Blood DNA methylation biomarkers predict clinical reactivity in food-sensitized infants

Journal of Allergy and Clinical Immunology

Volumn 135, Issue 5, 2015, Pages 1319-1328.e12

  Martino, David ^a,b,d,e   Dang, Thanh ^a,b   Sexton Oates, Alexandra ^b   Prescott, Susan ^a,c,e   Tang, Mimi L K ^a,b,d   Dharmage, Shyamali ^a,d   Gurrin, Lyle ^a,d   Koplin, Jennifer ^a,d   Ponsonby, Anne Louise ^a,b,d   Allen, Katrina J ^a,b,d,e,f   Saffery, Richard ^b,d  

^a MURDOCH CHILDREN'S RESEARCH INSTITUTE   (Australia)

^b ROYAL CHILDREN'S HOSPITAL   (Australia)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e World Universities Network (WUN)   (Australia)

^f UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

allergy epigenetics; biomarkers; DNA methylation profiling; epigenetic epidemiology; epigenetics; Food allergy; Infinium; methylation profiling; shrunken centroids

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 4; ATAXIN 3; BIOLOGICAL MARKER; CD4 ANTIGEN; COLLAGEN TYPE 3; CYCLIN G1; FK 506 BINDING PROTEIN; HIPPOCALCIN; HISTONE DEACETYLASE 4; IMMUNOGLOBULIN E; INTERLEUKIN 4; LYMPHOTOXIN BETA; MEMBRANE PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; NETRIN; NEUROFIBROMIN; OLIGODENDROCYTE MYELIN GLYCOPROTEIN; SOMATOMEDIN B RECEPTOR; TISSUE INHIBITOR OF METALLOPROTEINASE 2; TRANSIENT RECEPTOR POTENTIAL CHANNEL M1; ZINC FINGER PROTEIN;

ARTICLE; BLOOD SAMPLING; CHILD; CLINICAL FEATURE; CONTROLLED STUDY; DENDRITIC CELL; DNA METHYLATION; EGG ALLERGY; FLOW CYTOMETRY; FOOD ALLERGY; HUMAN; IMMUNOGLOBULIN BLOOD LEVEL; INFANT; MEMORY CELL; MICROARRAY ANALYSIS; MONONUCLEAR CELL; PEANUT ALLERGY; PRICK TEST; PRIORITY JOURNAL; REPLICATION STUDY; SENSITIVITY ANALYSIS; SENSITIZATION; SKIN TEST; BIOLOGICAL MODEL; BIOLOGY; BLOOD; CPG ISLAND; FOOD HYPERSENSITIVITY; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; PROGNOSIS; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FOOD HYPERSENSITIVITY; GENE EXPRESSION PROFILING; HUMANS; IMMUNOGLOBULIN E; INFANT; LEUKOCYTES, MONONUCLEAR; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; PROGNOSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84937511091     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2014.12.1933     Document Type: Article

References (25)

1. N.J. Osborne, J.J. Koplin, P.E. Martin, L.C. Gurrin, A.J. Lowe, M.C. Matheson, and et al. Prevalence of challenge-proven IgE-mediated food allergy using population-based sampling and predetermined challenge criteria in infants J Allergy Clin Immunol 127 2011 668 676 e1-2
2. S. Prescott, and K.J. Allen Food allergy: riding the second wave of the allergy epidemic Pediatr Allergy Immunol 22 2011 155 160
3. K. Ito Diagnosis of food allergies: the impact of oral food challenge testing Asia Pac Allergy 3 2013 59 69
4. A.F. Santos, and G. Lack Food allergy and anaphylaxis in pediatrics: update 2010-2012 Pediatr Allergy Immunol 23 2012 698 706
5. V.K. Rakyan, T.A. Down, D.J. Balding, and S. Beck Epigenome-wide association studies for common human diseases Nat Rev Genet 12 2011 529 541
6. D. Martino, D.A. Kesper, M. Amarasekera, H. Harb, H. Renz, and S. Prescott Epigenetics in immune development and in allergic and autoimmune diseases J Reprod Immunol 104-105 2014 43 48
7. D. Martino, J.E. Joo, A. Sexton-Oates, T. Dang, K. Allen, R. Saffery, and et al. Epigenome-wide association study reveals longitudinally stable DNA methylation differences in CD4+ T cells from children with IgE-mediated food allergy Epigenetics 9 2014 998 1006
8. R.L. Peters, S.C. Dharmage, L.C. Gurrin, J.J. Koplin, A.L. Ponsonby, A.J. Lowe, and et al. The natural history and clinical predictors of egg allergy in the first 2 years of life: a prospective, population-based cohort study J Allergy Clin Immunol 133 2014 485 491
9. M.H. Ho, W.H. Wong, R.G. Heine, C.S. Hosking, D.J. Hill, and K.J. Allen Early clinical predictors of remission of peanut allergy in children J Allergy Clin Immunol 121 2008 731 736
10. R.S. Pumphrey, and M.H. Gowland Further fatal allergic reactions to food in the United Kingdom, 1999-2006 J Allergy Clin Immunol 119 2007 1018 1019
11. N.J. Osborne, J.J. Koplin, P.E. Martin, L.C. Gurrin, L. Thiele, M.L. Tang, and et al. The HealthNuts population-based study of paediatric food allergy: validity, safety and acceptability Clin Exp Allergy 40 2010 1516 1522
12. J.J. Koplin, M.L. Tang, P.E. Martin, N.J. Osborne, A.J. Lowe, A.L. Ponsonby, and et al. Predetermined challenge eligibility and cessation criteria for oral food challenges in the HealthNuts population-based study of infants J Allergy Clin Immunol 129 2012 1145 1147
13. D. Martino, Y.J. Loke, L. Gordon, M. Ollikainen, M.N. Cruickshank, R. Saffery, and et al. Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance Genome Biol 14 2013 R42
14. M.J. Aryee, A.E. Jaffe, H. Corrada-Bravo, C. Ladd-Acosta, A.P. Feinberg, K.D. Hansen, and et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays Bioinformatics 30 2014 1363 1369
15. Y.A. Chen, M. Lemire, S. Choufani, D.T. Butcher, D. Grafodatskaya, B.W. Zanke, and et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray Epigenetics 8 2013 203 209
16. R. Tibshirani, T. Hastie, B. Narasimhan, and G. Chu Diagnosis of multiple cancer types by shrunken centroids of gene expression Proc Natl Acad Sci U S A 99 2002 6567 6572
17. J.D. Storey, and R. Tibshirani Statistical significance for genomewide studies Proc Natl Acad Sci U S A 100 2003 9440 9445
18. A. Subramanian, P. Tamayo, V.K. Mootha, S. Mukherjee, B.L. Ebert, M.A. Gillette, and et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc Natl Acad Sci U S A 102 2005 15545 15550
19. M.W. Coolen, A.L. Statham, M. Gardiner-Garden, and S.J. Clark Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements Nucleic Acids Res 35 2007 e119
20. B. Novakovic, R.K. Yuen, L. Gordon, M.S. Penaherrera, A. Sharkey, A. Moffett, and et al. Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors BMC Genomics 12 2011 529
21. J.E. Oh, N. Chambwe, S. Klein, J. Gal, S. Andrews, G. Gleason, and et al. Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment Transl Psychiatry 3 2013 e218
22. R.L. Peters, K.J. Allen, S.C. Dharmage, M.L. Tang, J.J. Koplin, A.L. Ponsonby, and et al. Skin prick test responses and allergen-specific IgE levels as predictors of peanut, egg, and sesame allergy in infants J Allergy Clin Immunol 132 2013 874 880
23. T.D. Dang, M. Tang, S. Choo, P.V. Licciardi, J.J. Koplin, P.E. Martin, and et al. Increasing the accuracy of peanut allergy diagnosis by using Ara h 2 J Allergy Clin Immunol 129 2012 1056 1063
24. E. Bair, and R. Tibshirani Semi-supervised methods to predict patient survival from gene expression data PLoS Biol 2 2004 E108
25. J.J. McCarthy, H.L. McLeod, and G.S. Ginsburg Genomic medicine: a decade of successes, challenges, and opportunities Sci Transl Med 5 2013 189sr4