Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age.,Genome Medicine

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Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age.
Genome Medicine ( IF 10.4 ) Pub Date : 2020-03-02 , DOI: 10.1186/s13073-020-0716-9
Simon Kebede Merid _{1,

2} , Alexei Novoloaca ₃ , Gemma C Sharp _{4,

5} , Leanne K Küpers _{5,

6,

7} , Alvin T Kho ₈ , Ritu Roy _{9,

10} , Lu Gao ₁₁ , Isabella Annesi-Maesano ₁₂ , Pooja Jain _{13,

14} , Michelle Plusquin _{13,

15} , Manolis Kogevinas _{16,

17,

18,

19} , Catherine Allard ₂₀ , Florianne O Vehmeijer _{21,

22} , Nabila Kazmi _{4,

5} , Lucas A Salas ₂₃ , Faisal I Rezwan ₂₄ , Hongmei Zhang ₂₅ , Sylvain Sebert _{26,

27,

28} , Darina Czamara ₂₉ , Sheryl L Rifas-Shiman ₃₀ , Phillip E Melton _{31,

32} , Debbie A Lawlor _{4,

5,

33} , Göran Pershagen _{1,

34} , Carrie V Breton ₁₁ , Karen Huen ₃₅ , Nour Baiz ₁₂ , Luigi Gagliardi ₃₆ , Tim S Nawrot _{13,

37} , Eva Corpeleijn ₇ , Patrice Perron _{20,

38} , Liesbeth Duijts _{21,

22} , Ellen Aagaard Nohr ₃₉ , Mariona Bustamante _{16,

17,

18} , Susan L Ewart ₄₀ , Wilfried Karmaus ₂₅ , Shanshan Zhao ₄₁ , Christian M Page ₄₂ , Zdenko Herceg ₃ , Marjo-Riitta Jarvelin _{26,

27,

43,

44} , Jari Lahti _{45,

46} , Andrea A Baccarelli ₄₇ , Denise Anderson ₄₈ , Priyadarshini Kachroo ₄₉ , Caroline L Relton _{4,

5,

33} , Anna Bergström _{1,

34} , Brenda Eskenazi ₅₀ , Munawar Hussain Soomro ₁₂ , Paolo Vineis ₅₁ , Harold Snieder ₇ , Luigi Bouchard _{20,

52,

53} , Vincent W Jaddoe _{21,

22} , Thorkild I A Sørensen _{4,

54,

55} , Martine Vrijheid _{16,

17,

18} , S Hasan Arshad _{56,

57} , John W Holloway ₅₈ , Siri E Håberg ₄₂ , Per Magnus ₄₂ , Terence Dwyer _{59,

60} , Elisabeth B Binder _{29,

61} , Dawn L DeMeo ₄₉ , Judith M Vonk _{7,

62} , John Newnham ₆₃ , Kelan G Tantisira ₄₉ , Inger Kull _{2,

64} , Joseph L Wiemels ₆₅ , Barbara Heude ₆₆ , Jordi Sunyer _{16,

17,

18,

19} , Wenche Nystad ₄₂ , Monica C Munthe-Kaas _{42,

67} , Katri Räikkönen ₄₂ , Emily Oken ₃₀ , Rae-Chi Huang ₄₈ , Scott T Weiss ₄₉ , Josep Maria Antó _{16,

17,

18,

19} , Jean Bousquet _{68,

69} , Ashish Kumar _{1,

70,

71} , Cilla Söderhäll ₇₂ , Catarina Almqvist _{73,

74} , Andres Cardenas ₇₅ , Olena Gruzieva _{1,

34} , Cheng-Jian Xu ₇₆ , Sarah E Reese ₄₁ , Juha Kere _{77,

78} , Petter Brodin _{72,

79,

80} , Olivia Solomon ₃₅ , Matthias Wielscher ₄₃ , Nina Holland ₃₅ , Akram Ghantous ₃ , Marie-France Hivert _{20,

30,

81} , Janine F Felix _{21,

22} , Gerard H Koppelman ₇₆ , Stephanie J London ₄₁ , Erik Melén _{1,

2,

82}

Affiliation

Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
Epigenetics Group, International Agency for Research on Cancer, Lyon, France.
MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
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.
Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
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.
Department of Preventive Medicine, University of Southern California, Los Angeles, USA.
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.
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.
Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.
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.
Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada.
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.
Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA.
School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK.
Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA.
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.
Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany.
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.
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.
Bristol NIHR Biomedical Research Centre, Bristol, UK.
Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden.
Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA.
Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy.
Department of Public Health & Primary Care, Leuven University, Leuven, Belgium.
Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada.
Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA.
Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA.
Norwegian Institute of Public Health, Oslo, Norway.
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.
Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Turku Institute for Advanced Studies, University of Turku, Turku, Finland.
Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA.
Telethon Kids Institute, University of Western Australia, Perth, Australia.
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA.
MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada.
Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada.
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.
Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK.
Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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.
Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA.
University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia.
Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden.
Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA.
INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France.
Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway.
University Hospital, Montpellier, France.
Department of Dermatology, Charité, Berlin, Germany.
University of Basel, Basel, Switzerland.
Swiss Tropical and Public Health Institute, Basel, Switzerland.
Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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.
Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
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.
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.
Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden.
Science for Life Laboratory, Stockholm, Sweden.
Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.

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.

中文翻译：

对新生儿和儿童血液 DNA 甲基化的全表观基因组荟萃分析确定了许多与胎龄相关的位点。

背景技术早产和较短的妊娠时间与新生儿和以后的发病率增加有关。由于表观基因组在胎儿发育过程中发挥着重要作用，我们研究了儿童孕龄与血液 DNA 甲基化之间的关联。方法我们对来自 17 个队列的 3648 名新生儿（没有常见妊娠并发症、引产或剖腹产）中的 3648 名新生儿的胎龄和脐带血 DNA 甲基化之间的关联进行了 Illumina 的 HumanMmethylation450 阵列的荟萃分析。我们还在其他儿科队列中探讨了胎龄与 4-18 岁时测量的 DNA 甲基化之间的关系。在脐带血中进行 DNA 甲基化和基因表达相关性的后续分析。还在与胎龄健康影响相关的组织（胎儿脑和肺）中探索了 DNA 甲基化谱。结果我们在脐带血中鉴定出 8899 个与胎龄（范围 27-42 周）相关的 CpG，具有 Bonferroni 显着性，P < 1.06 × 10-7，其中 3343 个是新的。这些被注释为 4966 个基因。在将发现限制为至少三个重要的相邻 CpG 后，我们确定了注释到 325 个基因的 1276 个 CpG。当分析仅限于足月出生时，结果总体上是一致的。脐带血检查结果往往不会持续到儿童期和青春期。通路分析确定了对胚胎发育至关重要的生物过程的富集。对已识别基因的跟踪显示胎龄与胎儿大脑和肺组织中 DNA 甲基化水平之间的相关性，以及与表达水平的相关性。结论我们确定了许多与出生胎龄相关的差异甲基化 CpG，这些 CpG 似乎反映了胎儿跨组织的发育过程。这些发现可能有助于理解胎龄与健康影响之间的联系机制。

更新日期：2020-04-22

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