The Epigenetics of Food Allergy

Trained innate immunity, epigenetics, and food allergy

In recent years the increased incidence of food allergy in Western culture has been associated with environmental factors and an inappropriate immune phenotype. While the adaptive immune changes in food allergy development and progression have been well-characterized, an increase in innate cell frequency and activation status has also recently received greater attention. Early in prenatal and neonatal development of human immunity there is a reliance on epigenetic and metabolic changes that stem from environmental factors, which are critical in training the immune outcomes. In the present review, we discuss how trained immunity is regulated by epigenetic, microbial and metabolic factors, and how these factors and their impact on innate immunity have been linked to the development of food allergy. We further summarize current efforts to use probiotics as a potential therapeutic approach to reverse the epigenetic and metabolic signatures and prevent the development of severe anaphylactic food allergy, as well as the potential use of trained immunity as a diagnostic and management strategy. Finally, trained immunity is presented as one of the mechanisms of action of allergen-specific immunotherapy to promote tolerogenic responses in allergic individuals.

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 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.

Immuno-epigenomic analysis identifies attenuated interferon responses in naïve CD4 T cells of adolescents with peanut and multi-food allergy

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.

An interdisciplinary approach to characterize peanut-allergic patients-First data from the FOOD@ consortium

Background

Peanut allergy is a frequent cause of food allergy and potentially life‐threatening. Within this interdisciplinary research approach, we aim to unravel the complex mechanisms of peanut allergy. As a first step were applied in an exploratory manner the analysis of peanut allergic versus non‐allergic controls.

Methods

Biosamples were studied regarding DNA methylation signatures, gut microbiome, adaptive and innate immune cell populations, soluble signaling molecules and allergen‐reactive antibody specificities. We applied a scalable systems medicine computational workflow to the assembled data.

Results

We identified combined cellular and soluble biomarker signatures that stratify donors into peanut‐allergic and non‐allergic with high specificity. DNA methylation profiling revealed various genes of interest and stool microbiota differences in bacteria abundances.

Conclusion

By extending our findings to a larger set of patients (e.g., children vs. adults), we will establish predictors for food allergy and tolerance and translate these as for example, indicators for interventional studies.

Trends in the contributions of atopic family history to pediatric food sensitization and allergy

OBJECTIVE

Family history of atopic diseases (FHA) contributes to food allergy (FA). But little is known whether FHA primarily increases IgE-mediated, non-IgE-mediated FA, or both. And the trends in the contributions of FHA to food sensitization (FS) and FA remain unclear. We aim to clarify the associations among FHA, FS and FA and to understand the trends in the contributions of FHA to FS and FA.

METHODS

We used chi-square test and mediating effect model to analyze the associations among FHA, FS and FA through comparisons between two cross-sectional investigations on FA in children under 2 years old in 2009 and 2019.

RESULTS

In 2009 and 2019, the positive FHA proportion tended to be increasing without significance (28.9% to 31.6%, P = 0.39). Subgroup analysis showed the FS rate in FA group decreased significantly (37/39 to 44/62, P = 0.003). In 2009, the FS rate and FA prevalence were higher in FHA (+) group than in FHA (-) group (26% vs. 14.7%, P = 0.008 and 15% vs. 7.7%, P = 0.03), and FS had a complete mediating effect on the association between FHA and FA (Z = 2.54, P = 0.011), but the results lost significance in 2019.

CONCLUSIONS

The association between FHA and FA was completely mediated by FS, which means FHA mainly increases IgE-mediated FA. And the contributions of FHA to FS and FA tended to be stabilized or even diminished, which means FHA alone could no longer be enough to screen high-risk children.

The use of biologics in food allergy

BACKGROUND

Food allergy continues to pose problems due to its increased frequency and its increasingly high severity. In this context, alongside the traditional avoidance strategies of allergenic foods and desensitization through the cautious progression of exposure to foods in the context of oral immunotherapy (OIT), alternative strategies have made their way in the last decades. We review the possibilities of intervention in food allergy with the use of biological drugs capable of interfering with the synthesis of IgE, with their mechanisms of action, or with complex biological mechanisms that lead to the establishment of a food allergy.

METHODS

Repeated Entrez PubMed searches using the template algorithm "Food allergy" and "biologics" or "Omalizumab" or "Dupilumab" or "milk desensitization" or "oral tolerance induction" or "oral immunotherapy" or "Etokimab" or "Tezepelumab" or "Quilizumab" or "Ligelizumab" or "Tralokinumab" or "Nemolizumab" or "Mepolizumab" or "Reslizumab" or "Benralizumab". The authors' clinical experience in paediatric allergy units of University hospitals was also drawn upon.

RESULTS

The landscape in this context has changed dramatically over the past 10 years. We have acquired knowledge mainly on the effect of different types of anti-IgE treatments in poliallergic patients with food allergy, and in patients treated with OIT. However, other mediators are being targeted by specific biologic treatments. Among them, the alarmins Il-33 and TSLP, IL-4 and IL-13, eosinophil-related molecules as IL-6, IL-8, IL-10, IL-12, and mostly IL-5, and integrins involved in the pathogenesis of eosinophilic gastrointestinal diseases (EGIDs), as SIGLEC-8.

CONCLUSIONS

The ever-better knowledge of the mechanisms of food allergy allowing these developments will improve not only the perspective of patients with the most serious immediate food allergies such as anaphylaxis, but also those of patients with related diseases such as atopic dermatitis, eosinophilic esophagitis, and EGIDs. Biologics are also intended to complement OIT strategies that have developed over the years.

DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life

DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.