoes from conception onwards. Challenges of the application of this concept to environmental-health association studies include a possibly high false-positive rate. OBJECTIVES We aimed to reduce the dimension of the exposome using information from DNA methylation as a way to more efficiently characterize the relation between exposome and child body mass index (BMI). METHODS Among 1,173 mother-child pairs from HELIX cohort, 216 exposures ("whole exposome") were characterized. BMI and DNA methylation from immune cells of peripheral blood were assessed in children at age 6-10 years. A priori reduction of the methylome to preselect BMI-relevant CpGs was performed using biological pathways. We then implemented a tailored Meet-in-the-Middle approach to identify from these CpGs candidate mediators in the exposome-BMI association, using univariate linear regression models corrected for multiple testing: this allowed to point out exposures most likely to be associated with BMI ("reduced exposome"). Associations of this reduced exposome with BMI were finally tested. The approach was compared to an agnostic exposome-wide association study (ExWAS) ignoring the methylome. RESULTS Among the 2284 preselected CpGs (0.6% of the assessed CpGs), 62 were associated with BMI. Four factors (3 postnatal and 1 prenatal) of the exposome were associated with at least one of these CpGs, among which postnatal blood level of copper and PFOS were directly associated with BMI, with respectively positive and negative estimated effects. The agnostic ExWAS identified 18 additional postnatal exposures, including many persistent pollutants, generally unexpectedly associated with decreased BMI. DISCUSSION Our approach incorporating a priori information identified fewer significant associations than an agnostic approach. We hypothesize that this smaller number corresponds to a higher specificity (and possibly lower sensitivity), compared to the agnostic approach. Indeed, the latter cannot distinguish causal relations from reverse causation, e.g. for persistent compounds stored in fat, whose circulating level is influenced by BMI.
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Affiliation(s)
- Solène Cadiou
- Team of Environmental Epidemiology, IAB, Institute for Advanced Biosciences, Inserm, CNRS, CHU-Grenoble-Alpes, University Grenoble-Alpes, Grenoble, France
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Lydiane Agier
- Team of Environmental Epidemiology, IAB, Institute for Advanced Biosciences, Inserm, CNRS, CHU-Grenoble-Alpes, University Grenoble-Alpes, Grenoble, France
| | - Sandra Andrusaityte
- Department of Environmental Sciences, Vytautas Magnus University, Kaunas, Lithuania
| | - Xavier Basagaña
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Angel Carracedo
- Fundación Pública Galega de Medicina Xenómica (SERGAS), IDIS, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | | | - Juan R Gonzalez
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Léa Maitre
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, United Kingdom
| | - Frédéric Millot
- CHU Poitiers, Clinical Investigation Centre, CIC 1402, Poitiers, France; Poitiers University, Clinical Investigation Centre CIC 1402, Poitiers, France
| | - Mark Nieuwenhuijsen
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Gillian Santorelli
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, United Kingdom
| | - Pierre-Jean Saulnier
- CHU Poitiers, Clinical Investigation Centre, CIC 1402, Poitiers, France; Poitiers University, Clinical Investigation Centre CIC 1402, Poitiers, France; INSERM, CIC 1402, F-86000 Poitiers, France; CHU Poitiers, Endocrinology, Diabetology, Nutrition Service, Poitiers, France
| | - Marta Vives
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, United Kingdom
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Rémy Slama
- Team of Environmental Epidemiology, IAB, Institute for Advanced Biosciences, Inserm, CNRS, CHU-Grenoble-Alpes, University Grenoble-Alpes, Grenoble, France.
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Howey R, Shin SY, Relton C, Davey Smith G, Cordell HJ. Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data. PLoS Genet 2020; 16:e1008198. [PMID: 32119656 PMCID: PMC7067488 DOI: 10.1371/journal.pgen.1008198] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 03/12/2020] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
Mendelian randomization (MR) implemented through instrumental variables analysis is an increasingly popular causal inference tool used in genetic epidemiology. But it can have limitations for evaluating simultaneous causal relationships in complex data sets that include, for example, multiple genetic predictors and multiple potential risk factors associated with the same genetic variant. Here we use real and simulated data to investigate Bayesian network analysis (BN) with the incorporation of directed arcs, representing genetic anchors, as an alternative approach. A Bayesian network describes the conditional dependencies/independencies of variables using a graphical model (a directed acyclic graph) with an accompanying joint probability. In real data, we found BN could be used to infer simultaneous causal relationships that confirmed the individual causal relationships suggested by bi-directional MR, while allowing for the existence of potential horizontal pleiotropy (that would violate MR assumptions). In simulated data, BN with two directional anchors (mimicking genetic instruments) had greater power for a fixed type 1 error than bi-directional MR, while BN with a single directional anchor performed better than or as well as bi-directional MR. Both BN and MR could be adversely affected by violations of their underlying assumptions (such as genetic confounding due to unmeasured horizontal pleiotropy). BN with no directional anchor generated inference that was no better than by chance, emphasizing the importance of directional anchors in BN (as in MR). Under highly pleiotropic simulated scenarios, BN outperformed both MR (and its recent extensions) and two recently-proposed alternative approaches: a multi-SNP mediation intersection-union test (SMUT) and a latent causal variable (LCV) test. We conclude that BN incorporating genetic anchors is a useful complementary method to conventional MR for exploring causal relationships in complex data sets such as those generated from modern "omics" technologies.
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Affiliation(s)
- Richard Howey
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
| | - So-Youn Shin
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom
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Gómez de Cedrón M, Mouhid L, García-Carrascosa E, Fornari T, Reglero G, Ramírez de Molina A. Marigold Supercritical Extract as Potential Co-adjuvant in Pancreatic Cancer: The Energetic Catastrophe Induced via BMP8B Ends Up With Autophagy-Induced Cell Death. Front Bioeng Biotechnol 2020; 7:455. [PMID: 32039173 PMCID: PMC6992545 DOI: 10.3389/fbioe.2019.00455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
The recent development of powerful "omics" technologies (genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has opened new avenues in nutritional sciences toward precision nutrition, which is a genotype-directed nutrition that takes into account the differential responses to nutritional interventions based on gene variation (nutrigenetics) and the effect of nutrients on gene expression (nutrigenomics). Current evidence demonstrates that up to one third of the deaths caused by cancer could be prevented by acting on key risk factors, with diet being one of the most important risk factors due to its association with obesity. Additional factors such as composition of gut microbiome, the immune system, and the nutritional status will have an impact on the final outcome. Nutrient components and bioactive compounds from natural sources can have an impact on cancer progression or even the risk of cancer development by regulating gene expression and/or associated risk factors such as obesity and chronic inflammation. Nowadays, among the different methods to produce natural extracts, the green technology of supercritical fluid extraction (SFE) is quite popular, with a special interest on the use of supercritical CO2 for the extraction of compounds with low polarity. The success of nutritional interventions based on the use of nutraceuticals requires several steps: (i) in vitro and preclinical demonstration of their antitumoral effects; (ii) knowledge of their mechanism of action and molecular targets, which will allow for identification of the specific subgroups of patients who will benefit from them; (iii) the study of genetic variants associated with the differential responses; and (iv) innovative approaches of formulations to improve the in vivo bioavailability of the bioactive ingredients. Herein, we investigate the antitumoral properties and mechanism of action of a supercritical CO2 extract from Calendula officinalis, commonly known as marigold (marigold SFE) in the context of pancreatic cancer. Mechanistically, marigold SFE induces the expression of BMP8B, which leads to an energetic catastrophe ending up with autophagy-induced cell death (AICD). As metabolic reprogramming is a well-recognized hallmark of cancer, the direct impact of marigold SFE on pancreatic cancer cell metabolism encourages further research of its potential as a coadjuvant in pancreatic cancer therapy. Finally, we discuss innovative formulation approaches to augment the clinical therapeutic potential of marigold SFE in nutritional interventions.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology and Nutritional Genomics of Cancer, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Lamia Mouhid
- Molecular Oncology and Nutritional Genomics of Cancer, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Elena García-Carrascosa
- Molecular Oncology and Nutritional Genomics of Cancer, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Tiziana Fornari
- Production and Characterization of Novel Foods Department, Institute of Food Science Research CIAL, CEI UAM + CSIC, Madrid, Spain
| | - Guillermo Reglero
- Production and Characterization of Novel Foods Department, Institute of Food Science Research CIAL, CEI UAM + CSIC, Madrid, Spain.,Production and Development of Foods for Health, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
| | - Ana Ramírez de Molina
- Molecular Oncology and Nutritional Genomics of Cancer, IMDEA-Food Institute, CEI UAM + CSIC, Madrid, Spain
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29
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Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. CURRENT GENETIC MEDICINE REPORTS 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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30
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Madley-Dowd P, Rai D, Zammit S, Heron J. Simulations and directed acyclic graphs explained why assortative mating biases the prenatal negative control design. J Clin Epidemiol 2019; 118:9-17. [PMID: 31689456 PMCID: PMC7001034 DOI: 10.1016/j.jclinepi.2019.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVE The negative control design can be used to provide evidence for whether a prenatal exposure-outcome association occurs by in utero mechanisms. Assortative mating has been suggested to influence results from negative control designs, although how and why has not yet been adequately explained. We aimed to explain why mutual adjustment of maternal and paternal exposure in regression models can account for assortative mating. STUDY DESIGN AND SETTING We used directed acyclic graphs to show how bias can occur when modeling maternal and paternal effects separately. We empirically tested our claims using a simulation study. We investigated how increasing assortative mating influences the bias of effect estimates obtained from models that do and do not use a mutual adjustment strategy. RESULTS In models without mutual adjustment, increasing assortative mating led to increased bias in effect estimates. The maternal and paternal effect estimates were biased by each other, making the difference between them smaller than the true difference. Mutually adjusted models did not suffer from such bias. CONCLUSIONS Mutual adjustment for maternal and paternal exposure prevents bias from assortative mating influencing the conclusions of a negative control design. We further discuss issues that mutual adjustment may not be able to resolve.
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Affiliation(s)
- Paul Madley-Dowd
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Biomedical Research Centre, University of Bristol, Bristol, UK.
| | - Dheeraj Rai
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Biomedical Research Centre, University of Bristol, Bristol, UK; Avon and Wiltshire Partnership NHS Mental Health Trust, Bristol, UK
| | - Stanley Zammit
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Biomedical Research Centre, University of Bristol, Bristol, UK; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jon Heron
- Centre for Academic Mental Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Biomedical Research Centre, University of Bristol, Bristol, UK
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31
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Zhao W, Ammous F, Ratliff S, Liu J, Yu M, Mosley TH, Kardia SLR, Smith JA. Education and Lifestyle Factors Are Associated with DNA Methylation Clocks in Older African Americans. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16173141. [PMID: 31466396 PMCID: PMC6747433 DOI: 10.3390/ijerph16173141] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/06/2019] [Accepted: 08/25/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation (DNAm) clocks are important biomarkers of cellular aging and are associated with a variety of age-related chronic diseases and all-cause mortality. Examining the relationship between education and lifestyle risk factors for age-related diseases and multiple DNAm clocks can increase the understanding of how risk factors contribute to aging at the cellular level. This study explored the association between education or lifestyle risk factors for age-related diseases and the acceleration of four DNAm clocks, including intrinsic (IEAA) and extrinsic epigenetic age acceleration (EEAA), PhenoAge acceleration (PhenoAA), and GrimAge acceleration (GrimAA) in the African American participants of the Genetic Epidemiology Network of Arteriopathy. We performed both cross-sectional and longitudinal analyses. In cross-sectional analyses, gender, education, BMI, smoking, and alcohol consumption were all independently associated with GrimAA, whereas only some of them were associated with other clocks. The effect of smoking and education on GrimAA varied by gender. Longitudinal analyses suggest that age and BMI continued to increase GrimAA, and that age and current smoking continued to increase PhenoAA after controlling DNAm clocks at baseline. In conclusion, education and common lifestyle risk factors were associated with multiple DNAm clocks. However, the association with each risk factor varied by clock, which suggests that different clocks may capture adverse effects from different environmental stimuli.
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Affiliation(s)
- Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiaxuan Liu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Miao Yu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas H Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS 39126, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
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32
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Current opportunities to catalyze research in nutrition and cancer prevention - an interdisciplinary perspective. BMC Med 2019; 17:148. [PMID: 31357989 PMCID: PMC6664739 DOI: 10.1186/s12916-019-1383-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/02/2019] [Indexed: 02/02/2023] Open
Abstract
Cancer Research UK and Ludwig Cancer Research convened an inaugural international Cancer Prevention and Nutrition Conference in London on December 3-4, 2018. Much of the discussion focused on the need for systematic, interdisciplinary approaches to better understand the relationships of nutrition, exercise, obesity and metabolic dysfunction with cancer development. Scientists at the meeting underscored the importance of studying the temporal natural history of exposures that may cumulatively impact cancer risk later in life.A robust dialogue identified obesity as a major risk for cancer, and the food environment, especially high energy and low nutrient processed foods, as strong and prevalent risk factors for obesity. Further engagement highlighted challenges in the post-diagnostic setting, where similar opportunities to understand the complex interplay of nutrition, physical activity, and weight will inform better health outcomes.Going forward, holistic research approaches, encompassing insights from multiple disciplines and perspectives, will catalyze progress urgently needed to prevent cancer and improve public health.
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33
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Chater-Diehl E, Ejaz R, Cytrynbaum C, Siu MT, Turinsky A, Choufani S, Goodman SJ, Abdul-Rahman O, Bedford M, Dorrani N, Engleman K, Flores-Daboub J, Genevieve D, Mendoza-Londono R, Meschino W, Perrin L, Safina N, Townshend S, Scherer SW, Anagnostou E, Piton A, Deardorff M, Brudno M, Chitayat D, Weksberg R. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. BMC Med Genomics 2019; 12:105. [PMID: 31288860 PMCID: PMC6617651 DOI: 10.1186/s12920-019-0555-y] [Citation(s) in RCA: 20] [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: 04/25/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures. METHODS Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as "pathogenic" or "benign". A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity. RESULTS We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as "pathogenic". A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient's unique clinical presentation. CONCLUSIONS Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary "benign" versus "pathogenic" scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.
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Affiliation(s)
- Eric Chater-Diehl
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, Ontario L8S 4L8 Canada
| | - Cheryl Cytrynbaum
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Michelle T. Siu
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Andrei Turinsky
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sarah J. Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE USA
| | - Melanie Bedford
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario M5S 3H7 Canada
| | | | - Kendra Engleman
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 66111 USA
| | - Josue Flores-Daboub
- Division of Pediatric Clinical Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - David Genevieve
- Service de génétique clinique, Département de génétique médicale, maladies rares, médecine personnalisée, Unité INSERM U1183, Université Montpellier, CHU Montpellier, 34000 Montpellier, France
| | - Roberto Mendoza-Londono
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Wendy Meschino
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
| | - Laurence Perrin
- AP-HP, Department of Genetics, Hôpital Robert Debré, 75019 Paris, France
| | - Nicole Safina
- University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108 USA
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
| | - Sharron Townshend
- Department of Health, Government of Western Australia, Genetic Services of Western Australia, Perth, WA Australia
| | - Stephen W. Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital Toronto, Toronto, Ontario M4G 1R8 Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Amelie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
- Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Matthew Deardorff
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- The Department of Pediatrics, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Michael Brudno
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario M5G 1X5 Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
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34
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Mansell T, Ponsonby AL, Januar V, Novakovic B, Collier F, Burgner D, Vuillermin P, Ryan J, Saffery R. Early-life determinants of hypoxia-inducible factor 3A gene (HIF3A) methylation: a birth cohort study. Clin Epigenetics 2019; 11:96. [PMID: 31262346 PMCID: PMC6604333 DOI: 10.1186/s13148-019-0687-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/27/2019] [Indexed: 12/17/2022] Open
Abstract
Background Methylation of the hypoxia-inducible factor 3α gene (HIF3A) has been linked to pregnancy exposures, infant adiposity and later BMI. Genetic variation influences HIF3A methylation levels and may modify these relationships. However, data in very early life are limited, particularly in association with adverse pregnancy outcomes. We investigated the relationship between maternal and gestational factors, infant anthropometry, genetic variation and HIF3A DNA methylation in the Barwon Infant Study, a population-based birth cohort. Methylation of two previously studied regions of HIF3A were tested in the cord blood mononuclear cells of 938 infants. Results No compelling evidence was found of an association between birth weight, adiposity or maternal gestational diabetes with methylation at the most widely studied HIF3A region. Male sex (− 4.3%, p < 0.001) and pre-eclampsia (− 5.4%, p = 0.02) negatively associated with methylation at a second region of HIF3A; while positive associations were identified for gestational diabetes (4.8%, p = 0.01) and gestational age (1.2% increase per week, p < 0.001). HIF3A genetic variation also associated strongly with methylation at this region (p < 0.001). Conclusions Pre- and perinatal factors impact HIF3A methylation, including pre-eclampsia. This provides evidence that specific pregnancy complications, previously linked to adverse outcomes for both mother and child, impact the infant epigenome in a molecular pathway critical to several vascular and metabolic conditions. Further work is required to understand the mechanisms and clinical relevance, particularly the differing effects of in utero exposure to gestational diabetes or pre-eclampsia. Electronic supplementary material The online version of this article (10.1186/s13148-019-0687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toby Mansell
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Vania Januar
- Murdoch Children's Research Institute, Parkville, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Fiona Collier
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - David Burgner
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Paediatrics, Monash University, Clayton, Australia
| | - Peter Vuillermin
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - Joanne Ryan
- Murdoch Children's Research Institute, Parkville, Australia.,School of Public Health & Preventive Medicine, Monash University, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Australia.
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35
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Potabattula R, Dittrich M, Schorsch M, Hahn T, Haaf T, El Hajj N. Male obesity effects on sperm and next-generation cord blood DNA methylation. PLoS One 2019; 14:e0218615. [PMID: 31246962 PMCID: PMC6597061 DOI: 10.1371/journal.pone.0218615] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The prevalence of metabolic disorders, in particular obesity has dramatically increased worldwide. Genetic variants explain only a minor part of the obesity epidemic induced by physical inactivity and over-nutrition. Epidemiological studies in humans and animal models indicate that epigenetic changes associated with adverse parental and/or intrauterine factors may contribute to the missing heritability of metabolic disorders. Possible adverse paternal effects are likely transmitted by sperm to the next-generation. To investigate this hypothesis, we have systematically analyzed the effects of male body mass index (BMI) on sperm epigenome and its association with next-generation fetal cord blood (FCB) DNA methylation. Methylation levels of maternally imprinted (PEG1, PEG4, PEG5, and PEG10), paternally imprinted (H19-IG DMR, IGF2-DMR0, and MEG3-IG DMR) regions, and obesity-related non-imprinted HIF3A gene were quantified by bisulphite pyrosequencing in sperm samples of 294 human donors undergoing in vitro fertilization or intracytoplasmic sperm injection, and in 113 FCBs of the resulting offspring. Multivariable regression analyses revealed that MEG3 intergenic differentially methylated region (IG DMR) showed positive correlation between sperm methylation and donor’s BMI. A gender-specific correlation between paternal BMI and FCB methylation was observed for MEG3-IG DMR, HIF3A, and IGF2-DMR0. The former two genes displayed same directional nominal association (as sperm) between paternal BMI and FCB methylation in male offspring. Hypomethylation of IGF2-DMR0 with increased paternal BMI was observed in FCBs from female offsprings. Our results suggest that male obesity is nominally associated with modification of sperm DNA methylome in humans, which may affect the epigenome of the next-generation. Nevertheless, it is important to note that none of the associated p-values survived multiple testing adjustments. Future work should test the effect of associated methylation aberrations in the offspring as DNA methylation was shown to control expression and/or imprint establishment across the studied genes.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- * E-mail: (RP); , (NEH)
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
- * E-mail: (RP); , (NEH)
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36
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Zar Kyaw T, Yamaguchi S, Imai C, Uematsu M, Sato N. The utility of post-test newborn blood spot screening cards for epigenetic association analyses: association between HIF3A methylation and birth weight-for-gestational age. J Hum Genet 2019; 64:795-801. [PMID: 31138846 PMCID: PMC6760750 DOI: 10.1038/s10038-019-0621-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/22/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
Abstract
Identification of disease-associated epigenetic markers in early life might be useful for pre-emptive intervention to prevent diseases. Epigenome-wide association analyses using newborn blood spot screening cards are an anticipated field of research in Japan. Here, in this study, post-test dried blood spot (DBS) samples were anonymized, with only three attributes of gender, gestational age, and birth weight identified. We isolated DNA from DBS (n = 300) archived for more than 3 years. The median DNA yield (ng) per individual was 429 (interquartile range 300–565). In a model epigenetic analysis, we conducted a confirmative study on the known association between birth weight and hypoxia-inducible factor 3A (HIF3A) gene methylation. DNA methylation levels and cis-acting SNP genotypes (rs8102595 and rs3826795) were measured using EpiTYPER and Taqman assays, respectively. HIF3A methylation was positively associated with birth weight-for-gestational age centile (p = 0.021). While HIF3A methylation was associated with cis-genotypes (rs8102595, p = 2.08E−13; rs3826795, p = 3.63E−09), the association with birth weight centile was retained after adjusting for cis-genotypes (p = 0.029). Thus, we successfully reproduced the results reported previously by others, and demonstrated the usefulness of archived DBS in secondary use for epigenetic association analyses.
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Affiliation(s)
- Tay Zar Kyaw
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Seiji Yamaguchi
- Department of Pediatrics, Shimane University School of Medicine, Izumo, Shimane, 693-8501, Japan
| | - Chihiro Imai
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Marina Uematsu
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Noriko Sato
- Department of Epigenetic Epidemiology/Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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37
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Lauschke VM, Zhou Y, Ingelman-Sundberg M. Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity. Pharmacol Ther 2019; 197:122-152. [PMID: 30677473 PMCID: PMC6527860 DOI: 10.1016/j.pharmthera.2019.01.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Individuals differ substantially in their response to pharmacological treatment. Personalized medicine aspires to embrace these inter-individual differences and customize therapy by taking a wealth of patient-specific data into account. Pharmacogenomic constitutes a cornerstone of personalized medicine that provides therapeutic guidance based on the genomic profile of a given patient. Pharmacogenomics already has applications in the clinics, particularly in oncology, whereas future development in this area is needed in order to establish pharmacogenomic biomarkers as useful clinical tools. In this review we present an updated overview of current and emerging pharmacogenomic biomarkers in different therapeutic areas and critically discuss their potential to transform clinical care. Furthermore, we discuss opportunities of technological, methodological and institutional advances to improve biomarker discovery. We also summarize recent progress in our understanding of epigenetic effects on drug disposition and response, including a discussion of the only few pharmacogenomic biomarkers implemented into routine care. We anticipate, in part due to exciting rapid developments in Next Generation Sequencing technologies, machine learning methods and national biobanks, that the field will make great advances in the upcoming years towards unlocking the full potential of genomic data.
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Affiliation(s)
- Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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38
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Byrne L, Drake AJ. Paediatrician's guide to epigenetics. Arch Dis Child 2019; 104:297-301. [PMID: 30655261 DOI: 10.1136/archdischild-2018-316054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 11/03/2022]
Abstract
Epigenetic regulation of gene expression is critical for normal development. Dysregulation of the epigenome can lead to the development and progression of a number of diseases relevant to paediatricians, including disorders of genomic imprinting and malignancies. It has long been recognised that early life events have implications for future disease risk, and epigenetic modifications may play a role in this, although further high-quality research is needed to better understand the underlying mechanisms. Research in the field of epigenetics will contribute to a greater understanding of growth, development and disease; however, paediatricians need to be able to interpret such research critically, in order to use the potential advances brought about through epigenetic studies while appreciating their limitations.
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Affiliation(s)
- Lauren Byrne
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Amanda Jane Drake
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK.,Department of Paediatric Endocrinology, Royal Hospital for Sick Children, Edinburgh, UK
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39
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Rohde K, Keller M, la Cour Poulsen L, Blüher M, Kovacs P, Böttcher Y. Genetics and epigenetics in obesity. Metabolism 2019; 92:37-50. [PMID: 30399374 DOI: 10.1016/j.metabol.2018.10.007] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/15/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Obesity is among the most threatening health burdens worldwide and its prevalence has markedly increased over the last decades. Obesity maybe considered a heritable trait. Identifications of rare cases of monogenic obesity unveiled that hypothalamic circuits and the brain-adipose axis play an important role in the regulation of energy homeostasis, appetite, hunger and satiety. For example, mutations in the leptin gene cause obesity through almost unsuppressed overeating. Common (multifactorial) obesity, most likely resulting from a concerted interplay of genetic, epigenetic and environmental factors, is clearly linked to genetic predisposition by multiple risk variants, which, however only account for a minor part of the general BMI variability. Although GWAS opened new avenues in elucidating the complex genetics behind common obesity, understanding the biological mechanisms relative to the specific risk contributing to obesity remains poorly understood. Non-genetic factors such as eating behavior or physical activity strongly modulate the individual risk for developing obesity. These factors may interact with genetic predisposition for obesity through epigenetic mechanisms. Thus, here, we review the current knowledge about monogenic and common (multifactorial) obesity highlighting the important recent advances in our knowledge on how epigenetic regulation is involved in the etiology of obesity.
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Affiliation(s)
- Kerstin Rohde
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway.
| | - Maria Keller
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Lars la Cour Poulsen
- Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway; Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
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40
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Cazaly E, Saad J, Wang W, Heckman C, Ollikainen M, Tang J. Making Sense of the Epigenome Using Data Integration Approaches. Front Pharmacol 2019; 10:126. [PMID: 30837884 PMCID: PMC6390500 DOI: 10.3389/fphar.2019.00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.
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Affiliation(s)
- Emma Cazaly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Joseph Saad
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Wenyu Wang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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41
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Grau-Perez M, Agha G, Pang Y, Bermudez JD, Tellez-Plaza M. Mendelian Randomization and the Environmental Epigenetics of Health: a Systematic Review. Curr Environ Health Rep 2019; 6:38-51. [DOI: 10.1007/s40572-019-0226-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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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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43
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Salvestrini V, Sell C, Lorenzini A. Obesity May Accelerate the Aging Process. Front Endocrinol (Lausanne) 2019; 10:266. [PMID: 31130916 PMCID: PMC6509231 DOI: 10.3389/fendo.2019.00266] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/10/2019] [Indexed: 12/27/2022] Open
Abstract
Lines of evidence from several studies have shown that increases in life expectancy are now accompanied by increased disability rate. The expanded lifespan of the aging population imposes a challenge on the continuous increase of chronic disease. The prevalence of overweight and obesity is increasing at an alarming rate in many parts of the world. Further to increasing the onset of metabolic imbalances, obesity leads to reduced life span and affects cellular and molecular processes in a fashion resembling aging. Nine key hallmarks of the aging process have been proposed. In this review, we will review these hallmarks and discuss pathophysiological changes that occur with obesity, that are similar to or contribute to those that occur during aging. We present and discuss the idea that obesity, in addition to having disease-specific effects, may accelerate the rate of aging affecting all aspects of physiology and thus shortening life span and health span.
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Affiliation(s)
- Valentina Salvestrini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Christian Sell
- Department of Pathology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Antonello Lorenzini
- Department of Biomedical and Neuromotor Sciences, Biochemistry Unit, University of Bologna, Bologna, Italy
- *Correspondence: Antonello Lorenzini
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44
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James P, Sajjadi S, Tomar AS, Saffari A, Fall CHD, Prentice AM, Shrestha S, Issarapu P, Yadav DK, Kaur L, Lillycrop K, Silver M, Chandak GR. Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism. Int J Epidemiol 2018; 47:1910-1937. [PMID: 30137462 PMCID: PMC6280938 DOI: 10.1093/ije/dyy153] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background Mounting evidence suggests that nutritional exposures during pregnancy influence the fetal epigenome, and that these epigenetic changes can persist postnatally, with implications for disease risk across the life course. Methods We review human intergenerational studies using a three-part search strategy. Search 1 investigates associations between preconceptional or pregnancy nutritional exposures, focusing on one-carbon metabolism, and offspring DNA methylation. Search 2 considers associations between offspring DNA methylation at genes found in the first search and growth-related, cardiometabolic and cognitive outcomes. Search 3 isolates those studies explicitly linking maternal nutritional exposure to offspring phenotype via DNA methylation. Finally, we compile all candidate genes and regions of interest identified in the searches and describe their genomic locations, annotations and coverage on the Illumina Infinium Methylation beadchip arrays. Results We summarize findings from the 34 studies found in the first search, the 31 studies found in the second search and the eight studies found in the third search. We provide details of all regions of interest within 45 genes captured by this review. Conclusions Many studies have investigated imprinted genes as priority loci, but with the adoption of microarray-based platforms other candidate genes and gene classes are now emerging. Despite a wealth of information, the current literature is characterized by heterogeneous exposures and outcomes, and mostly comprise observational associations that are frequently underpowered. The synthesis of current knowledge provided by this review identifies research needs on the pathway to developing possible early life interventions to optimize lifelong health.
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Affiliation(s)
- Philip James
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ashutosh Singh Tomar
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ayden Saffari
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Caroline H D Fall
- MRC Life course Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Prachand Issarapu
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Dilip Kumar Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Karen Lillycrop
- Research Centre for Biological Sciences, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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45
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Huang JV, Cardenas A, Colicino E, Schooling CM, Rifas-Shiman SL, Agha G, Zheng Y, Hou L, Just AC, Litonjua AA, DeMeo DL, Lin X, Oken E, Hivert MF, Baccarelli AA. DNA methylation in blood as a mediator of the association of mid-childhood body mass index with cardio-metabolic risk score in early adolescence. Epigenetics 2018; 13:1072-1087. [PMID: 30412002 PMCID: PMC6342073 DOI: 10.1080/15592294.2018.1543503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022] Open
Abstract
Obesity is associated with higher cardio-metabolic risk even in childhood and adolescence; whether this association is mediated by epigenetic mechanisms remains unclear. We examined the extent to which mid-childhood body mass index (BMI) z-score (median age 7.7 years) was associated with cardio-metabolic risk score in early adolescence (median age 12.9 years) via mid-childhood DNA methylation among 265 children in the Project Viva. We measured DNA methylation in leukocytes using the Infinium Human Methylation450K BeadChip. We assessed mediation CpG-by-CpG using epigenome-wide association analyses, high-dimensional mediation analysis, and natural effect models. We observed mediation by mid-childhood DNA methylation at 6 CpGs for the association between mid-childhood BMI z-score and cardio-metabolic risk score in early adolescence in the high-dimensional mediation analysis (accounting for 10% of the total effect) and in the natural effect model (β = 0.04, P = 3.2e-2, accounting for 13% of the total effect). The natural direct effect of BMI z-score on cardio-metabolic risk score was still evident (β = 0.27, P = 1.1e-25). We also observed mediation by mid-childhood DNA methylation at 5 CpGs that was in the opposite direction from the total effect (natural effect model: β = -0.04, P = 2.0e-2). Mediation in different directions implies a complex role of DNA methylation in the association between BMI and cardio-metabolic risk and needs further investigation. Future studies with larger sample size and greater variability in cardio-metabolic risk will further help elucidate the role of DNA methylation for cardio-metabolic risk.
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Affiliation(s)
- Jian V. Huang
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, NY, NY, USA
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Andres Cardenas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Elena Colicino
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - C. Mary Schooling
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, People’s Republic of China
- Graduate School of Public Health and Health Policy, City University of New York, New York, USA
| | - Sheryl L. Rifas-Shiman
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Golareh Agha
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, NY, NY, USA
| | - Yinan Zheng
- Center for Population Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Allan C. Just
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Augusto A. Litonjua
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, NY, NY, USA
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Population DNA methylation studies in the Developmental Origins of Health and Disease (DOHaD) framework. J Dev Orig Health Dis 2018; 10:306-313. [PMID: 30101736 DOI: 10.1017/s2040174418000442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic changes represent a potential mechanism underlying associations of early-life exposures and later life health outcomes. Population-based cohort studies starting in early life are an attractive framework to study the role of such changes. DNA methylation is the most studied epigenetic mechanism in population research. We discuss the application of DNA methylation in early-life population studies, some recent findings, key challenges and recommendations for future research. Studies into DNA methylation within the Developmental Origins of Health and Disease framework generally either explore associations between prenatal exposures and offspring DNA methylation or associations between offspring DNA methylation in early life and later health outcomes. Only a few studies to date have integrated prospective exposure, epigenetic and phenotypic data in order to explicitly test the role of DNA methylation as a potential biological mediator of environmental effects on health outcomes. Population epigenetics is an emerging field which has challenges in terms of methodology and interpretation of the data. Key challenges include tissue specificity, cell type adjustment, issues of power and comparability of findings, genetic influences, and exploring causality and functional consequences. Ongoing studies are working on addressing these issues. Large collaborative efforts of prospective cohorts are emerging, with clear benefits in terms of optimizing power and use of resources, and in advancing methodology. In the future, multidisciplinary approaches, within and beyond longitudinal birth and preconception cohorts will advance this complex, but highly promising, the field of research.
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Li S, Wong EM, Bui M, Nguyen TL, Joo JHE, Stone J, Dite GS, Dugué PA, Milne RL, Giles GG, Saffery R, Southey MC, Hopper JL. Inference about causation between body mass index and DNA methylation in blood from a twin family study. Int J Obes (Lond) 2018; 43:243-252. [PMID: 29777239 DOI: 10.1038/s41366-018-0103-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Several studies have reported DNA methylation in blood to be associated with body mass index (BMI), but few have investigated causal aspects of the association. We used a twin family design to assess this association at two life points and applied a novel analytical approach to appraise the evidence for causality. METHODS The methylation profile of DNA from peripheral blood was measured for 479 Australian women from 130 twin families. Linear regression was used to estimate the associations of DNA methylation at ~410,000 cytosine-guanine dinucleotides (CpGs), and of the average DNA methylation at ~20,000 genes, with current BMI, BMI at age 18-21 years, and the change between the two (BMI change). A novel regression-based methodology for twins, Inference about Causation through Examination of Familial Confounding (ICE FALCON), was used to assess causation. RESULTS At a 5% false discovery rate, nine, six and 12 CpGs at 24 loci were associated with current BMI, BMI at age 18-21 years and BMI change, respectively. The average DNA methylation of the BHLHE40 and SOCS3 loci was associated with current BMI, and of the PHGDH locus with BMI change. From the ICE FALCON analyses with BMI as the predictor and DNA methylation as the outcome, a woman's DNA methylation level was associated with her co-twin's BMI, and the association disappeared after conditioning on her own BMI, consistent with BMI causing DNA methylation. To the contrary, using DNA methylation as the predictor and BMI as the outcome, a woman's BMI was not associated with her co-twin's DNA methylation level, consistent with DNA methylation not causing BMI. CONCLUSION For middle-aged women, peripheral blood DNA methylation at several genomic locations is associated with current BMI, BMI at age 18-21 years and BMI change. Our study suggests that BMI has a causal effect on peripheral blood DNA methylation.
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Affiliation(s)
- Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ee Ming Wong
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Ji-Hoon Eric Joo
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Jennifer Stone
- Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, WA, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, VIC, Australia.
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Curtis EM, Suderman M, Phillips CM, Relton C, Harvey NC. Early-life dietary and epigenetic influences on childhood musculoskeletal health: Update on the UK component of the ALPHABET project. NUTR BULL 2018. [DOI: 10.1111/nbu.12322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- E. M. Curtis
- MRC Lifecourse Epidemiology Unit, University of Southampton; Southampton UK
| | - M. Suderman
- MRC Integrative Epidemiology Unit, University of Bristol; Bristol UK
| | - C. M. Phillips
- HRB Centre for Diet and Health Research, University College Dublin; Dublin Ireland
| | - C. Relton
- MRC Integrative Epidemiology Unit, University of Bristol; Bristol UK
| | - N. C. Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton; Southampton UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust; Southampton UK
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49
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Toghill BJ, Saratzis A, Freeman PJ, Sylvius N, Bown MJ. SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells. Clin Epigenetics 2018; 10:29. [PMID: 29507647 PMCID: PMC5833080 DOI: 10.1186/s13148-018-0460-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
Background Abdominal aortic aneurysm (AAA) is a deadly cardiovascular disease characterised by the gradual, irreversible dilation of the abdominal aorta. AAA is a complex genetic disease but little is known about the role of epigenetics. Our objective was to determine if global DNA methylation and CpG-specific methylation at known AAA risk loci is associated with AAA, and the functional effects of methylation changes. Results We assessed global methylation in peripheral blood mononuclear cell DNA from 92 individuals with AAA and 93 controls using enzyme-linked immunosorbent assays, identifying hyper-methylation in those with large AAA and a positive linear association with AAA diameter (P < 0.0001, R2 = 0.3175).We then determined CpG methylation status of regulatory regions in genes located at AAA risk loci identified in genome-wide association studies, using bisulphite next-generation sequencing (NGS) in vascular smooth muscle cells (VSMCs) taken from aortic tissues of 44 individuals (24 AAAs and 20 controls). In IL6R, 2 CpGs were hyper-methylated (P = 0.0145); in ERG, 13 CpGs were hyper-methylated (P = 0.0005); in SERPINB9, 6 CpGs were hypo-methylated (P = 0.0037) and 1 CpG was hyper-methylated (P = 0.0098); and in SMYD2, 4 CpGs were hypo-methylated (P = 0.0012).RT-qPCR was performed for each differentially methylated gene on mRNA from the same VSMCs and compared with methylation. This analysis revealed downregulation of SMYD2 and SERPINB9 in AAA, and a direct linear relationship between SMYD2 promoter methylation and SMYD2 expression (P = 0.038). Furthermore, downregulation of SMYD2 at the site of aneurysm in the aortic wall was further corroborated in 6 of the same samples used for methylation and gene expression analysis with immunohistochemistry. Conclusions This study is the first to assess DNA methylation in VSMCs from individuals with AAA using NGS, and provides further evidence there is an epigenetic basis to AAA. Our study shows that methylation status of the SMYD2 promoter may be linked with decreased SMYD2 expression in disease pathobiology. In support of our work, downregulated SMYD2 has previously been associated with adverse cardiovascular physiology and inflammation, which are both hallmarks of AAA. The identification of such adverse epigenetic modifications could potentially contribute towards the development of epigenetic treatment strategies in the future.
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Affiliation(s)
- Bradley J Toghill
- 1Department of Cardiovascular Sciences and the NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, LE2 7LX UK
| | - Athanasios Saratzis
- 1Department of Cardiovascular Sciences and the NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, LE2 7LX UK
| | - Peter J Freeman
- 2Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | - Nicolas Sylvius
- 2Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH UK
| | | | - Matthew J Bown
- 1Department of Cardiovascular Sciences and the NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, LE2 7LX UK
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50
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Keating ST, van Diepen JA, Riksen NP, El-Osta A. Epigenetics in diabetic nephropathy, immunity and metabolism. Diabetologia 2018; 61:6-20. [PMID: 29128937 PMCID: PMC6448927 DOI: 10.1007/s00125-017-4490-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/22/2017] [Indexed: 01/01/2023]
Abstract
When it comes to the epigenome, there is a fine line between clarity and confusion-walk that line and you will discover another fascinating level of transcription control. With the genetic code representing the cornerstone of rules for information that is encoded to proteins somewhere above the genome level there is a set of rules by which chemical information is also read. These epigenetic modifications show a different side of the genetic code that is diverse and regulated, hence modifying genetic transcription transiently, ranging from short- to long-term alterations. While this complexity brings exquisite control it also poses a formidable challenge to efforts to decode mechanisms underlying complex disease. Recent technological and computational advances have improved unbiased acquisition of epigenomic patterns to improve our understanding of the complex chromatin landscape. Key to resolving distinct chromatin signatures of diabetic complications is the identification of the true physiological targets of regulatory proteins, such as reader proteins that recognise, writer proteins that deposit and eraser proteins that remove specific chemical moieties. But how might a diverse group of proteins regulate the diabetic landscape from an epigenomic perspective? Drawing from an ever-expanding compendium of experimental and clinical studies, this review details the current state-of-play and provides a perspective of chromatin-dependent mechanisms implicated in diabetic complications, with a special focus on diabetic nephropathy. We hypothesise a codified signature of the diabetic epigenome and provide examples of prime candidates for chemical modification. As for the pharmacological control of epigenetic marks, we explore future strategies to expedite and refine the search for clinically relevant discoveries. We also consider the challenges associated with therapeutic strategies targeting epigenetic pathways.
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Affiliation(s)
- Samuel T Keating
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands.
| | - Janna A van Diepen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Assam El-Osta
- Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC, 3004, Australia.
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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