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Ochoa‐Avilés C, Ochoa‐Avilés A, Rivas‐Párraga R, Escandón S, Santos‐Jesus TD, Silva MDJ, Leão V, Salinas M, Vicuña Y, Baldeón L, Molina‐Cando MJ, Morillo D, Machuca M, Rodas C, Figueiredo C, Neira VA. Mother's smoking habits affects IL10 methylation but not asthma in Ecuadorian children. Mol Genet Genomic Med 2024; 12:e2438. [PMID: 38666495 PMCID: PMC11046467 DOI: 10.1002/mgg3.2438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
There is no evidence evaluating the IL10 epigenetic upregulation among mestizo children in a high-altitude Andean city in Latin America. OBJECTIVE To identify polymorphisms and methylation profiles in the IL10 gene associated with asthma in children aged 5 to 11. METHODS A case-control study was conducted with asthmatic and non-asthmatic children aged 5 to 11 years in Cuenca-Ecuador. Data on allergic diseases and risk factors were collected through a questionnaire for parents. Atopy was measured by skin prick test (SPT) to relevant aeroallergens. Three IL10 single nucleotide polymorphisms were evaluated in all participants, and methylation analysis was performed in 54 participants. Association between risk factors, allergic diseases and genetic factors were estimated using multivariate logistic regression. RESULTS The results of polymorphisms showed no differences between cases and controls when comparing the SNPs rs3024495, rs3024496, rs1800896 allelic and genotypic frequencies. In the methylation analysis, no differences in the IL10 methylation profile were found between cases and controls; however, the multivariate analysis showed an association between the mother's smoking habits and the IL10 methylation profile. CONCLUSION Smoking habit could be essential as an environmental exposure factor in regulating gene expression in children with asthma.
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Affiliation(s)
- Cristina Ochoa‐Avilés
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | | | - Roque Rivas‐Párraga
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Biomass to Resources GroupUniversidad Regional Amazónica IkiamTenaNapoEcuador
| | - Samuel Escandón
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
| | - Talita Dos Santos‐Jesus
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Milca de J. Silva
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Valderiene Leão
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Marco Salinas
- Biomass to Resources GroupUniversidad Regional Amazónica IkiamTenaNapoEcuador
| | - Yosselin Vicuña
- Instituto de Investigación en Biomedicina Facultad de Ciencias MédicasUniversidad Central del EcuadorQuitoPichinchaEcuador
| | - Lucy Baldeón
- Instituto de Investigación en Biomedicina Facultad de Ciencias MédicasUniversidad Central del EcuadorQuitoPichinchaEcuador
| | - María José Molina‐Cando
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad Internacional del EcuadorQuitoPichinchaEcuador
| | - Diana Morillo
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad Internacional del EcuadorQuitoPichinchaEcuador
| | - Marcos Machuca
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
| | - Claudia Rodas
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
| | - Camila Figueiredo
- Departamento de Biorregulação, Instituto de Ciências da SaúdeUniversidade Federal da BahiaSalvadorBahiaBrazil
| | - Vivian Alejandra Neira
- Departamento de BiocienciasUniversidad de CuencaCuencaAzuayEcuador
- Facultad de MedicinaUniversidad del AzuayCuencaAzuayEcuador
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Collins AR, Azqueta A, Schoeters G, Slingers G, Dusinska M, Langie SAS. In memory of Dr. Ir. Gudrun Koppen (1969-2024). MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 895:503751. [PMID: 38575250 DOI: 10.1016/j.mrgentox.2024.503751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- Andrew R Collins
- Norgenotech AS, Oslo Cancer Cluster Incubator, Oslo, Norway; & Department of Nutrition, University of Oslo, Oslo, Norway
| | - Amaya Azqueta
- Department of Pharmaceutical Science, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Greet Schoeters
- Prof. Em., Department of Biomedical Sciences & Toxicological Centre, University of Antwerp, Wilrijk, Belgium
| | - Gitte Slingers
- Environmental Intelligence, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Maria Dusinska
- Department of Environmental Chemistry and Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Sabine A S Langie
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
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3
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Davydova E, Perenkov A, Vedunova M. Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes (Basel) 2024; 15:425. [PMID: 38674360 PMCID: PMC11049545 DOI: 10.3390/genes15040425] [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: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.
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Affiliation(s)
- Ekaterina Davydova
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia (M.V.)
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What Have Mechanistic Studies Taught Us About Childhood Asthma? THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:684-692. [PMID: 36649800 DOI: 10.1016/j.jaip.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Childhood asthma is a chronic heterogeneous syndrome consisting of different disease entities or phenotypes. The immunologic and cellular processes that occur during asthma development are still not fully understood but represent distinct endotypes. Mechanistic studies have examined the role of gene expression, protein levels, and cell types in early life development and the manifestation of asthma, many under the influence of environmental stimuli, which can be both protective and risk factors for asthma. Genetic variants can regulate gene expression, controlled partly by different epigenetic mechanisms. In addition, environmental factors, such as living space, nutrition, and smoking, can contribute to these mechanisms. All of these factors produce modifications in gene expression that can alter the development and function of immune and epithelial cells and subsequently different trajectories of childhood asthma. These early changes in a partially immature immune system can have dramatic effects (e.g., causing dysregulation), which in turn contribute to different disease endotypes and may help to explain differential responsiveness to asthma treatment. In this review, we summarize published studies that have aimed to uncover distinct mechanisms in childhood asthma, considering genetics, epigenetics, and environment. Moreover, a discussion of new, powerful tools for single-cell immunologic assays for phenotypic and functional analysis is included, which promise new mechanistic insights into childhood asthma development and therapeutic and preventive strategies.
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5
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Lau CI, Yánez DC, Papaioannou E, Ross S, Crompton T. Sonic Hedgehog signalling in the regulation of barrier tissue homeostasis and inflammation. FEBS J 2022; 289:8050-8061. [PMID: 34614300 DOI: 10.1111/febs.16222] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 01/14/2023]
Abstract
Epithelial barrier tissues such as the skin and airway form an essential interface between the mammalian host and its external environment. These physical barriers are crucial to prevent damage and disease from environmental insults and allergens. Failure to maintain barrier function against such risks can lead to severe inflammatory disorders, including atopic dermatitis and asthma. Here, we discuss the role of the morphogen Sonic Hedgehog in postnatal skin and lung and the impact of Shh signalling on repair, inflammation, and atopic disease in these tissues.
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Affiliation(s)
- Ching-In Lau
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Diana C Yánez
- UCL Great Ormond Street Institute of Child Health, London, UK.,School of Medicine, Universidad San Francisco de Quito, Ecuador
| | - Eleftheria Papaioannou
- UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Susan Ross
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Tessa Crompton
- UCL Great Ormond Street Institute of Child Health, London, UK
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6
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Imran S, Neeland MR, Peng S, Vlahos A, Martino D, Dharmage SC, Tang MLK, Sawyer S, Dang TD, McWilliam V, Peters RL, Koplin JJ, Perrett KP, Novakovic B, Saffery R. Immuno-epigenomic analysis identifies attenuated interferon responses in naïve CD4 T cells of adolescents with peanut and multi-food allergy. Pediatr Allergy Immunol 2022; 33:e13890. [PMID: 36433861 DOI: 10.1111/pai.13890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND IgE-mediated food allergies have been linked to suboptimal naïve CD4 T (nCD4T) cell activation in infancy, underlined by epigenetic and transcriptomic variation. Similar attenuated nCD4T cell activation in adolescents with food allergy have also been reported, but these are yet to be linked to specific epigenetic or transcriptional changes. METHODS We generated genome-wide DNA methylation data in purified nCD4 T cells at quiescence and following activation in a cohort of adolescents (aged 10-15 years old) with peanut allergy (peanut only or peanut + ≥1 additional food allergy) (FA, n = 29), and age-matched non-food allergic controls (NA, n = 18). Additionally, we assessed transcriptome-wide gene expression and cytokine production in these cells following activation. RESULTS We found widespread changes in DNA methylation in both NA and FA nCD4T cells in response to activation, associated with the T cell receptor signaling pathway. Adolescents with FA exhibit unique DNA methylation signatures at quiescence and post-activation at key genes involved in Th1/Th2 differentiation (RUNX3, RXRA, NFKB1A, IL4R), including a differentially methylated region (DMR) at the TNFRSF6B promoter, linked to Th1 proliferation. Combined analysis of DNA methylation, transcriptomic data and cytokine output in the same samples identified an attenuated interferon response in nCD4T cells from FA individuals following activation, with decreased expression of several interferon genes, including IFN-γ and a DMR at a key downstream gene, BST2. CONCLUSION We find that attenuated nCD4T cell responses from adolescents with food allergy are associated with specific epigenetic variation, including disruption of interferon responses, indicating dysregulation of key immune pathways that may contribute to a persistent FA phenotype. However, we recognize the small sample size, and the consequent restraint on reporting adjusted p-value statistics as limitations of the study. Further study is required to validate these findings.
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Affiliation(s)
- Samira Imran
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Melanie R Neeland
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephen Peng
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Amanda Vlahos
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - David Martino
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Telethon Kids Institute, University of Western, Perth, Nedlands, Australia
| | - Shyamali C Dharmage
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Mimi L K Tang
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Susan Sawyer
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Centre for Adolescent Health, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
| | - Thanh D Dang
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Vicki McWilliam
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Rachel L Peters
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Jennifer J Koplin
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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7
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Koeck RM, Busato F, Tost J, Zandstra H, Remy S, Langie S, Gielen M, van Golde R, Dumoulin JCM, Brunner H, Zamani Esteki M, van Montfoort APA. At age 9, the methylome of assisted reproductive technology children that underwent embryo culture in different media is not significantly different on a genome-wide scale. Hum Reprod 2022; 37:2709-2721. [PMID: 36206092 DOI: 10.1093/humrep/deac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Can we detect DNA methylation differences between ART children that underwent embryo culture in different media? SUMMARY ANSWER We identified no significant differences in site-specific or regional DNA methylation between the different culture medium groups. WHAT IS KNOWN ALREADY Embryo culture in G3 or K-SICM medium leads to differences in embryonic, neonatal and childhood outcomes, including growth and weight. The methylome may mediate this association as the period of in vitro culture of ART treatments coincides with epigenetic reprogramming. STUDY DESIGN, SIZE, DURATION This study was conducted as a follow-up to a previous culture medium comparison study in which couples were pseudo-randomized to embryo culture in G3 or K-SICM medium. Of the resultant singletons, 120 (n = 65 G3, n = 55 K-SICM), were recruited at age 9. PARTICIPANTS/MATERIALS, SETTING, METHODS The ART children provided a saliva sample from which the methylome was analysed using the Infinium MethylationEPIC array. After quality and context filtering, 106 (n = 57 G3, n = 49 K-SICM) samples and 659 708 sites were retained for the analyses. Differential methylation analyses were conducted using mixed effects linear models corrected for age, sex, sample plate and cell composition. These were applied to all cytosine-guanine dinucleotide (CpG) sites, various genomic regions (genes, promoters, CpG Islands (CGIs)) and as a targeted analysis of imprinted genes and birth weight-associated CpG sites. Differential variance was assessed using the improved epigenetic variable outliers for risk prediction analysis (iEVORA) algorithm and methylation outliers were identified using a previously defined threshold (upper or lower quartile plus or minus three times the interquartile range, respectively). MAIN RESULTS AND THE ROLE OF CHANCE After correcting for multiple testing, we did not identify any significantly differentially methylated CpG sites, genes, promoters or CGIs between G3 and K-SICM children despite a lenient corrected P-value threshold of 0.1. Targeted analyses of (sites within) imprinted genes and birth weight-associated sites also did not identify any significant differences. The number of DNA methylation outliers per sample was comparable between the culture medium groups. iEVORA identified 101 differentially variable CpG sites of which 94 were more variable in the G3 group. LARGE SCALE DATA Gene Expression Omnibus (GEO) GSE196432. LIMITATIONS, REASONS FOR CAUTION To detect significant methylation differences with a magnitude of <10% between the groups many more participants would be necessary; however, the clinical relevance of such small differences is unclear. WIDER IMPLICATIONS OF THE FINDINGS The results of this study are reassuring, suggesting that if there is an effect of the culture medium on DNA methylation (and methylation-mediated diseases risk), it does not differ between the two media investigated here. The findings concur with other methylome studies of ART neonates and children that underwent embryo culture in different media, which also found no significant methylome differences. STUDY FUNDING/COMPETING INTEREST(S) Study funded by March of Dimes (6-FY13-153), EVA (Erfelijkheid Voortplanting & Aanleg) specialty programme (grant no. KP111513) of Maastricht University Medical Centre (MUMC+) and the Horizon 2020 innovation (ERIN) (grant no. EU952516) of the European Commission. The authors do not report any conflicts of interest relevant to this study. TRIAL REGISTRATION NUMBER Dutch Trial register-NL4083.
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Affiliation(s)
- Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Florence Busato
- Laboratory for Epigenetics & Environment, CEA-Centre National de Recherche en Genomique Humaine, Evry, France
| | - Jorg Tost
- Laboratory for Epigenetics & Environment, CEA-Centre National de Recherche en Genomique Humaine, Evry, France
| | - Heleen Zandstra
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Sylvie Remy
- Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Sabine Langie
- Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.,Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, The Netherlands
| | - Marij Gielen
- Department of Epidemiology and Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ron van Golde
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John C M Dumoulin
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aafke P A van Montfoort
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
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8
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Koeck RM, Busato F, Tost J, Consten D, van Echten-Arends J, Mastenbroek S, Wurth Y, Remy S, Langie S, Nawrot TS, Plusquin M, Alfano R, Bijnens EM, Gielen M, van Golde R, Dumoulin JCM, Brunner H, van Montfoort APA, Zamani Esteki M. Methylome-wide analysis of IVF neonates that underwent embryo culture in different media revealed no significant differences. NPJ Genom Med 2022; 7:39. [PMID: 35768464 PMCID: PMC9243125 DOI: 10.1038/s41525-022-00310-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
A growing number of children born are conceived through in vitro fertilisation (IVF), which has been linked to an increased risk of adverse perinatal outcomes, as well as altered growth profiles and cardiometabolic differences in the resultant individuals. Some of these outcomes have also been shown to be influenced by the use of different IVF culture media and this effect is hypothesised to be mediated epigenetically, e.g. through the methylome. As such, we profiled the umbilical cord blood methylome of IVF neonates that underwent preimplantation embryo development in two different IVF culture media (G5 or HTF), using the Infinium Human Methylation EPIC BeadChip. We found no significant methylation differences between the two groups in terms of: (i) systematic differences at CpG sites or regions, (ii) imprinted sites/genes or birth weight-associated sites, (iii) stochastic differences presenting as DNA methylation outliers or differentially variable sites, and (iv) epigenetic gestational age acceleration.
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Affiliation(s)
- Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Florence Busato
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Genomique Humaine, CEA - institut de Biologie François Jacob, Université Paris Saclay, 91000, Evry, France
| | - Jorg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Genomique Humaine, CEA - institut de Biologie François Jacob, Université Paris Saclay, 91000, Evry, France
| | - Dimitri Consten
- Center for Reproductive Medicine, St. Elisabeth-TweeSteden Hospital, Hilvarenbeekseweg 60, 5022, GC, Tilburg, the Netherlands
| | - Jannie van Echten-Arends
- Section of Reproductive Medicine, Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713, GZ, Groningen, the Netherlands
| | - Sebastiaan Mastenbroek
- Center for Reproductive Medicine, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Yvonne Wurth
- Center for Reproductive Medicine, St. Elisabeth-TweeSteden Hospital, Hilvarenbeekseweg 60, 5022, GC, Tilburg, the Netherlands
| | - Sylvie Remy
- Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400, Mol, Belgium
| | - Sabine Langie
- Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400, Mol, Belgium.,Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Public Health and Primary Care, Leuven University (KU Leuven), Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Esmée M Bijnens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
| | - Marij Gielen
- Department of Epidemiology and Nutrition and Toxicology Research Institute Maastricht (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ron van Golde
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - John C M Dumoulin
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aafke P A van Montfoort
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, Maastricht, The Netherlands.
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands. .,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
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9
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Declerck K, Novo CP, Grielens L, Van Camp G, Suter A, Vanden Berghe W. Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences. BMC Complement Med Ther 2021; 21:141. [PMID: 33980308 PMCID: PMC8114977 DOI: 10.1186/s12906-021-03310-5] [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: 05/09/2020] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Herbal remedies of Echinacea purpurea tinctures are widely used today to reduce common cold respiratory tract infections. Methods Transcriptome, epigenome and kinome profiling allowed a systems biology level characterisation of genomewide immunomodulatory effects of a standardized Echinacea purpurea (L.) Moench extract in THP1 monocytes. Results Gene expression and DNA methylation analysis revealed that Echinaforce® treatment triggers antiviral innate immunity pathways, involving tonic IFN signaling, activation of pattern recognition receptors, chemotaxis and immunometabolism. Furthermore, phosphopeptide based kinome activity profiling and pharmacological inhibitor experiments with filgotinib confirm a key role for Janus Kinase (JAK)-1 dependent gene expression changes in innate immune signaling. Finally, Echinaforce® treatment induces DNA hypermethylation at intergenic CpG, long/short interspersed nuclear DNA repeat elements (LINE, SINE) or long termininal DNA repeats (LTR). This changes transcription of flanking endogenous retroviral sequences (HERVs), involved in an evolutionary conserved (epi) genomic protective response against viral infections. Conclusions Altogether, our results suggest that Echinaforce® phytochemicals strengthen antiviral innate immunity through tonic IFN regulation of pattern recognition and chemokine gene expression and DNA repeat hypermethylated silencing of HERVs in monocytes. These results suggest that immunomodulation by Echinaforce® treatment holds promise to reduce symptoms and duration of infection episodes of common cold corona viruses (CoV), Severe Acute Respiratory Syndrome (SARS)-CoV, and new occurring strains such as SARS-CoV-2, with strongly impaired interferon (IFN) response and weak innate antiviral defense. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03310-5.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Claudina Perez Novo
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Lisa Grielens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp (UA) and University Hospital Antwerp (UZA), Antwerp, Belgium
| | | | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium.
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10
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Ntontsi P, Photiades A, Zervas E, Xanthou G, Samitas K. Genetics and Epigenetics in Asthma. Int J Mol Sci 2021; 22:ijms22052412. [PMID: 33673725 PMCID: PMC7957649 DOI: 10.3390/ijms22052412] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Asthma is one of the most common respiratory disease that affects both children and adults worldwide, with diverse phenotypes and underlying pathogenetic mechanisms poorly understood. As technology in genome sequencing progressed, scientific efforts were made to explain and predict asthma’s complexity and heterogeneity, and genome-wide association studies (GWAS) quickly became the preferred study method. Several gene markers and loci associated with asthma susceptibility, atopic and childhood-onset asthma were identified during the last few decades. Markers near the ORMDL3/GSDMB genes were associated with childhood-onset asthma, interleukin (IL)33 and IL1RL1 SNPs were associated with atopic asthma, and the Thymic Stromal Lymphopoietin (TSLP) gene was identified as protective against the risk to TH2-asthma. The latest efforts and advances in identifying and decoding asthma susceptibility are focused on epigenetics, heritable characteristics that affect gene expression without altering DNA sequence, with DNA methylation being the most described mechanism. Other less studied epigenetic mechanisms include histone modifications and alterations of miR expression. Recent findings suggest that the DNA methylation pattern is tissue and cell-specific. Several studies attempt to describe DNA methylation of different types of cells and tissues of asthmatic patients that regulate airway remodeling, phagocytosis, and other lung functions in asthma. In this review, we attempt to briefly present the latest advancements in the field of genetics and mainly epigenetics concerning asthma susceptibility.
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Affiliation(s)
- Polyxeni Ntontsi
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Andreas Photiades
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Eleftherios Zervas
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Georgina Xanthou
- Cellular Immunology Laboratory, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Konstantinos Samitas
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
- Cellular Immunology Laboratory, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-778-1720
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11
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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12
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Prevalence and risk factors for asthma, rhinitis, eczema, and atopy among preschool children in an Andean city. PLoS One 2020; 15:e0234633. [PMID: 32649729 PMCID: PMC7351199 DOI: 10.1371/journal.pone.0234633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Background Limited data are available on prevalence and associated risk factors for atopy and allergic diseases from high-altitude urban settings in Latin America. Objective To estimate the prevalence of atopy, asthma, rhinitis, and eczema, and associations with relevant risk factors in preschool children in the Andean city of Cuenca. Methods A cross-sectional study was undertaken using a representative sample of 535 children aged 3–5 years attending 30 nursery schools in the city of Cuenca, Ecuador. Data on allergic diseases and risk factors were collected by parental questionnaire. Atopy was measured by skin prick test (SPT) reactivity to a panel of relevant aeroallergens. Associations between risk factors and the prevalence of atopy and allergic diseases were estimated using multivariable logistic regression. Results Asthma symptoms were reported for 18% of children, rhinitis for 48%, and eczema for 28%, while SPT reactivity was present in 33%. Population fractions of asthma, rhinitis, and eczema attributable to SPT were 3.4%, 7.9%, and 2.9%, respectively. In multivariable models, an increased risk of asthma was observed among children with a maternal history of rhinitis (OR 1.85); rhinitis was significantly increased in children of high compared to low socioeconomic level (OR 2.09), among children with a maternal history of rhinitis (OR 2.29) or paternal history of eczema (OR 2.07), but reduced among children attending daycare (OR 0.64); eczema was associated with a paternal history of eczema (OR 3.73), and SPT was associated with having a dog inside the house (OR 1.67). Conclusions A high prevalence of asthma, rhinitis, and eczema symptoms were observed among preschool children in a high-altitude Andean setting. Despite a high prevalence of atopy, only a small fraction of symptoms was associated with atopy. Parental history of allergic diseases was the most consistent risk factor for symptoms in preschool children.
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13
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Van Den Heuvel R, Den Hond E, Colles A, Nelen V, Van Campenhout K, Schoeters G. Biobank@VITO: Biobanking the General Population in Flanders. Front Med (Lausanne) 2020; 7:37. [PMID: 32118021 PMCID: PMC7033607 DOI: 10.3389/fmed.2020.00037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 01/27/2020] [Indexed: 11/13/2022] Open
Abstract
During the last 15 years, VITO has established an infrastructure for biobanking a collection of biological samples from the general population in Flanders (Belgium). This biobank was set up to contribute to future, yet unspecified, research questions in the field of environment and health. Biobank@VITO is a population biobank in which bio-specimen including human peripheral blood, cord blood, and blood derivatives (e.g., serum, plasma, cells, RNA, DNA), urine, hair, nails, exhaled breath condensate, saliva DNA, and human breast milk collected from non-diseased populations are preserved. Currently, the biobank stores about 70,000 samples from 7,700 individuals. These biospecimen were collected since 2002 in different human biomonitoring studies comprising European (e.g., DEMOCOPHES, HBM4EU), national (e.g., WHO human breastmilk studies), Flemish (Flemish Environment and Health Study (FLEHS) campaigns), and local (e.g., hotspots, 3xG project) well-defined and ethically approved research projects. Participants to the surveys included different age groups (newborns, children, adolescents, and adults) and were representatively selected with regard to gender, age class, residence, and/or socioeconomic status (SES). In each campaign, samples were stored in the Biobank@VITO. The registration, preservation, and management of the samples in the biobank were done in a qualitative and uniform manner which guarantees the traceability of all samples. The samples in the biobank have an extended information backbone on the lifestyle, environment, and health status of the donor. The biological samples in the biobank are an invaluable archive that can be used to address specific policy and research questions in the future, to test old samples with new technology and according to the latest methods and insights or to measure newly identified pollutants in old samples looking for long-term trends.
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Affiliation(s)
- Rosette Van Den Heuvel
- Unit Health, Flanders' Research and Technology Organisation on Cleantech and Sustainable Development (VITO), Mol, Belgium
| | - Elly Den Hond
- Department of Environment, Provincial Institute for Hygiene (PIH), Antwerp, Belgium
| | - Ann Colles
- Unit Health, Flanders' Research and Technology Organisation on Cleantech and Sustainable Development (VITO), Mol, Belgium
| | - Vera Nelen
- Department of Environment, Provincial Institute for Hygiene (PIH), Antwerp, Belgium
| | | | - Greet Schoeters
- Unit Health, Flanders' Research and Technology Organisation on Cleantech and Sustainable Development (VITO), Mol, Belgium
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14
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Zhang C, Ge S, Wang J, Jing X, Li H, Mei S, Zhang J, Liang K, Xu H, Zhang X, Zhang C. Epigenomic profiling of DNA methylation for hepatocellular carcinoma diagnosis and prognosis prediction. J Gastroenterol Hepatol 2019; 34:1869-1877. [PMID: 31038805 DOI: 10.1111/jgh.14694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/31/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM DNA hypermethylation has emerged as a novel molecular biomarker for the diagnosis and prognosis prediction of many cancers. We aimed to identify clinically useful biomarkers regulated by DNA methylation in hepatocellular carcinoma (HCC). METHODS Genome-wide methylation analysis in HCCs and paired noncancerous tissues was performed using an Illumina Infinium HumanMethylation 450K BeadChip array. Methylation-specific polymerase chain reaction and pyrosequencing were used to validate the methylation status of selected genes in 100 paired HCCs and noncancerous samples. RESULTS A total of 97 027 (20.0%) out of 485 577 CpG sites significantly were differed between HCC and noncancerous tissues. Among all the significant CpG sites, 48.8% are hypermethylated and 51.2% are hypomethylated in HCCs. Multiple signaling pathways (AMP-activated protein kinase, estrogen, and adipocytokine) involved in gene methylation were identified in HCC. FES was selected for further analysis based on its high level of methylation confirmed by polymerase chain reaction and pyrosequencing. The result showed that FES hypermethylation was correlated with tumor size (0.001), serum alpha fetoprotein (0.023), and tumor differentiation (0.006). FES protein was significantly downregulated in 51/100 (51%) HCCs, and 94.12% (48/51) of them were due to promoter hypermethylation. Both FES hypermethylation and protein downregulation were associated with the progression-free survival and overall survival of HCC patients. Overexpressed and knockdown of FES confirmed its inhibitory effect on the proliferation and migration of HCC cells. CONCLUSIONS We identified many new differentially methylated CpGs in HCCs and demonstrate that FES functions as a tumor suppressor gene in HCC and its methylation status could be used as an indicator for prognosis of HCC.
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Affiliation(s)
- Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Shuang Ge
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Jun Wang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaotong Jing
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | | | - Shuyu Mei
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Juan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Ke Liang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Hui Xu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaoying Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
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15
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Langie SA, Timms JA, De Boever P, McKay JA. DNA methylation and the hygiene hypothesis: connecting respiratory allergy and childhood acute lymphoblastic leukemia. Epigenomics 2019; 11:1519-1537. [PMID: 31536380 DOI: 10.2217/epi-2019-0052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: The hygiene hypothesis states that a lack of infection in early-life suppresses immune system development, and is linked to respiratory allergy (RA) and childhood acute lymphoblastic leukemia (ALL) risk. Little is known about underlying mechanisms, but DNA methylation is altered in RA and ALL, and in response to infection. We investigated if aberrant methylation may be in common between these diseases and associated with infection. Materials & methods: RA and ALL disease-associated methylation signatures were compared and related to exposure-to-infection signatures. Results: A significant number of genes overlapped between RA and ALL signatures (p = 0.0019). Significant overlaps were observed between exposure-to-infection signatures and disease-associated signatures. Conclusion: DNA methylation may be a mediating mechanism through which the hygiene hypothesis is associated with RA and ALL risk.
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Affiliation(s)
- Sabine As Langie
- VITO-Health, 2400 Mol, Belgium.,Centre for Environmental Sciences, Hasselt University, Diepenbeek, 3590, Belgium
| | - Jessica A Timms
- Institute for Health & Society, Human Nutrition Research Centre, Newcastle University, NE2 4HH, UK.,Systems Cancer Immunology Lab, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Research Oncology, King's College London, Guy's Hospital, SE1 9RT, UK
| | - Patrick De Boever
- VITO-Health, 2400 Mol, Belgium.,Centre for Environmental Sciences, Hasselt University, Diepenbeek, 3590, Belgium
| | - Jill A McKay
- Institute for Health & Society, Human Nutrition Research Centre, Newcastle University, NE2 4HH, UK.,Faculty of Health & Life Sciences, Department of Applied Sciences, Northumbria University, NE1 8ST, UK
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16
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Popovic M, Fiano V, Fasanelli F, Trevisan M, Grasso C, Assumma MB, Gillio-Tos A, Polidoro S, De Marco L, Rusconi F, Merletti F, Zugna D, Richiardi L. Differentially methylated DNA regions in early childhood wheezing: An epigenome-wide study using saliva. Pediatr Allergy Immunol 2019; 30:305-314. [PMID: 30681197 DOI: 10.1111/pai.13023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Epigenetics may play a role in wheezing and asthma development. We aimed to examine infant saliva DNA methylation in association with early childhood wheezing. METHODS A case-control study was nested within the NINFEA birth cohort with 68 cases matched to 68 controls by sex, age (between 6 and 18 months, median: 10.3 months) and season at saliva sampling. Using a bumphunting region-based approach, we examined associations between saliva methylome measured using Illumina Infinium HumanMethylation450k array and wheezing between 6 and 18 months of age. We tested our main findings in independent publicly available data sets of childhood respiratory allergy and atopic asthma, with DNA methylation measured in different tissues and at different ages. RESULTS We identified one wheezing-associated differentially methylated region (DMR) spanning ten sequential CpG sites in the promoter-regulatory region of PM20D1 gene (family-wise error rate < 0.05). The observed associations were enhanced in children born to atopic mothers. In the publicly available data sets, hypermethylation in the same region of PM20D1 was consistently found at different ages and in all analysed tissues (cord blood, blood, saliva and nasal epithelia) of children with respiratory allergy/atopic asthma compared with controls. CONCLUSION This study suggests that PM20D1 hypermethylation is associated with early childhood wheezing. Directionally consistent epigenetic alteration observed in cord blood and other tissues at older ages in children with respiratory allergy and atopic asthma provides suggestive evidence that a long-term epigenetic modification, likely operating from birth, may be involved in childhood atopic phenotypes.
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Affiliation(s)
- Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Francesca Fasanelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | | | - Anna Gillio-Tos
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | | | - Laura De Marco
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Franca Rusconi
- Unit of Epidemiology, "Anna Meyer" Children's University Hospital, Florence, Italy
| | - Franco Merletti
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Daniela Zugna
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
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17
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Graw S, Henn R, Thompson JA, Koestler DC. pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS). BMC Bioinformatics 2019; 20:218. [PMID: 31035919 PMCID: PMC6489300 DOI: 10.1186/s12859-019-2804-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND When designing an epigenome-wide association study (EWAS) to investigate the relationship between DNA methylation (DNAm) and some exposure(s) or phenotype(s), it is critically important to assess the sample size needed to detect a hypothesized difference with adequate statistical power. However, the complex and nuanced nature of DNAm data makes direct assessment of statistical power challenging. To circumvent these challenges and to address the outstanding need for a user-friendly interface for EWAS power evaluation, we have developed pwrEWAS. RESULTS The current implementation of pwrEWAS accommodates power estimation for two-group comparisons of DNAm (e.g. case vs control, exposed vs non-exposed, etc.), where methylation assessment is carried out using the Illumina Human Methylation BeadChip technology. Power is calculated using a semi-parametric simulation-based approach in which DNAm data is randomly generated from beta-distributions using CpG-specific means and variances estimated from one of several different existing DNAm data sets, chosen to cover the most common tissue-types used in EWAS. In addition to specifying the tissue type to be used for DNAm profiling, users are required to specify the sample size, number of differentially methylated CpGs, effect size(s) (Δβ), target false discovery rate (FDR) and the number of simulated data sets, and have the option of selecting from several different statistical methods to perform differential methylation analyses. pwrEWAS reports the marginal power, marginal type I error rate, marginal FDR, and false discovery cost (FDC). Here, we demonstrate how pwrEWAS can be applied in practice using a hypothetical EWAS. In addition, we report its computational efficiency across a variety of user settings. CONCLUSION Both under- and overpowered studies unnecessarily deplete resources and even risk failure of a study. With pwrEWAS, we provide a user-friendly tool to help researchers circumvent these risks and to assist in the design and planning of EWAS. AVAILABILITY The web interface is written in the R statistical programming language using Shiny (RStudio Inc., 2016) and is available at https://biostats-shinyr.kumc.edu/pwrEWAS/ . The R package for pwrEWAS is publicly available at GitHub ( https://github.com/stefangraw/pwrEWAS ).
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Affiliation(s)
- Stefan Graw
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS USA
| | - Rosalyn Henn
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS USA
| | - Jeffrey A. Thompson
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS USA
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18
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Forno E, Celedón JC. Epigenomics and Transcriptomics in the Prediction and Diagnosis of Childhood Asthma: Are We There Yet? Front Pediatr 2019; 7:115. [PMID: 31001502 PMCID: PMC6454089 DOI: 10.3389/fped.2019.00115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/11/2019] [Indexed: 01/15/2023] Open
Abstract
Asthma is the most common non-communicable chronic disease of childhood. Despite its high prevalence, to date we lack methods that are both efficient and accurate in diagnosing asthma. Most traditional approaches have been based on garnering clinical evidence, such as risk factors and exposures. Given the high heritability of asthma, more recent approaches have looked at genetic polymorphisms as potential "risk factors." However, genetic variants explain only a small proportion of asthma risk, and have been less than optimal at predicting risk for individual subjects. Epigenomic studies offer significant advantages over previous approaches. Epigenetic regulation is highly tissue-specific, and can induce both short- and long-term changes in gene expression. Such changes can start in utero, can vary throughout the life span, and in some instances can be passed on from one generation to another. Most importantly, the epigenome can be modified by environmental factors and exposures, and thus epigenetic and transcriptomic profiling may yield the most accurate risk estimates for a given patient by incorporating environmental (and treatment) effects throughout the lifespan. Here we will review the most recent advances in the use of epigenetic and transcriptomic analysis for the early diagnosis of asthma and atopy, as well as challenges and future directions in the field as it moves forward. We will particularly focus on DNA methylation, the most studied mechanism of epigenetic regulation.
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Affiliation(s)
- Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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19
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Mørkve Knudsen T, Rezwan FI, Jiang Y, Karmaus W, Svanes C, Holloway JW. Transgenerational and intergenerational epigenetic inheritance in allergic diseases. J Allergy Clin Immunol 2018; 142:765-772. [PMID: 30040975 PMCID: PMC6167012 DOI: 10.1016/j.jaci.2018.07.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/07/2023]
Abstract
It has become clear that early life (including in utero exposures) is a key window of vulnerability during which environmental exposures can alter developmental trajectories and initiate allergic disease development. However, recent evidence suggests that there might be additional windows of vulnerability to environmental exposures in the parental generation before conception or even in previous generations. There is evidence suggesting that information of prior exposures can be transferred across generations, and experimental animal models suggest that such transmission can be conveyed through epigenetic mechanisms. Although the molecular mechanisms of intergenerational and transgenerationational epigenetic transmission have yet to be determined, the realization that environment before conception can alter the risks of allergic diseases has profound implications for the development of public health interventions to prevent disease. Future research in both experimental models and in multigenerational human cohorts is needed to better understand the role of intergenerational and transgenerational effects in patients with asthma and allergic disease. This will provide the knowledge basis for a new approach to efficient intervention strategies aimed at reducing the major public health challenge of these conditions.
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Affiliation(s)
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Cecilie Svanes
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway; Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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