Epigenome-wide association study reveals longitudinally stable DNA methylation differences in CD4+ T cells from children with IgE-mediated food allergy

Epigenetics

Volumn 9, Issue 7, 2014, Pages 998-1006

  Martino, David ^a,b   Joo, Jihoon E ^a   Sexton Oates, Alexandra ^a   Dang, Thanh ^a   Allen, Katrina ^a   Saffery, Richard ^a   Prescott, Susan ^c  

^a ROYAL CHILDREN'S HOSPITAL   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Allergic disease; EWAS; Food allergy; In utero programming; Infinium 450k; Metastable epialleles

Indexed keywords

ACYL COENZYME A DEHYDROGENASE; AGGRECAN; B CELL MATURATION ANTIGEN; B7 ANTIGEN; CALCIUM CHANNEL N TYPE; DUAL SPECIFICITY PHOSPHATASE 3; ENVELOPE PROTEIN; GAMMA GLUTAMYL HYDROLASE; HISTONE DEACETYLASE 4; HLA DQB1 ANTIGEN; HOMEODOMAIN PROTEIN; IMMUNOGLOBULIN E; LACTATE DEHYDROGENASE; LEUCINE ZIPPER PROTEIN; MICRORNA 26A; MITOCHONDRIAL PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; MYOSIN; NEUROPEPTIDE RECEPTOR; PROSTAGLANDIN E RECEPTOR 3; PROTAMINE; PROTEIN ARGININE DEIMINASE; RING FINGER PROTEIN; S6 KINASE; SMALL CONDUCTANCE CALCIUM ACTIVATED POTASSIUM CHANNEL; SUBTILISIN; THYROID PEROXIDASE; TRANSCRIPTION FACTOR SIN3A; UNINDEXED DRUG; URIDINE DIPHOSPHATE N ACETYLGLUCOSAMINE;

ARTICLE; CD4+ T LYMPHOCYTE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; FOLLOW UP; FOOD ALLERGY; GENE EXPRESSION; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; INFANT; MALE; MASS SPECTROMETRY; NEWBORN; OLFACTORY RECEPTOR; PRESCHOOL CHILD; PRICK TEST; RETROSPECTIVE STUDY; SINGLE NUCLEOTIDE POLYMORPHISM; CASE CONTROL STUDY; GENETIC EPIGENESIS; IMMUNOLOGY; METABOLISM; PATHOLOGY; PREGNANCY; SIGNAL TRANSDUCTION;

CASE-CONTROL STUDIES; CD4-POSITIVE T-LYMPHOCYTES; CHILD, PRESCHOOL; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; FOOD HYPERSENSITIVITY; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IMMUNOGLOBULIN E; INFANT; INFANT, NEWBORN; MALE; MAP KINASE SIGNALING SYSTEM; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; RETROSPECTIVE STUDIES;

EID: 84903726044     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.28945     Document Type: Article

References (28)

1. Osborne NJ, Koplin JJ, Martin PE, Gurrin LC, Lowe AJ, Matheson MC, Ponsonby A-L, Wake M, Tang MLK, Dharmage SC, et al.; HealthNuts Investigators. Prevalence of challenge-proven IgE-mediated food allergy using population-based sampling and predetermined challenge criteria in infants. J Allergy Clin Immunol 2011; 127:668, e1-668e2; PMID:21377036; http://dx.doi.org/10.1016/j.jaci.2011.01.039
2. Prescott S, Allen KJ. Food allergy: riding the second wave of the allergy epidemic. Pediatr Allergy Immunol 2011; 22:155 -160;PMID:21332796; http://dx.doi.org/10.1111/j.1399-3038.2011.01145.x
3. Morgan DK, Whitelaw E. The case for transgenerational epigenetic inheritance in humans. Mamm Genome 2008; 19:394-397;PMID:18663528; http://dx.doi.org/10.1007/s00335-008-9124-y
4. Trowbridge JJ, Snow JW, Kim J, Orkin SH. DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell 2009; 5:442-449; PMID:19796624; http://dx.doi.org/10.1016/j.stem.2009.08.016
5. Martino D, Maksimovic J, Joo JH, Prescott SL, Saffery R. Genome-scale profiling reveals a subset of genes regulated by DNA methylation that program somatic T-cell phenotypes in humans. Genes Immun 2012; 13:388-398;PMID:22495533; http://dx.doi.org/10.1038/gene.2012.7
6. Hollingsworth JW, Maruoka S, Boon K, Garantziotis S, Li Z, Tom Fohr J, Bailey N, Potts EN, Whitehead G, Brass DM, et al. In utero supplementation with methyl donors enhances allergic airway disease in mice. J Clin Invest 2008; 118:3462-3469;PMID:18802477
7. Chang H, Zhang T, Zhang Z, Bao R, Fu C, Wang Z, Bao Y, Li Y, Wu L, Zheng X, et al. Tissue-specific distribution of aberrant DNA methylation associated with maternal low-folate status in human neural tube defects. J Nutr Biochem 2011; 22:1172-1177;PMID:21333513; http://dx.doi.org/10.1016/j.jnutbio.2010.10.003
8. Perera F, Tang WY, Herbstman J, Tang D, Levin L, Miller R, Ho S-M. Relation of DNA methylation of 5′-CpG island of ACSL3 to transplacental exposure to airborne polycyclic aromatic hydrocarbons and childhood asthma. PLoS One 2009; 4:e4488; PMID:19221603; http://dx.doi.org/10.1371/journal.pone.0004488
9. Martino DJ, Prescott SL. Progress in understanding the epigenetic basis for immune development, immune function, and the rising incidence of allergic disease. Curr Allergy Asthma Rep 2013; 13:85-92;PMID:23054626; http://dx.doi.org/10.1007/s11882-012-0312-1
10. Nadeau K, McDonald-Hyman C, Noth EM, Pratt B, Hammond SK, Balmes J, Tager I. Ambient air pollution impairs regulatory T-cell function in asthma. J Allergy Clin Immunol 2010; 126:845, e10;PMID:20920773; http://dx.doi.org/10.1016/j.jaci.2010.08.008
11. Isidoro-García M, Dávila-González I, Pascual de Pedro M, Sanz-Lozano C, Lorente-Toledano F. Interactions between genes and the environment. Epigenetics in allergy. Allergol Immunopathol (Madr) 2007; 35:254-258;PMID:18047817; http://dx.doi.org/10.1157/13112992
12. Nestor CE, Barrenäs F, Wang H, Lentini A, Zhang H, Bruhn S, Jörnsten R, Langston MA, Rogers G, Gustafsson M, et al. DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure. PLoS Genet 2014; 10:e1004059; PMID: 24391521; http://dx.doi.org/10.1371/journal.pgen.1004059
13. Liang Y, Wang P, Zhao M, Liang G, Yin H, Zhang G, Wen H, Lu Q. Demethylation of the FCER1G promoter leads to FcεRI overexpression on monocytes of patients with atopic dermatitis. Allergy 2012; 67:424-430; PMID:22150093; http://dx.doi.org/10.1111/j.1398-9995.2011.02760.x
14. Martino DJ, Bosco A, McKenna KL, Hollams E, Mok D, Holt PG, Prescott SL. T-cell activation genes differentially expressed at birth in CD4+ T-cells from children who develop IgE food allergy. A llergy 2012; 67:191-200; PMID:22077487; http://dx.doi.org/10.1111/j.1398-9995.2011.02737.x
15. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet 2007; 3:1724-1735;PMID:17907809; http://dx.doi.org/10.1371/journal.pgen.0030161
16. Olson CM, Hedrick MN, Izadi H, Bates TC, Olivera ER, Anguita J. P38 mitogen-activated protein kinase controls NF-kappaB transcriptional activation and tumor necrosis factor alpha production through RelA phosphorylation mediated by mitogen- and stress-activated protein kinase 1 in response to Borrelia burgdorferi antigens. Infect Immun 2007; 75:270-277;PMID:17074860; http://dx.doi.org/10.1128/IAI.01412-06
17. Dodeller F, Schulze-Koops H. The p38 mitogen-activated protein kinase signaling cascade in CD4 T cells. Arthritis Res Ther 2006; 8:205;PMID:16542479; http://dx.doi.org/10.1186/ar1905
18. González-Navajas JM, Fine S, Law J, Datta SK, Nguyen KP, Yu M, Corr M, Katakura K, Eckman L, Lee J, et al. TLR4 signaling in effector CD4+ T cells regulates TCR activation and experimental colitis in mice. J Clin Invest 2010; 120:570-581; PMID:20051628; http://dx.doi.org/10.1172/JCI40055
19. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 2013; 10:949-955;PMID:24076989; http://dx.doi.org/10.1038/nmeth.2632
20. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol 2014; 15:R31;PMID:24495553; http://dx.doi.org/10.1186/gb-2014-15-2-r31
21. Docherty SJ, Davis OSP, Haworth CMA, Plomin R, Mill J. Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation. Epigenet Chromatin 2009; 2:3.
22. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg A P, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 2014; (Forthcoming);PMID:24478339; http://dx.doi.org/10.1093/bioinformatics/btu049
23. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5:R80;PMID:15461798; http://dx.doi.org/10.1186/gb-2004-5-10-r80
24. Maksimovic J, Gordon L, Oshlack A. SWA N: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol 2012; 13:R44;PMID:22703947; http://dx.doi.org/10.1186/gb-2012-13-6-r44
25. Chen Y-A, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013; 8:203-209;PMID:23314698; http://dx.doi.org/10.4161/epi.23470
26. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3:e3;PMID:16646809; http://dx.doi.org/10.2202/1544-6115.1027
27. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003; 100:9440-9445;PMID:12883005; http://dx.doi.org/10.1073/pnas.1530509100
28. Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44-57; PMID:19131956; http://dx.doi.org/10.1038/nprot.2008.211