1
|
Kular L. The lung-brain axis in multiple sclerosis: Mechanistic insights and future directions. Brain Behav Immun Health 2024; 38:100787. [PMID: 38737964 PMCID: PMC11087231 DOI: 10.1016/j.bbih.2024.100787] [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: 11/30/2023] [Revised: 03/23/2024] [Accepted: 05/02/2024] [Indexed: 05/14/2024] Open
Abstract
Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system with progressive lifelong disability. Current treatments are particularly effective at the early inflammatory stage of the disease but associate with safety concerns such as increased risk of infection. While clinical and epidemiological evidence strongly support the role of a bidirectional communication between the lung and the brain in MS in influencing disease risk and severity, the exact processes underlying such relationship appear complex and not fully understood. This short review aims to summarize key findings and future perspectives that might provide new insights into the mechanisms underpinning the lung-brain axis in MS.
Collapse
Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
2
|
Vasileva D, Greenwood CMT, Daley D. A Review of the Epigenetic Clock: Emerging Biomarkers for Asthma and Allergic Disease. Genes (Basel) 2023; 14:1724. [PMID: 37761864 PMCID: PMC10531327 DOI: 10.3390/genes14091724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergies. One method to study the role of DNAm is the epigenetic clock-an algorithm that uses DNAm levels at select age-informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such as asthma and allergic diseases, which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma. We delve into how in utero and early life exposures (e.g., smoking, air pollution, maternal BMI) result in methylation changes. Furthermore, we explore the potential for EAA to be used as a biomarker for asthma and allergic diseases and identify areas for further study.
Collapse
Affiliation(s)
- Denitsa Vasileva
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada;
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 0G4, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Denise Daley
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
- Department of Medicine, Respiratory Division, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
3
|
Wajda A, Bogucka D, Stypińska B, Radkowski MJ, Targowski T, Dudek E, Kmiołek T, Modzelewska E, Paradowska-Gorycka A. Expression of Prostaglandin Genes and β-Catenin in Whole Blood as Potential Markers of Muscle Degeneration. Int J Mol Sci 2023; 24:12885. [PMID: 37629065 PMCID: PMC10454559 DOI: 10.3390/ijms241612885] [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: 08/02/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Prostaglandin signaling pathways are closely related to inflammation, but also muscle regeneration and processes associated with frailty and sarcopenia, whereas β-catenin (CTNNB1 gene) as a part of Wnt signaling is also involved in the differentiation of muscle cells and fibrosis. The present study analyzed the association between selected prostaglandin pathway genes and clinical parameters in patients with sarcopenia and frailty syndrome. The present study was conducted on patients with sarcopenia, frailty syndrome, and control older patients (N = 25). Additionally, two healthy controls at the age of 25-30 years (N = 51) and above 50 years old (N = 42) were included. The expression of the PTRGER4, PTGES2 (COX2), PTGS2, and CTNNB1 genes in whole blood was checked by the qPCR method. The serum cytokine levels (IL-10, TNFα, IFN-y, IL-1α, IL-1β) in patients and controls were checked by the Q-Plex Human Cytokine Panel. The results showed a significant effect of age on PTGER4 gene expression (p = 0.01). A negative trend between the appendicular skeletal muscle mass parameter (ASSM) and the expression of PTGER4 has been noted (r = -0.224, p = 0.484). PTGES2 and PTGS2 expressions negatively correlated with creatine phosphokinase (r = -0.71, p = 0.009; r = -0.58, p = 0.047) and positively with the functional mobility test timed up and go scale (TUG) (r = 0.61, p = 0.04; r = 0.63, p = 0.032). In the older control group, a negative association between iron levels and the expression of PTGS2 (r = -0.47, p = 0.017) was observed. A similar tendency was noted in patients with sarcopenia (r = -0.112, p = 0.729). A negative trend between appendicular skeletal muscle mass (ASMM) and PTGER4 seems to confirm the impairment of muscle regeneration associated with sarcopenia. The expression of the studied genes revealed a trend in associations with the clinical picture of muscular dystrophy and weakening patients. Perhaps PTGS2 and PTGES2 is in opposition to the role of the PTGER4 receptor in muscle physiology. Nevertheless, further, including functional studies is needed.
Collapse
Affiliation(s)
- Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Diana Bogucka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Marcin Jerzy Radkowski
- Department of Geriatrics, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (M.J.R.); (T.T.)
| | - Tomasz Targowski
- Department of Geriatrics, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (M.J.R.); (T.T.)
| | - Ewa Dudek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Ewa Modzelewska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland; (D.B.); (B.S.); (E.D.); (T.K.); (E.M.); (A.P.-G.)
| |
Collapse
|
4
|
Roy R, Kuo PL, Candia J, Sarantopoulou D, Ubaida-Mohien C, Hernandez D, Kaileh M, Arepalli S, Singh A, Bektas A, Kim J, Moore AZ, Tanaka T, McKelvey J, Zukley L, Nguyen C, Wallace T, Dunn C, Wood W, Piao Y, Coletta C, De S, Sen J, Weng NP, Sen R, Ferrucci L. Epigenetic signature of human immune aging in the GESTALT study. eLife 2023; 12:e86136. [PMID: 37589453 PMCID: PMC10506794 DOI: 10.7554/elife.86136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
Age-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood-borne immune cell types (naive B, naive CD4+ and CD8+ T cells, granulocytes, monocytes, and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousands of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor (TF) motifs, respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to TF motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.
Collapse
Affiliation(s)
- Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Pei-Lun Kuo
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julián Candia
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | | | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on AgingBethesdaUnited States
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Arsun Bektas
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Jaekwan Kim
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ann Z Moore
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| | - Julia McKelvey
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Linda Zukley
- Clinical Research Core, National Institute on AgingBaltimoreUnited States
| | - Cuong Nguyen
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Tonya Wallace
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on AgingBaltimoreUnited States
| | - William Wood
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Christopher Coletta
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on AgingBaltimoreUnited States
| | - Jyoti Sen
- Laboratory of Clinical Investigation, National Institute on AgingBaltimoreUnited States
| | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on AgingBaltimoreUnited States
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on AgingBaltimoreUnited States
| |
Collapse
|
5
|
Alba-Linares JJ, Pérez RF, Tejedor JR, Bastante-Rodríguez D, Ponce F, Carbonell NG, Zafra RG, Fernández AF, Fraga MF, Lurbe E. Maternal obesity and gestational diabetes reprogram the methylome of offspring beyond birth by inducing epigenetic signatures in metabolic and developmental pathways. Cardiovasc Diabetol 2023; 22:44. [PMID: 36870961 PMCID: PMC9985842 DOI: 10.1186/s12933-023-01774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Obesity is a negative chronic metabolic health condition that represents an additional risk for the development of multiple pathologies. Epidemiological studies have shown how maternal obesity or gestational diabetes mellitus during pregnancy constitute serious risk factors in relation to the appearance of cardiometabolic diseases in the offspring. Furthermore, epigenetic remodelling may help explain the molecular mechanisms that underlie these epidemiological findings. Thus, in this study we explored the DNA methylation landscape of children born to mothers with obesity and gestational diabetes during their first year of life. METHODS We used Illumina Infinium MethylationEPIC BeadChip arrays to profile more than 770,000 genome-wide CpG sites in blood samples from a paediatric longitudinal cohort consisting of 26 children born to mothers who suffered from obesity or obesity with gestational diabetes mellitus during pregnancy and 13 healthy controls (measurements taken at 0, 6 and 12 month; total N = 90). We carried out cross-sectional and longitudinal analyses to derive DNA methylation alterations associated with developmental and pathology-related epigenomics. RESULTS We identified abundant DNA methylation changes during child development from birth to 6 months and, to a lesser extent, up to 12 months of age. Using cross-sectional analyses, we discovered DNA methylation biomarkers maintained across the first year of life that could discriminate children born to mothers who suffered from obesity or obesity with gestational diabetes. Importantly, enrichment analyses suggested that these alterations constitute epigenetic signatures that affect genes and pathways involved in the metabolism of fatty acids, postnatal developmental processes and mitochondrial bioenergetics, such as CPT1B, SLC38A4, SLC35F3 and FN3K. Finally, we observed evidence of an interaction between developmental DNA methylation changes and maternal metabolic condition alterations. CONCLUSIONS Our observations highlight the first six months of development as being the most crucial for epigenetic remodelling. Furthermore, our results support the existence of systemic intrauterine foetal programming linked to obesity and gestational diabetes that affects the childhood methylome beyond birth, which involves alterations related to metabolic pathways, and which may interact with ordinary postnatal development programmes.
Collapse
Affiliation(s)
- Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - David Bastante-Rodríguez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Francisco Ponce
- Health Research Institute INCLIVA, Valencia, Spain
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Nuria García Carbonell
- Health Research Institute INCLIVA, Valencia, Spain
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Rafael Gómez Zafra
- Health Research Institute INCLIVA, Valencia, Spain
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain.
| | - Empar Lurbe
- Health Research Institute INCLIVA, Valencia, Spain.
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III (ISCIII), Madrid, Spain.
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain.
| |
Collapse
|
6
|
Guo X, Qi H, Lin G, Yu J, Zhang M, Gao X. ARID3A plays a key regulatory role in palmitic acid-stimulated milk fat synthesis in mouse mammary epithelial cells. Cell Biol Int 2023; 47:1106-1117. [PMID: 36786478 DOI: 10.1002/cbin.12003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/18/2023] [Accepted: 02/05/2023] [Indexed: 02/15/2023]
Abstract
Palmitic acid (PA) can stimulate milk fat synthesis in mammary gland, but the specific mechanism is still unclear. In our research, we aim to explore the role and corresponding mechanism of AT-rich interaction domain 3A (ARID3A) in milk fat synthesis stimulated by PA. We found that ARID3A protein level in mouse mammary gland tissues during lactation was much higher than that during puberty and involution. ARID3A knockdown and gene activation showed that ARID3A stimulated the synthesis of triglycerides and cholesterol in HC11 cells, secretion of free fatty acids from cells and lipid droplet formation in cells. ARID3A also promoted the expression and maturation of SREBP1 in HC11 cells. PA stimulated ARID3A protein expression and SREBP1 expression and maturation in a dose-dependent manner, and the PI3K specific inhibitor LY294002 blocked the stimulation of PA on ARID3A expression. ARID3A knockdown blocked the stimulation of PA on SREBP1 protein expression and maturation. We further showed that ARID3A was localized in the nucleus and PA stimulated this localization, and ARID3A knockdown blocked the stimulation of PA on the mRNA expression of SREBP1. To sum up, our data reveal that ARID3A is a key mediator for PA to promote SREBP1 mRNA expression and stimulate milk fat synthesis in mammary epithelial cells.
Collapse
Affiliation(s)
- Xudong Guo
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hao Qi
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Gang Lin
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Jiaxiao Yu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Minghui Zhang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xuejun Gao
- College of Animal Science, Yangtze University, Jingzhou, China
| |
Collapse
|
7
|
Childhood Trauma and Epigenetics: State of the Science and Future. Curr Environ Health Rep 2022; 9:661-672. [PMID: 36242743 DOI: 10.1007/s40572-022-00381-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is a great deal of interest regarding the biological embedding of childhood trauma and social exposures through epigenetic mechanisms, including DNA methylation (DNAm), but a comprehensive understanding has been hindered by issues of limited reproducibility between studies. This review presents a summary of the literature on childhood trauma and DNAm, highlights issues in the field, and proposes some potential solutions. RECENT FINDINGS Investigations of the associations between DNAm and childhood trauma are commonly performed using candidate gene approaches, specifically involving genes related to neurological and stress pathways. Childhood trauma is defined in a wide range of ways in several societal contexts. However, although variations in DNAm are frequently found in stress-related genes, unsupervised epigenome-wide association studies (EWAS) have shown limited reproducibility both between studies and in relating these changes to exposures. The reproducibility of childhood trauma DNAm studies, and the field of social epigenetics in general, may be improved by increasing sample sizes, standardizing variables, making use of effect size thresholds, collecting longitudinal and intervention samples, appropriately accounting for known confounding factors, and applying causal analysis wherever possible, such as "two-step epigenetic Mendelian randomization."
Collapse
|
8
|
Charoenvicha C, Sirimaharaj W, Khwanngern K, Chattipakorn N, Chattipakorn SC. Alterations in DNA Methylation in Orofacial Clefts. Int J Mol Sci 2022; 23:ijms232112727. [PMID: 36361518 PMCID: PMC9654384 DOI: 10.3390/ijms232112727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Orofacial clefts are among the most common craniofacial anomalies with multifactorial etiologies, including genetics and environments. DNA methylation, one of the most acknowledged mechanisms of epigenetics, is involved in the development of orofacial clefts. DNA methylation has been examined in patients with non-syndromic cleft lip with cleft palate (nsCL/P) from multiple specimens, including blood, saliva, lip, and palate, as well as experimental studies in mice. The results can be reported in two different trends: hypomethylation and hypermethylation. Both hypomethylation and hypermethylation can potentially increase the risk of nsCL/P depending on the types of specimens and the specific regions on each gene and chromosome. This is the most up-to-date review, intending to summarize evidence of the alterations of DNA methylation in association with the occurrence of orofacial clefts. To make things straightforward to understand, we have systematically categorized the data into four main groups: human blood, human tissues, animal models, and the factors associated with DNA methylation. With this review, we are moving closer to the core of DNA methylation associated with nsCL/P development; we hope this is the initial step to find a genetic tool for early detection and prevention of the occurrence of nsCL/P.
Collapse
Affiliation(s)
- Chirakan Charoenvicha
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wimon Sirimaharaj
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Krit Khwanngern
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Siriporn C. Chattipakorn
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +011-66-53-944-451; Fax: +011-66-53-222-844
| |
Collapse
|
9
|
Olin A, Acevedo N, Lakshmikanth T, Chen Y, Johansson C, Alm J, Scheynius A, Brodin P. Longitudinal analyses of development of the immune system during the first five years of life in relation to lifestyle. Allergy 2022; 77:1583-1595. [PMID: 35094423 DOI: 10.1111/all.15232] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Changes in immune cell composition during the immunological window within the first years after birth are not fully understood, especially the effect that different lifestyles might have on immune cell functionality. METHODS Peripheral blood mononuclear cells from mothers and their children at birth and at two anvd five years were analyzed by mass cytometry. Immune cell composition and functionality was analyzed according to family lifestyle (anthroposophic and non-anthroposophic). RESULTS We found no significant differences in the proportions of major immune lineages between anthroposophic and non-anthroposophic children at each time point, but there were clear changes over time in the proportions of mononuclear leukocytes, especially in B-cells and T lymphocytes. Phenotypic distances between cord blood and maternal blood were high at birth but decreased sharply the first two years, indicating strong phenotypic convergence with maternal cells. We found that children exhibited similar stimulation responses at birth, but subsequently segregated into two discrete functional trajectories. Trajectory 1 was associated with a decrease in tumor necrosis factor alpha (TNFa) production by CD4+ T- and NK-cells, while Trajectory 2 depicted an increase in the production of IL-2 and interferon gamma (INFg) by T-cells. In both trajectories, there was an increase in IL-17A production by T-cells resulting in prominent differences at five years of age. CONCLUSIONS This exploratory study suggests that leukocyte frequencies and cell phenotypes change with age in the same way across all children, while functional development follows one of two discrete trajectories that largely segregate by family lifestyle, supporting the hypothesis that early environmental exposures imprint immune cell function which may contribute to IgE sensitization. Our results also support that the first two years are critical for the environmental exposures to imprint the immune cells. Further studies with larger sample sizes are required to validate our findings.
Collapse
Affiliation(s)
- Axel Olin
- Science for Life Laboratory Department of Women’s and Children's Health Karolinska Institutet Stockholm Sweden
| | - Nathalie Acevedo
- Department of Clinical Science and Education Karolinska Institutet Stockholm Sweden
- Sachs' Children and Youth Hospital Södersjukhuset Stockholm Sweden
- Institute for Immunological Research University of Cartagena Cartagena Colombia
| | - Tadepally Lakshmikanth
- Science for Life Laboratory Department of Women’s and Children's Health Karolinska Institutet Stockholm Sweden
| | - Yang Chen
- Science for Life Laboratory Department of Women’s and Children's Health Karolinska Institutet Stockholm Sweden
| | - Catharina Johansson
- Department of Clinical Science and Education Karolinska Institutet Stockholm Sweden
- Sachs' Children and Youth Hospital Södersjukhuset Stockholm Sweden
| | - Johan Alm
- Department of Clinical Science and Education Karolinska Institutet Stockholm Sweden
- Sachs' Children and Youth Hospital Södersjukhuset Stockholm Sweden
| | - Annika Scheynius
- Department of Clinical Science and Education Karolinska Institutet Stockholm Sweden
- Sachs' Children and Youth Hospital Södersjukhuset Stockholm Sweden
- Science for Life Laboratory Karolinska Institutet Stockholm Sweden
| | - Petter Brodin
- Science for Life Laboratory Department of Women’s and Children's Health Karolinska Institutet Stockholm Sweden
- Department of Newborn Medicine Karolinska University Hospital Stockholm Sweden
| |
Collapse
|
10
|
Lozano M, Yousefi P, Broberg K, Soler-Blasco R, Miyashita C, Pesce G, Kim WJ, Rahman M, Bakulski KM, Haug LS, Ikeda-Araki A, Huel G, Park J, Relton C, Vrijheid M, Rifas-Shiman S, Oken E, Dou JF, Kishi R, Gutzkow KB, Annesi-Maesano I, Won S, Hivert MF, Fallin MD, Vafeiadi M, Ballester F, Bustamante M, Llop S. DNA methylation changes associated with prenatal mercury exposure: A meta-analysis of prospective cohort studies from PACE consortium. ENVIRONMENTAL RESEARCH 2022; 204:112093. [PMID: 34562483 PMCID: PMC10879652 DOI: 10.1016/j.envres.2021.112093] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
Mercury (Hg) is a ubiquitous heavy metal that originates from both natural and anthropogenic sources and is transformed in the environment to its most toxicant form, methylmercury (MeHg). Recent studies suggest that MeHg exposure can alter epigenetic modifications during embryogenesis. In this study, we examined associations between prenatal MeHg exposure and levels of cord blood DNA methylation (DNAm) by meta-analysis in up to seven independent studies (n = 1462) as well as persistence of those relationships in blood from 7 to 8 year-old children (n = 794). In cord blood, we found limited evidence of differential DNAm at cg24184221 in MED31 (β = 2.28 × 10-4, p-value = 5.87 × 10-5) in relation to prenatal MeHg exposure. In child blood, we identified differential DNAm at cg15288800 (β = 0.004, p-value = 4.97 × 10-5), also located in MED31. This repeated link to MED31, a gene involved in lipid metabolism and RNA Polymerase II transcription function, may suggest a DNAm perturbation related to MeHg exposure that persists into early childhood. Further, we found evidence for association between prenatal MeHg exposure and child blood DNAm levels at two additional CpGs: cg12204245 (β = 0.002, p-value = 4.81 × 10-7) in GRK1 and cg02212000 (β = -0.001, p-value = 8.13 × 10-7) in GGH. Prenatal MeHg exposure was associated with DNAm modifications that may influence health outcomes, such as cognitive or anthropometric development, in different populations.
Collapse
Affiliation(s)
- Manuel Lozano
- Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain; Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain.
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Karin Broberg
- Unit of Metals and Health, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden; Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Raquel Soler-Blasco
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
| | - Chihiro Miyashita
- Center for Environmental and Health Sciences, Hokkaido University, Hokkaido, Japan
| | - Giancarlo Pesce
- INSERM UMR1018, Université Paris-Saclay, UVSQ, Centre for Epidemiology and Public Health (CESP), Villejuif, France
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, South Korea
| | - Mohammad Rahman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - Kelly M Bakulski
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Line S Haug
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Atsuko Ikeda-Araki
- Center for Environmental and Health Sciences, Hokkaido University, Hokkaido, Japan; Faculty of Health Sciences, Hokkaido University, Hokkaido, Japan
| | - Guy Huel
- INSERM UMR1018, Université Paris-Saclay, UVSQ, Centre for Epidemiology and Public Health (CESP), Villejuif, France
| | - Jaehyun Park
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Martine Vrijheid
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Sheryl Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States
| | - John F Dou
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Reiko Kishi
- Center for Environmental and Health Sciences, Hokkaido University, Hokkaido, Japan
| | - Kristine B Gutzkow
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Isabella Annesi-Maesano
- INSERM UMR1302, Montpellier University, Insitut Desbrest d'Épidémiologie et de Santé Publique (IDESP), Montpellier, France
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, South Korea; Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, United States; Diabetes Unit, Massachusetts General Hospital, Boston, MA, United States
| | - M Daniele Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Ferran Ballester
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; School of Nursing, Universitat de València, Valencia, Spain
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Sabrina Llop
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| |
Collapse
|
11
|
Lee KS, Lim YH, Lee YA, Shin CH, Kim BN, Hong YC, Kim JI. The association of prenatal and childhood pyrethroid pesticide exposure with school-age ADHD traits. ENVIRONMENT INTERNATIONAL 2022; 161:107124. [PMID: 35134717 DOI: 10.1016/j.envint.2022.107124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Pyrethroid insecticides are commonly used in residential settings, and their use has increased rapidly. Although research has been scarce, they have been reported to be associated with impaired neurodevelopment. Moreover, susceptible exposure windows and the long-term effects of pyrethroids have not been investigated. We examined the association between pyrethroid exposure and attention-deficit/hyperactivity disorder (ADHD) symptoms over time, with exposure windows spanning from the prenatal period to school-age. METHODS Using 524 mother-child pairs, we measured urinary concentrations of 3-phenoxybenzoic acid (3-PBA), a major pyrethroid metabolite, and asked parents to fill-out the ADHD Rating Scale IV (ARS). We used Poisson regression to identify the susceptible periods of pyrethroid exposure, by correlating various 3-PBA exposure windows (prenatal, ages 2, 4, 6 and 8) with ADHD symptoms at ages 6 and 8. RESULTS Doubling of prenatal and age 2 3-PBA concentrations was associated with increased ADHD symptoms at age 6 (2.7% change, 95% confidence interval [CI]: 0.3, 5.2; 5.2% change [95% CI: 0.5, 10.2], respectively). The 3-PBA concentrations at age 4 and age 6 were linked with ADHD symptoms at age 8 (2.7% change [95% CI: 0.3, 5.3]; 3.3% change [95% CI: 0.2, 6.4], respectively). There were no clear sex-specific patterns in association. DISCUSSION Both prenatal and early-childhood exposure to 3-PBA were found to be associated with ADHD symptoms. Exposure during pregnancy, and at ages 2 to 6 were found to be susceptible periods for pyrethroid neurotoxicity at ages 6 and 8.
Collapse
Affiliation(s)
- Kyung-Shin Lee
- Research Institue for Public Health, National Medical Center, Seoul, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea.
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea.
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University College of Medicine, Seoul, Korea.
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul, Korea; Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, South Korea.
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, Seoul, Republic of Korea.
| |
Collapse
|
12
|
Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
Collapse
Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
13
|
Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
Collapse
Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
| |
Collapse
|
14
|
Kim JI, Lee J, Lee KS, Lee YA, Shin CH, Hong YC, Kim BN, Lim YH. Association of phthalate exposure with autistic traits in children. ENVIRONMENT INTERNATIONAL 2021; 157:106775. [PMID: 34314979 DOI: 10.1016/j.envint.2021.106775] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Phthalates are synthetic chemicals with endocrine-disrupting properties. They are reportedly associated with various neurotoxic outcomes. Studies on exposure to phthalates and children's autistic traits have shown inconsistent results with respect to sex and susceptible time periods. We investigated the association of phthalate exposure during the prenatal period and childhood with autistic traits over time using a birth cohort in South Korea. METHODS Five phthalate metabolites were measured during mid-term pregnancy and children's follow-up at ages of 4, 6, and 8 years among a total of 547 mother-child pairs. The social communication questionnaire (SCQ) was used to assess autistic traits of children at each time point. The relationship between phthalate metabolites and SCQ scores were analyzed by exposure windows and sex. RESULTS A 2.7 fold increase in di-(2-ethylhexyl) phthalate metabolite levels, mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) and mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) during pregnancy was associated with increased SCQ scores at 4 years by 8.5% (95% confidence intervals [CI]: 1.9%, 15.5%) and 7.4% (95% CI: 0.3%, 15.0%), respectively, but not at the age of 6 or 8 years. Moreover, MEHHP levels at ages of 4 and 8 years were associated with increased SCQ scores at 8 years by 9.9% (95% CI: 1.8%, 18.6%) and 9.6% (95% CI: 1.3%, 18.6%), respectively. Boys showed stronger associations between phthalate exposure and SCQ scores than girls. CONCLUSION The study suggested different susceptible time windows of phthalate exposure: exposure during pregnancy is associated with autistic traits in young children, whereas exposure during early childhood years leads to autistic traits in school-aged children, particularly boys.
Collapse
Affiliation(s)
- Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, Seoul, Republic of Korea
| | - Jung Lee
- Integrative Care Hub, Children's Hospital, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, South Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
15
|
Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
Collapse
Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| |
Collapse
|
16
|
Liu L, Liu J, Lin Q. Histone demethylase KDM2A: Biological functions and clinical values (Review). Exp Ther Med 2021; 22:723. [PMID: 34007332 DOI: 10.3892/etm.2021.10155] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
Histone lysine demethylation modification is a critical epigenetic modification. Lysine demethylase 2A (KDM2A), a Jumonji C domain-containing demethylase, demethylates the dimethylated H3 lysine 36 (H3K36) residue and exerts little or no activity on monomethylated and trimethylated H3K36 residues. KDM2A expression is regulated by several factors, such as microRNAs, and the phosphorylation of KDM2A also plays a vital role in its function. KDM2A mainly recognizes the unmethylated region of CpG islands and subsequently demethylates histone H3K36 residues. In addition, KDM2A recognizes and binds to phosphorylated proteins, and promotes their ubiquitination and degradation. KDM2A plays an important role in chromosome remodeling and gene transcription, and is involved in cell proliferation and differentiation, cell metabolism, heterochromosomal homeostasis and gene stability. Notably, KDM2A is crucial for tumorigenesis and progression. In the present review, the documented biological functions of KDM2A in physiological and pathological processes are comprehensively summarized.
Collapse
Affiliation(s)
- Lisheng Liu
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, Jinan, Shandong 250014, P.R. China.,Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Qinghai Lin
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| |
Collapse
|
17
|
Maden SK, Thompson RF, Hansen KD, Nellore A. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genom Bioinform 2021; 3:lqab025. [PMID: 33937763 PMCID: PMC8061458 DOI: 10.1093/nargab/lqab025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina's 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
Collapse
Affiliation(s)
- Sean K Maden
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| |
Collapse
|
18
|
Wiencke JK, Zhang Z, Koestler DC, Salas LA, Molinaro AM, Christensen BC, Kelsey KT. Identification of a foetal epigenetic compartment in adult human kidney. Epigenetics 2021; 17:335-355. [PMID: 33783321 DOI: 10.1080/15592294.2021.1900027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The mammalian kidney has extensive repair capacity; however, identifying adult renal stem cells has proven elusive. We applied an epigenetic marker of foetal cell origin (FCO) in diverse human tissues as a probe for developmental cell persistence, finding a 5.4-fold greater FCO proportion in kidney. Normal kidney FCO proportions averaged 49% with extensive interindividual variation. FCO proportions were significantly negatively correlated with immune-related gene expression and positively correlated with genes expressed in the renal medulla, including those involved in renal organogenesis (e.g., FGF2, PAX8, and HOXB7). FCO associated genes also mapped to medullary nephron segments in mouse and rat, suggesting evolutionary conservation of this cellular compartment. Renal cancer patients whose tumours contained non-zero FCO scores survived longer. The kidney appears unique in possessing substantial foetal epigenetic features. Further study of FCO-related gene methylation may elucidate regenerative regulatory programmes in tissues without apparent discrete stem cell compartments.
Collapse
Affiliation(s)
- John K Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Ze Zhang
- Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Lucas A Salas
- Department of Epidemiology, Department of Molecular and Systems Biology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Brock C Christensen
- Department of Epidemiology, Department of Molecular and Systems Biology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI, USA
| |
Collapse
|
19
|
Ong LTC, Schibeci SD, Fewings NL, Booth DR, Parnell GP. Age-dependent VDR peak DNA methylation as a mechanism for latitude-dependent multiple sclerosis risk. Epigenetics Chromatin 2021; 14:9. [PMID: 33541415 PMCID: PMC7863270 DOI: 10.1186/s13072-021-00383-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/28/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The mechanisms linking UV radiation and vitamin D exposure to the risk of acquiring the latitude and critical period-dependent autoimmune disease, multiple sclerosis, is unclear. We examined the effect of vitamin D on DNA methylation and DNA methylation at vitamin D receptor binding sites in adult and paediatric myeloid cells. This was accomplished through differentiating CD34+ haematopoietic progenitors into CD14+ mononuclear phagocytes, in the presence and absence of calcitriol. RESULTS Few DNA methylation changes occurred in cells treated with calcitriol. However, several VDR-binding sites demonstrated increased DNA methylation in cells of adult origin when compared to cells of paediatric origin. This phenomenon was not observed at other transcription factor binding sites. Genes associated with these sites were enriched for intracellular signalling and cell activation pathways involved in myeloid cell differentiation and adaptive immune system regulation. CONCLUSION These results suggest vitamin D exposure at critical periods during development may contribute to latitude-related differences in autoimmune disease incidence.
Collapse
Affiliation(s)
- Lawrence T C Ong
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia. .,Department of Immunology, Westmead Hospital, Cnr Darcy and Hawkesbury Rds, Westmead, NSW, 2145, Australia.
| | - Stephen D Schibeci
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Nicole L Fewings
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, The University of Sydney, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| |
Collapse
|
20
|
Pischedda S, O'Connor D, Fairfax BP, Salas A, Martinon-Torres F, Pollard AJ, Trück J. Changes in epigenetic profiles throughout early childhood and their relationship to the response to pneumococcal vaccination. Clin Epigenetics 2021; 13:29. [PMID: 33541404 PMCID: PMC7860179 DOI: 10.1186/s13148-021-01012-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Background Pneumococcal infections are a major cause of morbidity and mortality in young children and immaturity of the immune system partly underlies poor vaccine responses seen in the young. Emerging evidence suggests a key role for epigenetics in the maturation and regulation of the immune system in health and disease. The study aimed to investigate epigenetic changes in early life and to understand the relationship between the epigenome and antigen-specific antibody responses to pneumococcal vaccination. Methods The epigenetic profiles from 24 healthy children were analyzed at 12 months prior to a booster dose of the 13-valent pneumococcal conjugate vaccine (PCV-13), and at 24 months of age, using the Illumina Methylation 450 K assay and assessed for differences over time and between high and low vaccine responders. Results Our analysis revealed 721 significantly differentially methylated positions between 12 and 24 months (FDR < 0.01), with significant enrichment in pathways involved in the regulation of cell–cell adhesion and T cell activation. Comparing high and low vaccine responders, we identified differentially methylated CpG sites (P value < 0.01) associated with HLA-DPB1 and IL6. Conclusion These data imply that epigenetic changes that occur during early childhood may be associated with antigen-specific antibody responses to pneumococcal vaccines.
Collapse
Affiliation(s)
- Sara Pischedda
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain. .,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Galicia, Spain.
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Benjamin P Fairfax
- MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Antonio Salas
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain.,Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Galicia, Spain
| | - Federico Martinon-Torres
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK. .,Division of Immunology and Children's Research Center, University Children's Hospital Zurich, University of Zurich (UZH), Zurich, Switzerland.
| |
Collapse
|
21
|
The SWI/SNF subunit SMARCD3 regulates cell cycle progression and predicts survival outcome in ER+ breast cancer. Breast Cancer Res Treat 2020; 185:601-614. [PMID: 33180234 DOI: 10.1007/s10549-020-05997-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE Chromatin remodeling plays an essential role in regulating transcriptional networks and timing of gene expression. Chromatin remodelers such as SWItch/Sucrose Non-Fermentable (SWI/SNF) harbor many protein components, with the catalytic subunit providing ATPase activity to displace histones along or from the DNA molecules, and associated subunits ensuring tissue specificity and transcriptional or co-transcriptional activities. Mutations in several of the SWI/SNF subunits have been linked to cancer. Here, we investigate between SMARCD3/Baf60c expression and hormone-positive (ER+) breast cancer. METHODS The level of SMARCD3 was detected by immunohistochemistry in breast cancer patient samples, and expression levels of SMARCD1, SMARCD2, and SMARCD3 were investigated using publicly available datasets from large cohorts of breast cancer patients. Using molecular biology and microscopy, we interrogated the cellular consequences of lower SMARCD3 expression. RESULTS Lower proliferation rates were observed in SMARCD3-depleted cells, which reflects a failure of the cell cycle progression and an increase in endoreplication. In the absence of SMARCD3, p21 accumulates in cells, but does not halt the cell cycle, and DNA damage accumulates and remains unrepaired. CONCLUSION Taken together, our data begin to explain why ER+ breast cancer patients with low-SMARCD3 expressing tumors exhibit reduced survival rates compared to patients expressing normal or higher levels of SMARCD3. SMARCD3 might act as a tumor suppressor through regulation of cell cycle checkpoints and could be a reliable and specific breast cancer prognostic biomarker.
Collapse
|
22
|
Hynes-Smith RW, Wittorf KJ, Buckley SM. Regulation of Normal and Malignant Hematopoiesis by FBOX Ubiquitin E3 Ligases. Trends Immunol 2020; 41:1128-1140. [PMID: 33160841 DOI: 10.1016/j.it.2020.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]
Abstract
Hematopoiesis is responsible for numerous functions, ranging from oxygen transportation to host defense, to injury repair. This process of hematopoiesis is maintained throughout life by hematopoietic stem cells and requires a controlled balance between self-renewal, differentiation, and quiescence. Disrupting this balance can result in hematopoietic malignancies, including anemia, immune deficiency, leukemia, and lymphoma. Recent work has shown that FBOX E3 ligases, a substrate recognition component of the ubiquitin proteasome system (UPS), have an integral role in maintaining this balance. In this review, we detail how FBOX proteins target specific proteins for degradation to regulate hematopoiesis through cell processes, such as cell cycle, development, and apoptosis.
Collapse
Affiliation(s)
- R Willow Hynes-Smith
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Karli J Wittorf
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon M Buckley
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
23
|
Gutierrez MJ, Nino G, Hong X, Wang X. Epigenomics and Early Life Human Humoral Immunity: Novel Paradigms and Research Opportunities. Front Immunol 2020; 11:1766. [PMID: 32983086 PMCID: PMC7492271 DOI: 10.3389/fimmu.2020.01766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
The molecular machinery controlling immune development has been extensively investigated. Studies in animal models and adult individuals have revealed fundamental mechanisms of disease and have been essential to understanding how humans sense and respond to cellular stress, tissue damage, pathogens and their environment. Nonetheless, our understanding of how immune responses originate during human development is just starting to emerge. In particular, studies to unveil how environmental and other non-heritable factors shape the immune system at the beginning of life offer great promise to yield important knowledge about determinants of normal inter-individual immune variation and to prevent and treat many human diseases. In this review, we summarize our current understanding of some of the mechanisms determining early life antibody production as a model of an immune process with sequential molecular checkpoints susceptible to influence by non-heritable factors. We discuss the potential of epigenomics as a valuable approach that may reveal not only relevant gene-environment interactions but important clues about immune developmental processes and homeostasis in early life. We then highlight the novel paradigm of human immunology as a complex field that nowadays requires a longitudinal systems-biology approach to understand normal variation and developmental changes during the first few years of life.
Collapse
Affiliation(s)
- Maria J Gutierrez
- Division of Pediatric Allergy, Immunology and Rheumatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children's National Medical Center, George Washington University, Washington, DC, United States.,Center for Genetic Medicine, Children's National Medical Center, Washington, DC, United States
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Division of General Pediatrics and Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
24
|
Abstract
Multiple sclerosis (MS), a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system, is today a leading cause of unpredictable lifelong disability in young adults. The treatment of patients in progressive stages remains highly challenging, alluding to our limited understanding of the underlying pathological processes. In this review, we provide insights into the mechanisms underpinning MS progression from a perspective of epigenetics, that refers to stable and mitotically heritable, yet reversible, changes in the genome activity and gene expression. We first recapitulate findings from epigenetic studies examining the brain tissue of progressive MS patients, which support a contribution of DNA and histone modifications in impaired oligodendrocyte differentiation, defective myelination/remyelination and sustained neuro-axonal vulnerability. We next explore possibilities for identifying factors affecting progression using easily accessible tissues such as blood by comparing epigenetic signatures in peripheral immune cells and brain tissue. Despite minor overlap at individual methylation sites, nearly 30% of altered genes reported in peripheral immune cells of progressive MS patients were found in brain tissue, jointly converging on alterations of neuronal functions. We further speculate about the mechanisms underlying shared epigenetic patterns between blood and brain, which likely imply the influence of internal (genetic control) and/or external (e.g. smoking and ageing) factors imprinting a common signature in both compartments. Overall, we propose that epigenetics might shed light on clinically relevant mechanisms involved in disease progression and open new avenues for the treatment of progressive MS patients in the future.
Collapse
Affiliation(s)
- L Kular
- From the, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Jagodic
- From the, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
25
|
Sunny SK, Zhang H, Rezwan FI, Relton CL, Henderson AJ, Merid SK, Melén E, Hallberg J, Arshad SH, Ewart S, Holloway JW. Changes of DNA methylation are associated with changes in lung function during adolescence. Respir Res 2020; 21:80. [PMID: 32264874 PMCID: PMC7140357 DOI: 10.1186/s12931-020-01342-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Adolescence is a significant period for the gender-dependent development of lung function. Prior studies have shown that DNA methylation (DNA-M) is associated with lung function and DNA-M at some cytosine-phosphate-guanine dinucleotide sites (CpGs) changes over time. This study examined whether changes of DNA-M at lung-function-related CpGs are associated with changes in lung function during adolescence for each gender, and if so, the biological significance of the detected CpGs. METHODS Genome-scale DNA-M was measured in peripheral blood samples at ages 10 (n = 330) and 18 years (n = 476) from the Isle of Wight (IOW) birth cohort in United Kingdom, using Illumina Infinium arrays (450 K and EPIC). Spirometry was conducted at both ages. A training and testing method was used to screen 402,714 CpGs for their potential associations with lung function. Linear regressions were applied to assess the association of changes in lung function with changes of DNA-M at those CpGs potentially related to lung function. Adolescence-related and personal and family-related confounders were included in the model. The analyses were stratified by gender. Multiple testing was adjusted by controlling false discovery rate of 0.05. Findings were further examined in two independent birth cohorts, the Avon Longitudinal Study of Children and Parents (ALSPAC) and the Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) cohort. Pathway analyses were performed on genes to which the identified CpGs were mapped. RESULTS For females, 42 CpGs showed statistically significant associations with change in FEV1/FVC, but none for change in FEV1 or FVC. No CpGs were identified for males. In replication analyses, 16 and 21 of the 42 CpGs showed the same direction of associations among the females in the ALSPAC and BAMSE cohorts, respectively, with 11 CpGs overlapping across all the three cohorts. Through pathway analyses, significant biological processes were identified that have previously been related to lung function development. CONCLUSIONS The detected 11 CpGs in all three cohorts have the potential to serve as the candidate epigenetic markers for changes in lung function during adolescence in females.
Collapse
Affiliation(s)
- Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Faisal I. Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield Bedfordshire, MK43 0AL England
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- Population Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Simon Kebede Merid
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - Jenny Hallberg
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - S. Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Parkhurst Road, Newport, Isle of Wight PO30 5TG UK
| | - Susan Ewart
- Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
| |
Collapse
|
26
|
Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
Collapse
Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - 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
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B 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, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - 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
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
| |
Collapse
|
27
|
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features, immune infiltrates, and response prediction to immunotherapy in melanoma. EBioMedicine 2020; 52:102647. [PMID: 32028068 PMCID: PMC6997575 DOI: 10.1016/j.ebiom.2020.102647] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Immunotherapy, including checkpoint inhibition, has remarkably improved prognosis in advanced melanoma. Despite this success, acquired resistance is still a major challenge. The T cell costimulatory receptor TNFRSF9 (also known as 4-1BB and CD137) is a promising new target for immunotherapy and two agonistic antibodies are currently tested in clinical trials. However, little is known about epigenetic regulation of the encoding gene. In this study we investigate a possible correlation of TNFRSF9 DNA methylation with gene expression, clinicopathological parameters, molecular and immune correlates, and response to anti-PD-1 immunotherapy to assess the validity of TNFRSF9 methylation to serve as a biomarker. METHODS We performed a correlation analyses of methylation at twelve CpG sites within TNFRSF9 with regard to transcriptional activity, immune cell infiltration, mutation status, and survival in a cohort of N = 470 melanoma patients obtained from The Cancer Genome Atlas. Furthermore, we used quantitative methylation-specific PCR to confirm correlations in a cohort of N = 115 melanoma patients' samples (UHB validation cohort). Finally, we tested the ability of TNFRSF9 methylation and expression to predict progression-free survival (PFS) and response to anti-PD-1 immunotherapy in a cohort comprised of N = 121 patients (mRNA transcription), (mRNA ICB cohort) and a case-control study including N = 48 patients (DNA methylation, UHB ICB cohort). FINDINGS We found a significant inverse correlation between TNFRSF9 DNA methylation and mRNA expression levels at six of twelve analyzed CpG sites (P ≤ 0.005), predominately located in the promoter flank region. Consistent with its role as costimulatory receptor in immune cells, TNFRSF9 mRNA expression and hypomethylation positively correlated with immune cell infiltrates and an interferon-γ signature. Furthermore, elevated TNFRSF9 mRNA expression and TNFRSF9 hypomethylation correlated with superior overall survival. In patients receiving anti-PD-1 immunotherapy (mRNA ICB cohort), we found that TNFRSF9 hypermethylation and reduced mRNA expression correlated with poor PFS and response. INTERPRETATION Our study suggests that TNFRSF9 mRNA expression is regulated via DNA methylation. The observed correlations between TNFRSF9 DNA methylation or mRNA expression with known features of response to immune checkpoint blockage suggest TNFRSF9 methylation could serve as a biomarker in the context of immunotherapies. Concordantly, we identified a correlation between TNFRSF9 DNA methylation and mRNA expression with disease progression in patients under immunotherapy. Our study provides rationale for further investigating TNFRSF9 DNA methylation as a predictive biomarker for response to immunotherapy. FUNDING AF was partly funded by the Mildred Scheel Foundation. SF received funding from the University Hospital Bonn BONFOR program (O-105.0069). DN was funded in part by DFG Cluster of Excellence ImmunoSensation (EXC 1023). The funders had no role in study design, data collection and analysis, interpretation, decision to publish, or preparation of the manuscript; or any aspect pertinent to the study.
Collapse
|
28
|
Han L, Zhang H, Kaushal A, Rezwan FI, Kadalayil L, Karmaus W, Henderson AJ, Relton CL, Ring S, Arshad SH, Ewart SL, Holloway JW. Changes in DNA methylation from pre- to post-adolescence are associated with pubertal exposures. Clin Epigenetics 2019; 11:176. [PMID: 31791392 PMCID: PMC6888960 DOI: 10.1186/s13148-019-0780-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adolescence is a period characterized by major biological development, which may be associated with changes in DNA methylation (DNA-M). However, it is unknown to what extent DNA-M varies from pre- to post-adolescence, whether the pattern of changes is different between females and males, and how adolescence-related factors are associated with changes in DNA-M. METHODS Genome-scale DNA-M at ages 10 and 18 years in whole blood of 325 subjects (n = 140 females) in the Isle of Wight (IOW) birth cohort was analyzed using Illumina Infinium arrays (450K and EPIC). Linear mixed models were used to examine DNA-M changes between pre- and post-adolescence and whether the changes were gender-specific. Adolescence-related factors and environmental exposure factors were assessed on their association with DNA-M changes. Replication of findings was attempted in the comparable Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. RESULTS In the IOW cohort, after controlling for technical variation and cell compositions at both pre- and post-adolescence, 15,532 cytosine-phosphate-guanine (CpG) sites (of 400,825 CpGs, 3.88%) showed statistically significant DNA-M changes from pre-adolescence to post-adolescence invariant to gender (false discovery rate (FDR) = 0.05). Of these 15,532 CpGs, 10,212 CpGs (66%) were replicated in the ALSPAC cohort. Pathway analysis using Ingenuity Pathway Analysis (IPA) identified significant biological pathways related to growth and development of the reproductive system, emphasizing the importance of this period of transition on epigenetic state of genes. In addition, in IOW, we identified 1179 CpGs with gender-specific DNA-M changes. In the IOW cohort, body mass index (BMI) at age 10 years, age of growth spurt, nonsteroidal drugs use, and current smoking status showed statistically significant associations with DNA-M changes at 15 CpGs on 14 genes such as the AHRR gene. For BMI at age 10 years, the association was gender-specific. Findings on current smoking status were replicated in the ALSPAC cohort. CONCLUSION Adolescent transition is associated with changes in DNA-M at more than 15K CpGs. Identified pathways emphasize the importance of this period of transition on epigenetic state of genes relevant to cell growth and immune system development.
Collapse
Affiliation(s)
- Luhang Han
- Department of Mathematical Sciences, University of Memphis, Memphis, TN 38152 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN 38152 USA
| | | | - Faisal I. Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL UK
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN 38152 USA
| | - A. John Henderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 1QU UK
| | - Caroline L. Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 1QU UK
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 1QU UK
| | - Susan Ring
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 1QU UK
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 1QU UK
| | - S. Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG UK
| | - Susan L. Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824 USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
| |
Collapse
|
29
|
Potential of epigenetic events in human thyroid cancer. Cancer Genet 2019; 239:13-21. [PMID: 31472323 DOI: 10.1016/j.cancergen.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/27/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
Thyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have revealed promise for their diagnostic, prognostic and therapeutic capacity but still need further confirmation. Among different types of mechanisms, the current article reviews the importance of epigenetic modifications in thyroid cancer. Increasing data from previous reports demonstrate that acquired epigenetic abnormalities together with genetic changes plays an important role in alteration of gene expression patterns. Aberrant DNA methylation has been well known in the CpG regions and profile of microRNAs (mi-RNAs) expression also involved in cancer development. In addition, the gene expression through epigenetic control contribution to thyroid cancer is analyzed and it is semi considered in the clinic. However the epigenetic of the thyroid cancer is yet remains in its early stages, and it carries encouraging potential thyroid cancer detections in its early stages, assessment of prognosis and targeted cancer treatment.
Collapse
|
30
|
Gruzieva O, Merid SK, Chen S, Mukherjee N, Hedman AM, Almqvist C, Andolf E, Jiang Y, Kere J, Scheynius A, Söderhäll C, Ullemar V, Karmaus W, Melén E, Arshad SH, Pershagen G. DNA Methylation Trajectories During Pregnancy. Epigenet Insights 2019; 12:2516865719867090. [PMID: 31453433 PMCID: PMC6696836 DOI: 10.1177/2516865719867090] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/10/2019] [Indexed: 01/03/2023] Open
Abstract
There is emerging evidence on DNA methylation (DNAm) variability over time; however, little is known about dynamics of DNAm patterns during pregnancy. We performed an epigenome-wide longitudinal DNAm study of a well-characterized sample of young women from the Swedish Born into Life study, with repeated blood sampling before, during and after pregnancy (n = 21), using the Illumina Infinium MethylationEPIC array. We conducted a replication in the Isle of Wight third-generation birth cohort (n = 27), using the Infinium HumanMethylation450k BeadChip. We identified 196 CpG sites displaying intra-individual longitudinal change in DNAm with a false discovery rate (FDR) P < .05. Most of these (91%) showed a decrease in average methylation levels over the studied period. We observed several genes represented by ⩾3 differentially methylated CpGs: HOXB3, AVP, LOC100996291, and MicroRNA 10a. Of 36 CpGs available in the replication cohort, 17 were replicated, all but 2 with the same direction of association (replication P < .05). Biological pathway analysis demonstrated that FDR-significant CpGs belong to genes overrepresented in metabolism-related pathways, such as adipose tissue development, regulation of insulin receptor signaling, and mammary gland fat development. These results contribute to a better understanding of the biological mechanisms underlying important physiological alterations and adaptations for pregnancy and lactation.
Collapse
Affiliation(s)
- Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden,Olena Gruzieva, Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, SE-171 77 Stockholm, Sweden.
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Su Chen
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Anna M Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Ellika Andolf
- Department of Clinical Sciences, Division of Obstetrics and Gynaecology, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland,School of Basic & Medical Biosciences, King’s College London, London, UK
| | - Annika Scheynius
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden,Sachs’ Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden,Clinical Genomics, Science for Life Laboratory, Stockholm, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden,Sachs’ Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Syed Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, Newport, UK,Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| |
Collapse
|
31
|
Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts. Int J Mol Sci 2019; 20:ijms20133229. [PMID: 31262088 PMCID: PMC6651091 DOI: 10.3390/ijms20133229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic health via epigenetic mechanisms. To understand how the timing of HF diet intake impacts DNA methylation and metabolism, male Sprague–Dawley rats were exposed to either maternal HF (MHF) or post-weaning HF diet (PHF). At post-natal week 12, PHF rats had similar body weights but greater hepatic lipid accumulation compared to the MHF rats. Genome-wide DNA methylation was evaluated, and analysis revealed 1744 differentially methylation regions (DMRs) between the groups with the majority of the DMR located outside of gene-coding regions. Within differentially methylated genes (DMGs), intragenic DNA methylation closer to the transcription start site was associated with lower gene expression, whereas DNA methylation further downstream was positively correlated with gene expression. The insulin and phosphatidylinositol (PI) signaling pathways were enriched with 25 DMRs that were associated with 20 DMGs, including PI3 kinase (Pi3k), pyruvate kinase (Pklr), and phosphodiesterase 3 (Pde3). Together, these results suggest that the timing of HF diet intake determines DNA methylation and gene expression patterns in hepatic metabolic pathways that target specific genomic contexts.
Collapse
|
32
|
Kochmanski J, Goodrich JM, Peterson KE, Lumeng JC, Dolinoy DC. Neonatal bloodspot DNA methylation patterns are associated with childhood weight status in the Healthy Families Project. Pediatr Res 2019; 85:848-855. [PMID: 30425339 PMCID: PMC6494701 DOI: 10.1038/s41390-018-0227-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 09/19/2018] [Accepted: 10/14/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND This study measured longitudinal DNA methylation dynamics at growth-related genes during childhood, and then tested whether DNA methylation at various stages of childhood was associated with obesity status. METHODS Using neonatal bloodspot (n = 132) and matched childhood blood samples (n = 65), DNA methylation was quantified at a repetitive element (long interspersed nuclear element-1 (LINE-1)), two imprinted genes (IGF2, H19), and four non-imprinted genes (LEP, PPARA, ESR1, SREBF1) related to growth and adiposity. Logistic regression was used to test whether neonatal bloodspot DNA methylation at target genes was associated with log odds of obesity (Y/N) in children recruited from three age groups-12-24 months old (n = 40), 3-5 years of age (n = 40), and 10-12 years of age (n = 52). RESULTS In 3-5 year olds, neonatal bloodspot LINE-1 methylation was negatively associated with obesity (log odds = -0.40, p = 0.04). Across childhood age group in matched blood samples, DNA methylation levels in blood decreased (p < 0.05) at LINE-1, PPARA, ESR1, SREBF1, IGF2, and H19, and increased (p < 0.05) at LEP. CONCLUSIONS Our results suggest that age-related epigenetic changes occur at growth-related genes in the first decade of life, and that gene-specific neonatal bloodspot DNA methylation may be a useful biomarker of obesity likelihood during childhood.
Collapse
Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Karen E Peterson
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julie C Lumeng
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
33
|
Alfano R, Guida F, Galobardes B, Chadeau-Hyam M, Delpierre C, Ghantous A, Henderson J, Herceg Z, Jain P, Nawrot TS, Relton C, Vineis P, Castagné R, Plusquin M. Socioeconomic position during pregnancy and DNA methylation signatures at three stages across early life: epigenome-wide association studies in the ALSPAC birth cohort. Int J Epidemiol 2019; 48:30-44. [PMID: 30590607 PMCID: PMC6443021 DOI: 10.1093/ije/dyy259] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Socioeconomic experiences are recognized determinants of health, and recent work has shown that social disadvantages in early life may induce sustained biological changes at molecular level that are detectable later in life. However, the dynamics and persistence of biological embedding of socioeconomic position (SEP) remains vastly unexplored. METHODS Using the data from the ALSPAC birth cohort, we performed epigenome-wide association studies of DNA methylation changes at three life stages (birth, n = 914; childhood at mean age 7.5 years, n = 973; and adolescence at mean age 15.5 years, n = 974), measured using the Illumina HumanMethylation450 Beadchip, in relation to pregnancy SEP indicators (maternal and paternal education and occupation). RESULTS Across the four early life SEP metrics investigated, only maternal education was associated with methylation levels at birth, and four CpGs mapped to SULF1, GLB1L2 and RPUSD1 genes were identified [false discovery rate (FDR)-corrected P-value <0.05]. No epigenetic signature was found associated with maternal education in child samples, but methylation levels at 20 CpG loci were found significantly associated with maternal education in adolescence. Although no overlap was found between the differentially methylated CpG sites at different ages, we identified two CpG sites at birth and during adolescence which are 219 bp apart in the SULF1 gene that encodes an heparan sulphatase involved in modulation of signalling pathways. Using data from an independent birth cohort, the ENVIRONAGE cohort, we were not able to replicate these findings. CONCLUSIONS Taken together, our results suggest that parental SEP, and particularly maternal education, may influence the offspring's methylome at birth and adolescence.
Collapse
Affiliation(s)
- Rossella Alfano
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Florence Guida
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
| | - Bruna Galobardes
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Cyrille Delpierre
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - John Henderson
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Pooja Jain
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- IIGM, Italian Institute for Genomic Medicine, Turin, Italy
| | - Raphaële Castagné
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Michelle Plusquin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
34
|
Tian W, Du Y, Ma Y, Zhang B, Gu L, Zhou J, Deng D. miR663a‑TTC22V1 axis inhibits colon cancer metastasis. Oncol Rep 2019; 41:1718-1728. [PMID: 30664167 PMCID: PMC6365692 DOI: 10.3892/or.2019.6969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 01/10/2019] [Indexed: 12/12/2022] Open
Abstract
An increasing number of studies have demonstrated that microRNAs (miRs) may act as oncogenes or anti‑oncogenes in various types of cancer, including colon cancer (CC). However, the clinical and biological significance of miR663a in the prognosis of CC and its underlying molecular mechanisms remain unknown. Using the reverse transcription‑quantitative polymerase chain reaction on CC and surgical margin tissue samples from 172 patients with CC, it was identified that miR663a was significantly downregulated in CC (P<0.001), particularly in metastatic CC (P=0.044). miR663a overexpression inhibited the proliferation and migration/invasion of CC cells in vitro, and also tumor growth and metastasis of CC cells in vivo. Additionally, miR663a target genes were analyzed. Inverse changes in tetratricopeptide repeat domain 22 variant 1 (TTC22V1) in response to alterations in miR663a expression were observed. miR663a decreased the reporter activity of the wild‑type TTC22V1‑3' untranslated region (UTR), but did not decrease that of a 3'UTR mutant. miR663a completely abolished cell migration/invasion induced by TTC22V1 containing the wild‑type 3'UTR sequence, but not that induced by TTC22V1 containing the 3'UTR mutant. An inverse correlation between miR663a and TTC22 mRNA levels was observed in CC tissues. These results suggest that TTC22V1 mRNA is a crucial miR663a target that directly promotes cell migration/invasion. TTC22, which, to the best of our knowledge, has rarely been investigated, is located in the nuclei of epithelial cells in colon stem cell niches at crypt bases, and is significantly downregulated in CC, particularly in non‑metastatic CC. High TTC22V1 expression is a significant poor survival factor for patients with CC. Collectively, the results of the present study suggested that TTC22V1 may be a metastasis‑associated gene and that the miR663a‑TTC22V1 axis inhibited CC metastasis.
Collapse
Affiliation(s)
- Wei Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Yantao Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Yuwan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| |
Collapse
|
35
|
Pérez RF, Santamarina P, Tejedor JR, Urdinguio RG, Álvarez-Pitti J, Redon P, Fernández AF, Fraga MF, Lurbe E. Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes. J Transl Med 2019; 17:15. [PMID: 30626398 PMCID: PMC6327427 DOI: 10.1186/s12967-018-1751-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
Background Early life is a period of drastic epigenetic remodeling in which the epigenome is especially sensitive to extrinsic and intrinsic influence. However, the epigenome-wide dynamics of the DNA methylation changes that occur during this period have not been sufficiently characterized in longitudinal studies. Methods To this end, we studied the DNA methylation status of more than 750,000 CpG sites using Illumina MethylationEPIC arrays on 33 paired blood samples from 11 subjects at birth and at 5 and 10 years of age, then characterized the chromatin context associated with these loci by integrating our data with histone, chromatin-state and enhancer-element external datasets, and, finally, validated our results through bisulfite pyrosequencing in two independent longitudinal cohorts of 18 additional subjects. Results We found abundant DNA methylation changes (110,726 CpG sites) during the first lustrum of life, while far fewer alterations were observed in the subsequent 5 years (460 CpG sites). However, our analysis revealed persistent DNA methylation changes at 240 CpG sites, indicating that there are genomic locations of considerable epigenetic change beyond immediate birth. The chromatin context of hypermethylation changes was associated with repressive genomic locations and genes with developmental and cell signaling functions, while hypomethylation changes were linked to enhancer regions and genes with immunological and mRNA and protein metabolism functions. Significantly, our results show that genes that suffer simultaneous hyper- and hypomethylation are functionally distinct from exclusively hyper- or hypomethylated genes, and that enhancer-associated methylation is different in hyper- and hypomethylation scenarios, with hypomethylation being more associated to epigenetic changes at blood tissue-specific enhancer elements. Conclusions These data show that epigenetic remodeling is dramatically reduced after the first 5 years of life. However, there are certain loci which continue to manifest DNA methylation changes, pointing towards a possible functionality beyond early development. Furthermore, our results deepen the understanding of the genomic context associated to hyper- or hypomethylation alterations during time, suggesting that hypomethylation of blood tissue-specific enhancer elements could be of importance in the establishment of functional states in blood tissue during early-life. Electronic supplementary material The online version of this article (10.1186/s12967-018-1751-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Pablo Santamarina
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Mario F Fraga
- Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain. .,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
36
|
Verhoeven D. Influence of Immunological Maturity on Respiratory Syncytial Virus-Induced Morbidity in Young Children. Viral Immunol 2018; 32:76-83. [PMID: 30499759 DOI: 10.1089/vim.2018.0121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a very frequent viral respiratory pathogen of the young (<5 years old) with a significant portion of young toddlers having been infected before 2 years of age. Although we understand that some of the morbidity associated with RSV in neonates is due to immunological maturation that favors immunosuppression over antiviral innate and/or adaptive immune responses, the rapid development of the immune system right after birth suggests that each age group (newborn, early infant, older infant, toddler, and older) may respond to the virus in different ways. In this study, we summarize the morbidity associated with infection in young children in the context of immunological maturation of monocytes/macrophages and the ramifications for poor innate control of viral pathogenesis. We also summarize key mechanisms that contribute to the diminished antiviral innate immune responses of these young children.
Collapse
Affiliation(s)
- David Verhoeven
- Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames , Iowa
| |
Collapse
|
37
|
DNA methylation-based age prediction using massively parallel sequencing data and multiple machine learning models. Forensic Sci Int Genet 2018; 37:215-226. [DOI: 10.1016/j.fsigen.2018.09.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
|
38
|
Goronzy JJ, Hu B, Kim C, Jadhav RR, Weyand CM. Epigenetics of T cell aging. J Leukoc Biol 2018; 104:691-699. [PMID: 29947427 PMCID: PMC6162101 DOI: 10.1002/jlb.1ri0418-160r] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 02/06/2023] Open
Abstract
T cells are a heterogeneous population of cells that differ in their differentiation stages. Functional states are reflected in the epigenome that confers stability in cellular identity and is therefore important for naïve as well as memory T cell function. In many cellular systems, changes in chromatin structure due to alterations in histone expression, histone modifications and DNA methylation are characteristic of the aging process and cause or at least contribute to cellular dysfunction in senescence. Here, we review the epigenetic changes in T cells that occur with age and discuss them in the context of canonical epigenetic marks in aging model systems as well as recent findings of chromatin accessibility changes in T cell differentiation. Remarkably, transcription factor networks driving T cell differentiation account for many of the age-associated modifications in chromatin structures suggesting that loss of quiescence and activation of differentiation pathways are major components of T cell aging.
Collapse
Affiliation(s)
- Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Bin Hu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Chulwoo Kim
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Rohit R. Jadhav
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| |
Collapse
|
39
|
Salas LA, Wiencke JK, Koestler DC, Zhang Z, Christensen BC, Kelsey KT. Tracing human stem cell lineage during development using DNA methylation. Genome Res 2018; 28:1285-1295. [PMID: 30072366 PMCID: PMC6120629 DOI: 10.1101/gr.233213.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/27/2018] [Indexed: 12/22/2022]
Abstract
Stem cell maturation is a fundamental, yet poorly understood aspect of human development. We devised a DNA methylation signature deeply reminiscent of embryonic stem cells (a fetal cell origin signature, FCO) to interrogate the evolving character of multiple human tissues. The cell fraction displaying this FCO signature was highly dependent upon developmental stage (fetal versus adult), and in leukocytes, it described a dynamic transition during the first 5 yr of life. Significant individual variation in the FCO signature of leukocytes was evident at birth, in childhood, and throughout adult life. The genes characterizing the signature included transcription factors and proteins intimately involved in embryonic development. We defined and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature traces the lineage of cells and informs the study of stem cell heterogeneity in humans under homeostatic conditions.
Collapse
Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - John K Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Ze Zhang
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
| |
Collapse
|
40
|
Plusquin M, Chadeau-Hyam M, Ghantous A, Alfano R, Bustamante M, Chatzi L, Cuenin C, Gulliver J, Herceg Z, Kogevinas M, Nawrot TS, Pizzi C, Porta D, Relton CL, Richiardi L, Robinson O, Sunyer J, Vermeulen R, Vriens A, Vrijheid M, Henderson J, Vineis P. DNA Methylome Marks of Exposure to Particulate Matter at Three Time Points in Early Life. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5427-5437. [PMID: 29597345 DOI: 10.1021/acs.est.7b06447] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Maternal exposure to airborne particulate matter (PM) has been associated with restricted fetal growth and reduced birthweight. Here, we performed methylome-wide analyses of cord and children's blood DNA in relation to residential exposure to PM smaller than 10 μm (PM10). This study included participants of the Avon Longitudinal Study of Pregnancy and Childhood (ALSPAC, cord blood, n = 780; blood at age 7, n = 757 and age 15-17, n = 850) and the EXPOsOMICS birth cohort consortium including cord blood from ENVIR ONAGE ( n = 197), INMA ( n = 84), Piccolipiù ( n = 99) and Rhea ( n = 75). We could not identify significant CpG sites, by meta-analyzing associations between maternal PM10 exposure during pregnancy and DNA methylation in cord blood, nor by studying DNA methylation and concordant annual exposure at 7 and 15-17 years. The CpG cg21785536 was inversely associated with PM10 exposure using a longitudinal model integrating the three studied age groups (-1.2% per 10 μg/m3; raw p-value = 3.82 × 10-8). Pathway analyses on the corresponding genes of the 100 strongest associated CpG sites of the longitudinal model revealed enriched pathways relating to the GABAergic synapse, p53 signaling and NOTCH1. We provided evidence that residential PM10 exposure in early life affects methylation of the CpG cg21785536 located on the EGF Domain Specific O-Linked N-Acetylglucosamine Transferase gene.
Collapse
Affiliation(s)
- Michelle Plusquin
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology , Utrecht University , Utrecht , The Netherlands
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - Rossella Alfano
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Mariona Bustamante
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona , Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
| | - Leda Chatzi
- Department of Preventive Medicine , University of Southern California , Los Angeles , California 90007 , United States
- Department of Social Medicine , University of Crete , Heraklion, Crete , Greece
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - John Gulliver
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
- IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Spain
| | - Tim S Nawrot
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Environment & Health Unit Leuven University , Leuven , Belgium
| | - Costanza Pizzi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences , University of Turin and CPO-Piemonte , Torino , Italy
| | - Daniela Porta
- Department of Epidemiology of the Lazio Regional Health Service , Rome , Italy
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School , University of Bristol , Bristol , U.K
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences , University of Turin and CPO-Piemonte , Torino , Italy
| | - Oliver Robinson
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Jordi Sunyer
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Spain
| | - Roel Vermeulen
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology , Utrecht University , Utrecht , The Netherlands
| | - Annette Vriens
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
| | - Martine Vrijheid
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
| | - John Henderson
- Department of Population Health Sciences, Bristol Medical School , University of Bristol , Bristol , U.K
| | - Paolo Vineis
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- IIGM, Italian Institute for Genomic Medicine , Turin , Italy
| |
Collapse
|
41
|
Vogt TJ, Gevensleben H, Dietrich J, Kristiansen G, Bootz F, Landsberg J, Goltz D, Dietrich D. Detailed analysis of adenosine A2a receptor ( ADORA2A) and CD73 (5'-nucleotidase, ecto, NT5E) methylation and gene expression in head and neck squamous cell carcinoma patients. Oncoimmunology 2018; 7:e1452579. [PMID: 30221045 PMCID: PMC6136855 DOI: 10.1080/2162402x.2018.1452579] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 12/15/2022] Open
Abstract
Background: The adenosine A2a receptor (A2aR) and the adenosine synthesizing enzyme CD73 have recently evolved as a novel immunotherapeutic target. However, little is known about epigenetic modification of the encoding genes ADORA2A and NT5E. Methods: In the present study, we evaluated methylation at 23 loci of ADORA2A and 17 loci of NT5E with regard to transcriptional activity, human papilloma virus (HPV) status, immune cell infiltration, and outcome in a cohort of 279 head and neck squamous carcinoma (HNSCC) patients obtained from The Cancer Genome Atlas (TCGA). Methylation and mRNA expression were generated by the Infinium HumanMethylation450 BeadChip and Illumina HiSeq 2000 RNA Sequencing Version 2 analysis (Illumina, Inc., San Diego, CA, USA). HPV status was assessed by RNA-Seq data analysis of the viral genes E6 and E7. Results: Thirteen out of 23 ADORA2A loci and 15/17 NT5E loci were significantly correlated with mRNA levels (p < 0.05). Inverse correlations were predominately found in promoter regions, while positive correlations were more profound at intragenic loci. ADORA2A hypermethylation was significantly associated with poor overall survival (OS, p ≤ 0.030), whereas NT5E hypomethylation was associated with decreased OS in HPV-positive tumors (p ≤ 0.024) and increased OS in HPV-negative HNSCC (p ≤ 0.029). Further, we found significant correlations between methylation and immune cell infiltrates. Conclusion: Our data might point towards a significant role of the A2aR/CD73 axis during cancer progression in HNSCC.
Collapse
Affiliation(s)
- Timo J. Vogt
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Jörn Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| |
Collapse
|
42
|
Naumova OY, Dozier M, Dobrynin PV, Grigorev K, Wallin A, Jeltova I, Lee M, Raefski A, Grigorenko EL. Developmental dynamics of the epigenome: A longitudinal study of three toddlers. Neurotoxicol Teratol 2017; 66:125-131. [PMID: 29247702 DOI: 10.1016/j.ntt.2017.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/20/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022]
Abstract
Epigenetic regulation plays an important role in development, at the embryonic stages and later during the lifespan. Some epigenetic marks are highly conserved throughout the lifespan whereas others are closely associated with specific age periods and/or particular environmental factors. Little is known about the dynamics of epigenetic regulation during childhood, especially during the period of rapid early development. Our study was aimed to determine whether the developmental program at the early stages of human development is accompanied by significant changes in the systems of genome regulation, specifically, by genome-wide changes in DNA methylation. Using a sequencing approach (MBD-seq) we investigated genome-wide DNA methylation patterns in the T-lymphocytes of three healthy toddlers at two timepoints within the second year of life. Pairwise comparison of the methylation patterns across the individuals and time points was conducted to determine common longitudinal changes in the DNA methylation patterns. Despite relatively high interindividual variability in their epigenetic profiles and the dynamics of these profiles during the second year of life, all children showed consistent changes in the DNA methylation patterns of genes involved in the control of the immune system and genes related to the development of the CNS. Thereby, we provide evidence that early development might be accompanied by epigenetic changes in specific functional groups of genes; many such epigenetic changes appear to be related to the rapid development of the CNS.
Collapse
Affiliation(s)
- Oxana Yu Naumova
- Dept. of Psychology, University of Houston, Houston, TX, USA; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia
| | - Mary Dozier
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Pavel V Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Kirill Grigorev
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Allison Wallin
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Ida Jeltova
- Private Psychological Practice, Ridgewood, NJ, USA
| | - Maria Lee
- Child Study Center, Yale University, New Haven, CT, USA
| | - Adam Raefski
- Child Study Center, Yale University, New Haven, CT, USA
| | - Elena L Grigorenko
- Dept. of Psychology, University of Houston, Houston, TX, USA; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia; Child Study Center, Yale University, New Haven, CT, USA; Office of the Rector, Moscow State University of Psychology and Education, Moscow, Russia.
| |
Collapse
|
43
|
Muurinen M, Hannula-Jouppi K, Reinius LE, Söderhäll C, Merid SK, Bergström A, Melén E, Pershagen G, Lipsanen-Nyman M, Greco D, Kere J. Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children. Sci Rep 2017; 7:15693. [PMID: 29146936 PMCID: PMC5691194 DOI: 10.1038/s41598-017-16070-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 11/07/2017] [Indexed: 01/03/2023] Open
Abstract
Silver-Russell syndrome (SRS) is a growth retardation syndrome in which loss of methylation on chromosome 11p15 (11p15 LOM) and maternal uniparental disomy for chromosome 7 [UPD(7)mat] explain 20–60% and 10% of the syndrome, respectively. To search for a molecular cause for the remaining SRS cases, and to find a possible common epigenetic change, we studied DNA methylation pattern of more than 450 000 CpG sites in 44 SRS patients. Common to all three SRS subgroups, we found a hypomethylated region at the promoter region of HOXA4 in 55% of the patients. We then tested 39 patients with severe growth restriction of unknown etiology, and found hypomethylation of HOXA4 in 44% of the patients. Finally, we found that methylation at multiple CpG sites in the HOXA4 promoter region was associated with height in a cohort of 227 healthy children, suggesting that HOXA4 may play a role in regulating human growth by epigenetic mechanisms.
Collapse
Affiliation(s)
- Mari Muurinen
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Katariina Hannula-Jouppi
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Dermatology, Skin and Allergy Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Marita Lipsanen-Nyman
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Dario Greco
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Faculty of Medicine and Life Sciences & Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. .,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK.
| |
Collapse
|
44
|
DNA methylation in blood from neonatal screening cards and the association with BMI and insulin sensitivity in early childhood. Int J Obes (Lond) 2017; 42:28-35. [PMID: 29064478 DOI: 10.1038/ijo.2017.228] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/13/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND/OBJECTIVES There is increasing evidence that metabolic diseases originate in early life, and epigenetic changes have been implicated as key drivers of this early life programming. This led to the hypothesis that epigenetic marks present at birth may predict an individual's future risk of obesity and type 2 diabetes. In this study, we assessed whether epigenetic marks in blood of newborn children were associated with body mass index (BMI) and insulin sensitivity later in childhood. SUBJECTS/METHODS DNA methylation was measured in neonatal blood spot samples of 438 children using the Illumina Infinium 450 k BeadChip. Associations were assessed between DNA methylation at birth and BMI z-scores, body fat mass, fasting plasma glucose, insulin and homeostatic model assessment of insulin resistance (HOMA-IR) at age 5 years, as well as birth weight, maternal BMI and smoking status. RESULTS No individual methylation sites at birth were associated with obesity or insulin sensitivity measures at 5 years. DNA methylation in 69 genomic regions at birth was associated with BMI z-scores at age 5 years, and in 63 regions with HOMA-IR. The methylation changes were generally small (<5%), except for a region near the non-coding RNA nc886 (VTRNA2-1) where a clear link between methylation status at birth and BMI in childhood was observed (P=0.001). Associations were also found between DNA methylation, maternal smoking and birth weight. CONCLUSIONS We identified a number of DNA methylation regions at birth that were associated with obesity or insulin sensitivity measurements in childhood. These findings support the mounting evidence on the role of epigenetics in programming of metabolic health. Whether many of these small changes in DNA methylation are causally related to the health outcomes, and of clinical relevance, remains to be determined, but the nc886 region represents a promising obesity risk marker that warrants further investigation.
Collapse
|
45
|
Verschoor CP, McEwen LM, Kohli V, Wolfson C, Bowdish DM, Raina P, Kobor MS, Balion C. The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study. BMC Genet 2017. [PMID: 28637423 PMCID: PMC5480116 DOI: 10.1186/s12863-017-0525-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The levels of circulating cytokines fluctuate with age, acute illness, and chronic disease, and are predictive of mortality; this is also true for patterns of DNA (CpG) methylation. Given that immune cells are particularly sensitive to changes in the concentration of cytokines in their microenvironment, we hypothesized that serum levels of TNF, IL-6, IL-8 and IL-10 would correlate with genome-wide alterations in the DNA methylation levels of blood leukocytes. To test this, we evaluated community-dwelling adults (n = 14; 48–78 years old) recruited to a pilot study for the Canadian Longitudinal Study on Aging (CLSA), examining DNA methylation patterns in peripheral blood mononuclear cells using the Illumina HumanMethylation 450 K BeadChip. Results We show that, apart from age, serum IL-10 levels exhibited the most substantial association to DNA methylation patterns, followed by TNF, IL-6 and IL-8. Furthermore, while the levels of these cytokines were higher in elderly adults, no associations with epigenetic accelerated aging, derived using the epigenetic clock, were observed. Conclusions As a preliminary study with a small sample size, the conclusions drawn from this work must be viewed with caution; however, our observations are encouraging and certainly warrant more suitably powered studies of this relationship. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0525-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chris P Verschoor
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada. .,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada. .,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. .,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada.
| | - Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Vikas Kohli
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada
| | - Christina Wolfson
- Canadian Longitudinal Study on Aging, Hamilton, ON, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Dawn Me Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada.,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada.,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| |
Collapse
|
46
|
Sharp GC, Ho K, Davies A, Stergiakouli E, Humphries K, McArdle W, Sandy J, Davey Smith G, Lewis SJ, Relton CL. Distinct DNA methylation profiles in subtypes of orofacial cleft. Clin Epigenetics 2017; 9:63. [PMID: 28603561 PMCID: PMC5465456 DOI: 10.1186/s13148-017-0362-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Background Epigenetic data could help identify risk factors for orofacial clefts, either by revealing a causal role for epigenetic mechanisms in causing clefts or by capturing information about causal genetic or environmental factors. Given the evidence that different subtypes of orofacial cleft have distinct aetiologies, we explored whether children with different cleft subtypes showed distinct epigenetic profiles. Methods In whole-blood samples from 150 children from the Cleft Collective cohort study, we measured DNA methylation at over 450,000 sites on the genome. We then carried out epigenome-wide association studies (EWAS) to test the association between methylation at each site and cleft subtype (cleft lip only (CLO) n = 50; cleft palate only (CPO) n = 50; cleft lip and palate (CLP) n = 50). We also compared methylation in the blood to methylation in the lip or palate tissue using genome-wide data from the same 150 children and conducted an EWAS of CLO compared to CLP in lip tissue. Results We found four genomic regions in blood differentially methylated in CLO compared to CLP, 17 in CPO compared to CLP and 294 in CPO compared to CLO. Several regions mapped to genes that have previously been implicated in the development of orofacial clefts (for example, TBX1, COL11A2, HOXA2, PDGFRA), and over 250 associations were novel. Methylation in blood correlated with that in lip/palate at some regions. There were 14 regions differentially methylated in the lip tissue from children with CLO and CLP, with one region (near KIAA0415) showing up in both the blood and lip EWAS. Conclusions Our finding of distinct methylation profiles in different orofacial cleft (OFC) subtypes represents a promising first step in exploring the potential role of epigenetic modifications in the aetiology of OFCs and/or as clinically useful biomarkers of OFC subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0362-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Karen Ho
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Amy Davies
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Kerry Humphries
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Jonathan Sandy
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| |
Collapse
|
47
|
Persistent DNA methylation changes associated with prenatal mercury exposure and cognitive performance during childhood. Sci Rep 2017; 7:288. [PMID: 28325913 PMCID: PMC5428306 DOI: 10.1038/s41598-017-00384-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Prenatal exposure to mercury, a known neurotoxic metal, is associated with lower cognitive performance during childhood. Disruption of fetal epigenetic programming could explain mercury’s neurodevelopmental effects. We screened for epigenome-wide methylation differences associated with maternal prenatal blood mercury levels in 321 cord blood DNA samples and examined the persistence of these alterations during early (n = 75; 2.9–4.9 years) and mid-childhood (n = 291; 6.7–10.5 years). Among males, prenatal mercury levels were associated with lower regional cord blood DNA methylation at the Paraoxonase 1 gene (PON1) that persisted in early childhood and was attenuated in mid-childhood blood. Cord blood methylation at the PON1 locus predicted lower cognitive test scores measured during early childhood. Methylation at the PON1 locus was associated with PON1 expression in an independent set of cord blood samples. The observed persistent epigenetic disruption of the PON1 gene may modulate mercury toxicity in humans and might serve as a biomarker of exposure and disease susceptibility.
Collapse
|
48
|
Epigenetic Silencing of the Human 18 kDa Translocator Protein in a T Cell Leukemia Cell Line. DNA Cell Biol 2017; 36:103-108. [DOI: 10.1089/dna.2016.3385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
49
|
Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH. The emerging landscape of dynamic DNA methylation in early childhood. BMC Genomics 2017; 18:25. [PMID: 28056824 PMCID: PMC5217260 DOI: 10.1186/s12864-016-3452-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/21/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. RESULTS By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1.14 × 10-7. Genes with an increase in age-differential methylation were enriched in pathways related to 'development', and were more often located in bivalent transcription start site (TSS) regions, which can silence or activate expression of developmental genes. Genes with a decrease in age-differential methylation were involved in cell signalling, and enriched on H3K27ac, which can predict developmental state. Maternal smoking tended to decrease methylation levels at the identified da-DMSs. We also found 101 a-DMSs (0.71%) that were regulated by genetic variants using cis-differential Methylation Quantitative Trait Locus (cis-dMeQTL) mapping. Moreover, a-DMS-associated genes during early development were significantly more likely to be linked with disease. CONCLUSION Our study provides new insights into the dynamic epigenetic landscape of the first 8 years of life.
Collapse
Affiliation(s)
- Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Soesma A Jankipersadsing
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pieter van der Vlies
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bianca van Rijkom
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jocelyne Just
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France.,Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Inger Kull
- Department of Clinical Science and Education, Stockholm South General Hospital, Karolinska Institutet, and Sachs' Children's Hospital, SE-118 83, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Institute of Genetics and Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Josep Maria Antó
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France.,MACVIA-France, Contre les Maladies Chroniques pour un VIeillissement Actif en France, European Innovation Partnership on Active and Healthy Ageing Reference Site, Paris, France.,INSERM, VIMA: Ageing and chronic diseases. Epidemiological and public health approaches, U1168, Paris, France.,UVSQ, UMR-S 1168, Université Versailles St-Quentin-en-Yvelines, Versailles, France
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Jordi Sunyer
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Erik Melén
- Department of Paediatric Pulmonology and Paediatric Allergy, Beatrix Children's Hospital, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Dirkje S Postma
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- Department of Paediatric Pulmonology and Paediatric Allergy, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, GRIAC Research Institute, Groningen, The Netherlands
| |
Collapse
|
50
|
Feerick CL, McKernan DP. Understanding the regulation of pattern recognition receptors in inflammatory diseases - a 'Nod' in the right direction. Immunology 2016; 150:237-247. [PMID: 27706808 DOI: 10.1111/imm.12677] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/15/2016] [Accepted: 09/28/2016] [Indexed: 12/11/2022] Open
Abstract
Nucleotide-binding oligomerization domain (NOD) -like receptors (NLRs) are a family of 23 receptors known as pattern recognition receptors; they are expressed in many cell types and play a key role in the innate immune response. The NLRs are activated by pathogen-associated molecular patterns, which include structurally conserved molecules present on the surfaces of bacteria. The activation of these NLRs by pathogens results in the downstream activation of signalling kinases and transcription factors, culminating in the transcription of genes coding for pro-inflammatory factors. Expression of NLR is altered in many cellular, physiological and disease states. There is a lack of understanding of the mechanisms by which NLR expression is regulated, particularly in chronic inflammatory states. Genetic polymorphisms and protein interactions are included in such mechanisms. This review seeks to examine the current knowledge regarding the regulation of this family of receptors and their signalling pathways as well as how their expression changes in disease states with particular focus on NOD1 and NOD2 in inflammatory bowel diseases among others.
Collapse
Affiliation(s)
- Claire L Feerick
- Pharmacology & Therapeutics, National University of Ireland, Galway, Ireland
| | - Declan P McKernan
- Pharmacology & Therapeutics, National University of Ireland, Galway, Ireland
| |
Collapse
|