Epigenome alterations in food allergy: A systematic review of candidate gene and epigenome‐wide association studies

Objective The aim of this study was to systematically review the evidence across studies that assessed DNA methylome variations in association with food allergy (FA). Design A systematic review of the literature and meta‐analysis were carried out within several databases. However, the risk of bias i...

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Published in:Clinical and experimental allergy 2023-03, Vol.53 (3), p.259-275
Main Authors: Safar, Ramia, Oussalah, Abderrahim, Mayorga, Lina, Vieths, Stefan, Barber, Domingo, Torres, Maria Jose, Guéant, Jean‐Louis
Format: Article
Language:English
Subjects:
Allergens
Animals
Cattle
CD14 antigen
Cell differentiation
Cell Line, Tumor
Cow's milk
Cow's milk allergy
Cytokine storm
Dendritic cells
DNA methylome
DNA-Binding Proteins
Epigenome
epigenome‐wide association study
ESR1 protein
Female
Food allergies
food allergy
Food Hypersensitivity
Foxp3 protein
GATA-3 protein
Gene clusters
Genes
Helper cells
Interleukin 10
Literature reviews
Lymphocytes
Lymphocytes T
Meta-analysis
Milk
Milk Hypersensitivity
Peanut allergy
Phosphorylation
Receptor mechanisms
Retinoid X receptor α
Ryanodine receptors
Signal transduction
Systematic review
Systematic Reviews as Topic
TLR2 protein
Toll-like receptors
Transcription Factors
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Summary:Objective The aim of this study was to systematically review the evidence across studies that assessed DNA methylome variations in association with food allergy (FA). Design A systematic review of the literature and meta‐analysis were carried out within several databases. However, the risk of bias in the included articles was not evaluated. Data sources PubMed, Cochrane Database of Systematic Reviews, and Web of Science were used to search up to July 2022. Eligibility criteria We included targeted and epigenome‐wide association studies (EWASs) that assessed DNA methylome alterations in association with FA in adult or paediatric populations. Results Among 366 publications, only 16 were retained, which were mainly focused on FA in children. Seven candidate gene‐targeted studies found associations in Th1/Th2 imbalance (IL4, IL5, IL10, INFG, IL2 and IL12B genes), regulatory T cell function (FOXP3 gene), Toll‐like receptors pathway (TLR2, CD14 genes) and digestive barrier integrity (FLG gene). Nine EWAS assessed the association with peanut allergy (n = 3), cow's milk allergy (n = 2) or various food allergens (n = 4). They highlighted 11 differentially methylated loci in at least two studies (RPS6KA2, CAMTA1, CTBP2, RYR2, TRAPPC9, DOCK1, GALNTL4, HDAC4, UMODL1, ZAK and TNS3 genes). Among them, CAMTA1 and RPS6KA2, and CTBP2 are involved in regulatory T cell function and Th2 cell differentiation, respectively. Gene‐functional analysis revealed two enriched gene clusters involved in immune responses and protein phosphorylation. ChIP‐X Enrichment Analysis 3 showed eight significant transcription factors (RXRA, ZBTB7A, ESR1, TCF3, MYOD1, CTCF, GATA3 and CBX2). Ingenuity Pathway Analysis identified canonical pathways involved, among other, in B cell development, pathogen‐induced cytokine storm signalling pathway and dendritic cell maturation. Conclusion This review highlights the involvement of epigenomic alterations of loci in Th1/Th2 and regulatory T cell differentiation in both candidate gene studies and EWAS. These alterations provide a better insight into the mechanistic aspects in FA pathogenesis and may guide the development of epigenome‐based biomarkers for FA. Data were extracted from seven candidate gene and nine epigenome‐wide association studies on food allergy. Eleven genes with epivariations were common to at least two epigenome‐wide association studies. This review highlights the involvement of epigenomic alterations of loci in Th1/Th2 and regulatory T
ISSN:0954-7894
1365-2222
DOI:10.1111/cea.14277