Current insights into the genetics of food allergy

Update on the genetics of allergic diseases

The field of genetic etiology of allergic diseases has advanced significantly in recent years. Shared risk loci reflect the contribution of genetic factors to the sequential development of allergic conditions across the atopic march, while unique risk loci provide opportunities to understand tissue specific manifestations of allergic disease. Most identified risk variants are noncoding, indicating that they likely influence gene expression through gene regulatory mechanisms. Despite recent advances, challenges persist, particularly regarding the need for increased ancestral diversity in research populations. Further, while polygenic risk scores show promise for identifying individuals at higher genetic risk for allergic diseases, their predictive accuracy varies across different ancestries and can be difficult to translate to an individual's absolute risk of developing a disease. Methodologies, including "nearest gene," 3D chromatin interaction analysis, expression quantitative trait locus analysis, experimental screens, and integrative bioinformatic models, have established connections between genetic variants and their regulatory targets, enhancing our understanding of disease risk and phenotypic variability. In this review, we focus on the state of knowledge of allergic sensitization and 5 allergic diseases: asthma, atopic dermatitis, allergic rhinitis, food allergy, and eosinophilic esophagitis. We summarize recent progress and highlight opportunities for advancing our understanding of their genetic etiology.

Scientific developments in understanding food allergy prevention, diagnosis, and treatment

Food allergies (FAs) are adverse immune reactions to normally innocuous foods. Their prevalence has been increasing in recent decades. They can be IgE-mediated, non-IgE mediated, or mixed. Of these, the mechanisms underlying IgE-mediated FA are the best understood and this has assisted in the development of therapeutics. Currently there are two approved drugs for the treatment of FA, Palforzia and Omalizumab. Palfornia is a characterized peanut product used as immunotherapy for peanut allergy. Immunotherapy, involves exposure of the patient to small but increasing doses of the allergen and slowly builds immune tolerance to the allergen and increases a patient's allergic threshold. Omalizumab, a biologic, is an anti-IgE antibody which binds to IgE and prevents release of proinflammatory allergenic mediators on exposure to allergen. Other biologics, investigational vaccines, nanoparticles, Janus Kinase and Bruton's tyrosine kinase inhibitors, or DARPins are also being evaluated as potential therapeutics. Oral food challenges (OFC) are the gold standard for the diagnosis for FA. However, they are time-consuming and involve risk of anaphylaxis; therefore, alternative diagnostic methods are being evaluated. This review will discuss how the immune system mediates an allergic response to specific foods, as well as FA risk factors, diagnosis, prevention, and treatments for FA.

Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma

Background

Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.

Objective

To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study (TWAS) to discover candidate asthma genes.

Methods

We developed and validated gene expression prediction databases for unstimulated CD4+ T cells (CD4+T) and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma. For detailed Methods, please see the Supplemental Methods.

Results

Novel databases for CD4+T and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From TWAS, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.

Conclusions

Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+T and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.

RELMβ sets the threshold for microbiome-dependent oral tolerance

Tolerance to dietary antigens is critical for avoiding deleterious type 2 immune responses resulting in food allergy (FA) and anaphylaxis1,2. However, the mechanisms resulting in both the maintenance and failure of tolerance to food antigens are poorly understood. Here we demonstrate that the goblet-cell-derived resistin-like molecule β (RELMβ)3,4 is a critical regulator of oral tolerance. RELMβ is abundant in the sera of both patients with FA and mouse models of FA. Deletion of RELMβ protects mice from FA and the development of food-antigen-specific IgE and anaphylaxis. RELMβ disrupts food tolerance through the modulation of the gut microbiome and depletion of indole-metabolite-producing Lactobacilli and Alistipes. Tolerance is maintained by the local production of indole derivatives driving FA protective RORγt+ regulatory T (Treg) cells5 through activation of the aryl hydrocarbon receptor. RELMβ antagonism in the peri-weaning period restores oral tolerance and protects genetically prone offspring from developing FA later in life. Together, we show that RELMβ mediates a gut immune-epithelial circuit regulating tolerance to food antigens-a novel mode of innate control of adaptive immunity through microbiome editing-and identify targetable candidates in this circuit for prevention and treatment of FA.

Genome-Wide Association Study Reveals a Causal Relationship Between Allergic Rhinitis and Hazelnut Allergy

BACKGROUND

Little is known about the genetics of food allergy (FA) to various allergens and the heterogeneity of FA in adults.

OBJECTIVE

We aimed to investigate genetic susceptibility to FA in an adult population and to assess the association between secondary FA and allergic rhinitis (AR).

METHODS

FA and allergen-specific FA were defined based on in-depth questionnaires and a previously published FA algorithm in the Lifelines. We performed a series of genome-wide association studies (GWAS) on FA and nine allergen-specific (e.g., hazelnut) FA in 21,353 adults in Lifelines. Single nucleotide polymorphisms (SNPs) (p < 1E-5) were replicated in a second independent set of 15,518 adults participating in the Lifelines followed by meta-analysis of the results of the two datasets. We subsequently investigated the causal relationship of AR to FA using Mendelian randomization (MR) analysis.

RESULTS

We observed co-occurrence of tree nuts and apple FA, with over 80% of this group also reporting AR. After meta-analysis, we identified one genome-wide significant locus near HLA-DPA1 associated with self-reported hazelnut allergy (hazelnutFA), of which the top SNP is rs5025825 (p = 2.51E-9, OR = 1.43). Two-sample MR indicated that AR is a significant causal risk factor for hazelnutFA (p-IVW = 5.27E-10, β = 5.90, p-pleiotropy = 0.46).

CONCLUSION

Our questionnaire enabled a large GWAS on self-reported FA in Dutch adults. We report one novel locus in the human leukocyte antigens (HLA) region associated with hazelnutFA, implying an association with antigen recognition. Our findings genetically link secondary FA to AR in adults.

Food Allergy Genetics and Epigenetics: A Review of Genome-Wide Association Studies

In this review, we provide an overview of food allergy genetics and epigenetics aimed at clinicians and researchers. This includes a brief review of the current understanding of genetic and epigenetic mechanisms, inheritance of food allergy, as well as a discussion of advantages and limitations of the different types of studies in genetic research. We specifically focus on the results of genome-wide association studies in food allergy, which have identified 16 genetic variants that reach genome-wide significance, many of which overlap with other allergic diseases, including asthma, atopic dermatitis, and allergic rhinitis. Identified genes for food allergy are mainly involved in epithelial barrier function (e.g., FLG, SERPINB7) and immune function (e.g., HLA, IL4). Epigenome-wide significant findings at 32 loci are also summarized as well as 14 additional loci with significance at a false discovery of < 1 × 10-4. Integration of epigenetic and genetic data is discussed in the context of disease mechanisms, many of which are shared with other allergic diseases. The potential utility of genetic and epigenetic discoveries is deliberated. In the future, genetic and epigenetic markers may offer ways to predict the presence or absence of clinical IgE-mediated food allergy among sensitized individuals, likelihood of development of natural tolerance, and response to immunotherapy.

Zéro allergie research clinic: a clinical and research initiative in oral immunotherapy for managing IgE-mediated food allergy

BACKGROUND AND METHODS

The Zéro allergie research clinic (Saguenay, Canada) is a clinical and research initiative in oral immunotherapy (OIT) for managing IgE-mediated food allergy (FA). A total of 183 children with FA and 27 non-allergic siblings were recruited to date in the Zéro allergie cohort (ZAC) to better understand biological mechanisms underlying FA and OIT prognosis. The primary aims are to (a) better understand the genetic, epigenetic, transcriptomic, metabolomic, and microbial diversity associated with FA; (b) establish the multi-omics and microbial diversity profiles of children following OIT to identify predictive prognosis biomarkers, (c) make OIT more accessible to the population of the Saguenay-Lac-Saint-Jean region, and (d) build a biobank of data and biological material.

RESULTS

The ZAC constitutes a unique and rich biobank of biological samples (blood, buccal swabs, microbiota samples [intestinal, buccal, nasal, and cutaneous]) combined with clinical data and more than 75 phenotypic characteristics.

CONCLUSIONS

This represents an innovative interdisciplinary initiative by researchers, allergists, and paediatricians to make FA care accessible to a greater number of children with IgE-mediated FA. Ultimately, it will contribute to provide more accessible treatment options with greater chances of success through a better understanding of the biological nature of FA and OIT.

Diagnosis and management of shrimp allergy

Shrimp allergy, the most common food allergy in the United States, affects up to 2% of the population. Its etiology is multi-factorial with the combination of genetic predisposition and environmental exposures. This review summarizes the latest diagnosis and management strategies for shrimp allergy. Currently, the double-blind, placebo-controlled food challenge is the gold standard for diagnosis. Moreover, mainstream and experimental management strategies include food allergen avoidance, the FDA-approved omalizumab, and oral immunotherapy. Herein, we emphasize the urgent need to develop more effective diagnostic tools and therapies for shrimp allergy.

Skin and oral intervention for food allergy prevention based on dual allergen exposure hypothesis

Early-onset atopic dermatitis increases an individual's risk of food allergies, suggesting that transcutaneous sensitization may occur through inflamed skin. Regarding food allergy causation, the dual allergen exposure hypothesis proposes that oral allergen exposure leads to immune tolerance, whereas allergen exposure via inflamed skin causes food allergies. This hypothesis suggests that it is important to induce oral immune tolerance and prevent allergic food sensitization through the skin. This review focuses on the breakthrough evidence based on the dual allergen exposure hypothesis that involves both skin and oral interventions for food allergy prevention.

IL10 and CXCL10 mRNA expression in food protein-induced enterocolitis syndrome

BACKGROUND

Food protein-induced enterocolitis syndrome (FPIES) is a rare non-IgE-mediated food allergy that mainly impacts babies and 7toddlers. The exact mechanism of FPIES is not completely understood. By studying the expression of IL-10 and CXCL10 in pediatric FPIES patients, researchers can gain insights into the immune mechanisms underlying this disorder.

METHODS

Peripheral venous blood was collected and subsequently stabilized with RNA pro. Total RNA was extracted and mRNA levels of CXCL10 and IL-10 was determined with real time PCR.

RESULTS

Children with FPIES had significantly higher values than the healthy control group (HC) for CXCL10 while FPIES had a significant lower values than the control group for IL-10.

CONCLUSIONS

Our results show a high production of CXCL10 and a concomitant reduced production of IL-10 in FPIES subjects who have not yet reached tolerance. These data may represent a molecular diagnostic marker for FPIES.

Maternal influences on offspring food allergy

The prevalence of allergies has been globally escalating. While allergies could appear at any age, they often develop in early life. However, the significant knowledge gap in the field is the mechanisms by which allergies affect certain people but not others. Investigating early factors and events in neonatal life that have a lasting impact on determining the susceptibilities of children to develop allergies is a significant area of the investigation as it promotes the understanding of neonatal immune system that mediates tolerance versus allergies. This review focuses on the research over the recent 10 years regarding the potential maternal factors that influence offspring allergies with a view to food allergy, a potentially life-threatening cause of anaphylaxis. The role of breast milk, maternal diet, maternal antibodies, and microbiota that have been suggested as key maternal factors regulating offspring allergies are discussed here. We also suggest future research area to expand our knowledge of maternal-offspring interactions on the pathogenesis of food allergy.

Loss of tolerance to dietary proteins: From mouse models to human model diseases

The critical importance of the immunoregulatory mechanisms, which prevent adverse responses to dietary proteins is demonstrated by the consequences of their failure in two common but distinct human pathological conditions, food allergy and celiac disease. The mechanisms of tolerance to dietary proteins have been extensively studied in mouse models but the extent to which the results in mice can be extrapolated to humans remains unclear. Here, after summarizing the mechanisms known to control oral tolerance in mouse models, we discuss how the monogenic immune disorders associated with food allergy on the one hand, and celiac disease, on the other hand, represent model diseases to gain insight into the key immunoregulatory pathways that control immune responses to food antigens in humans. The spectrum of monogenic disorders, in which the dysfunction of a single gene, is strongly associated with TH2-mediated food allergy suggests an important overlap between the mechanisms that regulate TH2 and IgE responses to food antigens in humans and mice. In contrast, celiac disease provides a unique example of the link between autoimmunity and loss of tolerance to a food antigen.

Regulation of immune responses to food by commensal microbes

The increasing prevalence of immune-mediated non-communicable chronic diseases, such as food allergies, has prompted a deeper investigation into the role of the gut microbiome in modulating immune responses. Here, we explore the complex interactions between commensal microbes and the host immune system, highlighting the critical role of gut bacteria in maintaining immune homeostasis. We examine how modern lifestyle practices and environmental factors have disrupted co-evolved host-microbe interactions and discuss how changes in microbiome composition impact epithelial barrier function, responses to food allergens, and susceptibility to allergic diseases. Finally, we examine the potential of bioengineered microbiome-based therapies, and live biotherapeutic products, for reestablishing immune homeostasis to prevent or treat food allergies.

Prevention of IgE-Mediated Food Allergy: Emerging Strategies Through Maternal and Neonatal Interventions

Whereas the early introduction of highly allergenic foods has been shown to be effective at preventing the onset of food allergy (FA) in high-risk infants, sensitization to food antigens can occur prior to complementary food introduction, and thus, additional earlier FA prevention strategies are urgently needed. Currently, aside from early introduction of peanut and egg, no therapies are strongly recommended by international professional allergy societies for the primary prevention of FA. This review focuses on maternal- and neonatal-directed interventions that are being actively investigated and developed, including maternal dietary factors and supplementation, specific elimination diets, breastfeeding, cow's milk formula supplementation, microbiome manipulations, bacterial lysate therapy, and skin barrier therapies. Evaluating how these factors and various prenatal/early life environmental exposures may impact the development of FA is crucial for accurately counseling caregivers in the prevention of FA.

HLA variants and their association with IgE-Mediated banana allergy: A cross-sectional study

Background

Banana allergy is on the rise in tropical regions. Advances in genomics and candidate gene identification have increased interest in genetic factors in food allergies. However, the genetic basis of IgE-mediated banana allergy is underexplored.

Objective

To characterize HLA variants and their association with IgE-mediated banana allergy.

Methods

This cross-sectional study recruited banana-allergic adults, confirmed by allergology tests, with non-allergic individuals as controls. Genomic DNA extraction and sequencing BAM files for HLA typing were conducted. Allele frequency was calculated using the direct counting method, and odds ratio (OR) with 95 % confidence interval (CI) were determined. Fisher's exact or chi-square tests were used to assess associations with Bonferroni's correction for multiple tests. The allele frequency of the Thai population from The Allele Frequency Net Database was used to compute the allele enrichment ratio (ER).

Results

A total of 59 cases and 64 controls were recruited. HLA genotyping indicated potential associations of HLA-B*15:25 (OR 11.872; p-value 0.027), HLA-C*04:03 (OR 7.636; p-value 0.033), and HLA-DQB1*06:09 (OR 11.558; p-value 0.039) with banana allergy. However, after Bonferroni correction, none of these associations reached statistical significance. Comparing allele frequency with the general population from The Allele Frequency Net Database, our ER analysis revealed a higher prevalence in the banana allergy group for B*15:25 (ER 1.849), C*04:03 (ER 1.332), and DQB1*06:09 (ER 6.602) alleles.

Conclusions

This study provides initial genetic insights into banana allergy, suggesting potential links with specific HLA alleles. Despite 12 initially identifying alleles, none were statistically significant after multiple testing correction. Larger studies are needed to detect possible significant correlations.

The pathogenesis of food allergy and protection offered by dietary compounds from the perspective of epigenetics

Food allergy is a global food safety concern, with an increasing prevalence in recent decades. However, the immunological and cellular mechanisms involved in allergic reactions remain incompletely understood, which impedes the development of effective prevention and treatment strategies. Current evidence supports those epigenetic modifications regulate the activation of immune cells, and their dysregulation can contribute to the development of food allergies. Patients with food allergy show epigenetic alterations that lead to the onset, duration and recovery of allergic disease. Moreover, many preclinical studies have shown that certain dietary components exert nutriepigenetic effects in changing the course of food allergies. In this review, we provide an up-to-date overview of DNA methylation, noncoding RNA and histone modification, with a focus on their connections to food allergies. Following this, we discuss the epigenetic mechanisms that regulate the activation and differentiation of innate and adapted immune cell in the context of food allergies. Subsequently, this study specifically focuses on the multidimensional epigenetic effects of dietary components in modulating the immune response, which holds promise for preventing food allergies in the future.

Genetic and Immunological Pathogenesis of Atopic Dermatitis

Type 2 immune-mediated diseases give a clear answer to the issue of nature (genetics) versus nurture (environment). Both genetics and environment play vital complementary roles in the development of atopic dermatitis (AD). As a key component of the atopic march, AD demonstrates the interactive nature of genetic and environmental contributions to atopy. From sequence variants in the epithelial barrier gene encoding FLG to the hygiene hypothesis, AD combines a broad array of contributions into a single syndrome. This review will focus on the genetic contribution to AD and where genetics facilitates the elicitation or enhancement of AD pathogenesis.

A Positive Causal Effect of Shrimp Allergy on Major Depressive Disorder Mediated by Allergy- and Immune-Related Pathways in the East Asian Population

BACKGROUND

Observational studies have implied a potential correlation between allergic diseases and major depressive disorder (MDD). However, the relationship is still inconclusive as it is likely to be interfered with by substantial confounding factors and potential reverse causality. The present study aimed to investigate causal correlation of the two diseases by a Mendelian randomization (MR) study and further elucidate the underlying molecular mechanisms.

METHODS

With the biggest summary datasets of a genome-wide association study (GWAS) in the East Asian population, we conducted a two-sample, bidirectional MR study to assess the causal correlation between shrimp allergy (SA) and MDD. Subsequently, we identified the pleiotropic genes' susceptibility to the two diseases at whole-genome and tissue-specific levels, respectively. Enriched GO sets and KEGG pathways were also discovered to elucidate the potential underlying mechanisms.

RESULTS

With the most suitable MR method, SA was identified as a causal risk factor for MDD based on three different groups of independent genetic instruments, respectively (p < 2.81 × 10-2). In contrast, we did not observe a significant causal effect of MDD on SA. The GWAS-pairwise program successfully identified seven pleiotropic genetic variants (PPA3 > 0.8), indicating that the two diseases indeed have a shared genetic basis. At a whole-genome level, the MAGMA program identified 44 pleiotropic genes, which were enriched in allergy-related pathways, such as antigen processing and presentation pathway (p = 1.46 × 10-2). In brain-specific tissue, the S-MultiXcan program found 17 pleiotropic genes that were significantly enriched in immune-related pathways and GO sets, including asthma-related pathway, T-cell activation-related, and major histocompatibility complex protein-related GO sets. Regarding whole-blood tissue, the program identified six pleiotropic genes that are significantly enriched in tolerance induction-related GO sets.

CONCLUSIONS

The present study for the first time indicated a significant causal effect of SA on the occurrence of MDD, but the reverse was not true. Enrichment analyses of pleiotropic genes at whole-genome and tissue-specific levels implied the involvement of allergy and immune-related pathways in the shared genetic mechanism of the two diseases. Elucidating the causal effect and the acting direction may be beneficial in reducing the incidence rate of MDD for the massive group of SA patients in the East Asian region.

Emerging Pharmaceutical Therapies to Address the Inadequacy of a Gluten-Free Diet for Celiac Disease

Celiac disease (CeD) is a chronic autoimmune disorder triggered by the ingestion of gluten, affecting around 1% of the global population. It is a multifactorial disease involving both genetics and environmental factors. Nowadays, the only available treatment for CeD is a life-long gluten-free diet (GFD), which can cause a significant burden for patients, since symptoms and mucosal injury can persist despite apparent compliance with a GFD. This could also lead to psychological consequences and affect the quality of life of these patients. Thankfully, recent advances in understanding the pathogenesis of CeD and the availability of various targets have made it feasible to explore pharmaceutical treatments specific to CeD. Recently, the FDA has highlighted the unmet needs of adult patients on a GFD who experience ongoing symptoms attributed to CeD and also show persistent duodenal villous atrophy. This review will outline the limitations of a GFD, describe the targets of potential novel treatment of CeD and provide an overview of the primary clinical trials involving oral and injectable agents for a non-dietary treatment of CeD.

Early-life risk factors for food allergy: Dietary and environmental factors revisited

There appears a steep increase in the prevalence of food allergy worldwide in the past few decades. It is believed that, rather than genetic factors, the recently altered dietary and environmental factors are the driving forces behind the rapid increase of this disease. Accumulating evidence has implied that external exposures that occurred in prenatal and postnatal periods could affect the development of oral tolerance in later life. Understanding the potential risk factors for food allergy would greatly benefit the progress of intervention and therapy. In this review, we present updated knowledge on the dietary and environmental risk factors in early life that have been shown to impact the development of food allergy. These predominantly include dietary habits, microbial exposures, allergen exposure routes, environmental pollutants, and so on. The key evidence, conflicts, and potential research topics of each theory are discussed, and associated interventional strategies to prevent the disease development and ameliorate treatment burden are included. Accumulating evidence has supported the causative role of certain dietary and environmental factors in the establishment of oral tolerance in early life, especially the time of introducing allergenic foods, skin barrier function, and microbial exposures. In addition to certain immunomodulatory factors, increasing interest is raised toward modern dietary patterns, where adequately powered studies are required to identify contributions of those modifiable risk factors. This review broadens our understanding of the connections between diet, environment, and early-life immunity, thus benefiting the progress of intervention and therapy of food allergy.

Intestinal factors promoting the development of RORγt+ cells and oral tolerance

The gastrointestinal tract has to harmonize the two seemingly opposite functions of fulfilling nutritional needs and avoiding the entry of pathogens, toxins and agents that can cause physical damage. This balance requires a constant adjustment of absorptive and defending functions by sensing environmental changes or noxious substances and initiating adaptive or protective mechanisms against them through a complex network of receptors integrated with the central nervous system that communicate with cells of the innate and adaptive immune system. Effective homeostatic processes at barrier sites take the responsibility for oral tolerance, which protects from adverse reactions to food that cause allergic diseases. During a very specific time interval in early life, the establishment of a stable microbiota in the large intestine is sufficient to prevent pathological events in adulthood towards a much larger bacterial community and provide tolerance towards diverse food antigens encountered later in life. The beneficial effects of the microbiome are mainly exerted by innate and adaptive cells that express the transcription factor RORγt, in whose generation, mediated by different bacterial metabolites, retinoic acid signalling plays a predominant role. In addition, recent investigations indicate that food antigens also contribute, analogously to microbial-derived signals, to educating innate immune cells and instructing the development and function of RORγt+ cells in the small intestine, complementing and expanding the tolerogenic effect of the microbiome in the colon. This review addresses the mechanisms through which microbiota-produced metabolites and dietary antigens maintain intestinal homeostasis, highlighting the complementarity and redundancy between their functions.

Influence of Lifestyle and Dietary Habits on the Prevalence of Food Allergies: A Scoping Review

Changes in behavior, lifestyle, and nutritional patterns have influenced many potential risk variables globally. In recent decades, food allergies (FAs) have been elevated to a severe public health issue both in developed countries and developing countries (third-world countries). This study aims to evaluate the effects caused by certain factors such as lifestyle and dietary habits on food allergies, review the association of lifestyle and dietary habit status with FAs, and outline why more people are allergic to food sources as a result of lifestyle changes and dietary habits. We searched electronic international databases including Scopus, PubMed, Google Scholar, and Web of Science using combinations of keywords. Utilizing Excel, the relevant studies were included and the irrelevant studies were excluded, and Mendeley was used for referencing and also to remove duplicates. The framework proposed by Arksey and O'Malley was used for this scoping review. The papers published in the databases from 2016 to 2020 were extracted. A total of eight studies were extracted, and this scoping review was carried out according to the risk factors. In our review, we found that some lifestyle choices (Caesarean section and antibiotics) and dietary habits (n-3 PUFA, fast food, duration of dietary intervention, and vitamin D), were important contributing factors for FA.

Peanut butter feeding induces oral tolerance in genetically diverse collaborative cross mice

Background

Early dietary introduction of peanut has shown efficacy in clinical trials and driven pediatric recommendations for early introduction of peanut to children with heightened allergy risk worldwide. Unfortunately, tolerance is not induced in every case, and a subset of patients are allergic prior to introduction. Here we assess peanut allergic sensitization and oral tolerance in genetically diverse mouse strains.

Objective

We aimed to determine whether environmental adjuvant-driven airway sensitization and oral tolerance to peanut could be induced in various genetically diverse mouse strains.

Methods

C57BL/6J and 12 Collaborative Cross (CC) mouse strains were fed regular chow or ad libitum peanut butter to induce tolerance. Tolerance was tested by attempting to sensitize mice via intratracheal exposure to peanut and lipopolysaccharide (LPS), followed by intraperitoneal peanut challenge. Peanut-specific immunoglobulins and peanut-induced anaphylaxis were assessed.

Results

Without oral peanut feeding, most CC strains (11/12) and C57BL/6J induced peanut-specific IgE and IgG1 following airway exposure to peanut and LPS. With oral peanut feeding none of the CC strains nor C57BL/6J mice became sensitized to peanut or experienced anaphylaxis following peanut challenge.

Conclusion

Allergic sensitization and oral tolerance to peanut can be achieved across a range of genetically diverse mice. Notably, the same strains that became allergic via airway sensitization were tolerized by feeding high doses of peanut butter before sensitization, suggesting that the order and route of peanut exposure are critical for determining the allergic fate.

Multi-omics profiling approach in food allergy

The prevalence of food allergy (FA) among children is increasing, affecting nearly 8% of children, and FA is the most common cause of anaphylaxis and anaphylaxis-related emergency department visits in children. Importantly, FA is a complex, multi-system, multifactorial disease mediated by food-specific immunoglobulin E (IgE) and type 2 immune responses and involving environmental and genetic factors and gene-environment interactions. Early exposure to external and internal environmental factors largely influences the development of immune responses to allergens. Genetic factors and gene-environment interactions have established roles in the FA pathophysiology. To improve diagnosis and identification of FA therapeutic targets, high-throughput omics approaches have emerged and been applied over the past decades to screen for potential FA biomarkers, such as genes, transcripts, proteins, and metabolites. In this article, we provide an overview of the current status of FA omics studies, namely genomic, transcriptomic, epigenomic, proteomic, exposomic, and metabolomic. The current development of multi-omics integration of FA studies is also briefly discussed. As individual omics technologies only provide limited information on the multi-system biological processes of FA, integration of population-based multi-omics data and clinical data may lead to robust biomarker discovery that could translate into advances in disease management and clinical care and ultimately lead to precision medicine approaches.

Changes in risk factors for food sensitization in early life: Analysis over a period of 10 years

Background

Although epidemiological trends of childhood food sensitization (FS) in IgE-mediated food allergy were reported in China, few studies have examined at changes in its risk factors.

Objective

To investigate the change in early-life risk factors associated with childhood food sensitization during 2009–2019 in China.

Methods

Data from two cross-sectional surveys conducted in 2009 and 2019 (401 and 513 children, respectively) were analyzed. The results of skin prick tests and information on food sensitization-related risk factors in children were summarized, including family history of atopic disease (FHA), demographic characteristics, method of delivery, feeding patterns, sibship size, pet ownership, and vitamin D supplementation. Binary logistic regression was used to calculate the odds ratio and the regression coefficient β-value of risk factors in the 2009 and 2019 surveys separately. Then, coefficient β-value differences between the two surveys were analyzed by the bdiff command in STATA to describe the change in risk factors over 10 years.

Results

The 2009 survey revealed that FHA, age, only child, and feeding patterns were associated with food sensitization. The 2019 survey showed that food sensitization was affected by age, sex, and feeding patterns. However, from 2009 to 2019, the probability of food sensitization in the only-child group significantly increased by 226.0% (β-value difference = 0.81, P = 0.024) and decreased by 65.0% in female children (β-value difference = −1.06, P = 0.008). The effect of age on food sensitization decreased by 50.0% (β-value difference = −0.69, P &lt; 0.001) over 10 years.

Conclusion

The effect of FHA and common lifestyle factors on food sensitization did not significantly change during 2009−2019. However, the influence of demographic characteristics on food sensitization has changed since 2009; that is, older age, male gender, and only child are more likely to develop food sensitization, which needs to be considered in future epidemiological surveys.

Clinical Trial Registration

http://www.chictr.org.cn/, identifier ChiCTR1900024338.

Advances and potential of omics studies for understanding the development of food allergy

The prevalence of food allergy continues to rise globally, carrying with it substantial safety, economic, and emotional burdens. Although preventative strategies do exist, the heterogeneity of allergy trajectories and clinical phenotypes has made it difficult to identify patients who would benefit from these strategies. Therefore, further studies investigating the molecular mechanisms that differentiate these trajectories are needed. Large-scale omics studies have identified key insights into the molecular mechanisms for many different diseases, however the application of these technologies to uncover the drivers of food allergy development is in its infancy. Here we review the use of omics approaches in food allergy and highlight key gaps in knowledge for applying these technologies for the characterization of food allergy development.

Allergic sensitization to foods in India and other Low-Middle-income countries

Food allergy is an important cause of morbidity, significantly affecting the quality of life of the sufferer. Most food allergy research has been undertaken in high-income countries. Here, we summarize literature regarding food allergy in India and other low-middle-income countries (LMIC). We provide summaries of self-reported adverse food reactions and food sensitization in these regions by reviewing published community-based studies of prevalence, burden, and risk factors. We identified 2 community-based studies of food allergy prevalence in Karnataka, India, which estimate that food allergy affects just 0.14% of children and 1.2% of adults. The overall prevalence of allergic sensitization to 'any' food was 26.5% in adults and 19.1% in children by serum-specific IgE; but only 4.48% in children by skin prick test. We identified a further 28 studies in other LMICs, mainly from China but also Turkey, South Africa, Ghana, Mexico, Brazil, Thailand, Philippines, and Korea. The overall prevalence of allergic sensitization to 'any' food ranged from 0.11% to 16.8% in children using serum-specific IgE and 0.14% to 9.6% in children by skin prick test. The questionnaires and skin prick testing materials used and number of allergens tested varied significantly between studies. Other than Karnataka, there is no information on prevalence of food sensitization and probable food allergy in the community in India. Similar lack of information is noted among the majority of the 136 LMICs. Where community-based studies have been undertaken, there is wide variation in the prevalence and patterns of food sensitization across different LMICs, at least partly due to variations in study methodology. International collaboration is required in order to formally assess food allergy prevalence and burden across representative samples from multiple LMICs.

Environmental Exposures may Hold the Key; Impact of Air Pollution, Greenness, and Rural/Farm Lifestyle on Allergic Outcomes

PURPOSE OF REVIEW

There has been an increased prevalence of allergy. Due to this relatively rapid rise, changes in environmental exposures are likely the main contributor. In this review, we highlight literature from the last 3 years pertaining to the role of air pollution, greenness, and the rural/farm lifestyle and their association with the development of allergic sensitization, atopic dermatitis, food allergy, and allergic rhinitis in infancy and childhood. Because asthma has a more complex pathophysiology, it was excluded from this review.

RECENT FINDINGS

Recent studies support a role for air pollution, greenness, and rural/farming lifestyle influencing atopic outcomes that continue to be defined. While many studies have examined singular environmental exposures, the interconnectedness of these exposures and others points to a need for future work to consider an individual's whole exposure. Environmental exposures' influence on atopic disease development remains an ongoing and important area of study.

Incorporating genetics in identifying peanut allergy risk and tailoring allergen immunotherapy: A perspective on the genetic findings from the LEAP trial

Examining the genetics of peanut allergy (PA) in the context of clinical trial interventions and outcomes provides an opportunity to not only understand gene-environment interactions for PA risk but to also understand the benefit of allergen immunotherapy. A consistent theme in the genetics of food allergy is that in keeping with the dual allergen exposure hypothesis, barrier- and immune-related genes are most commonly implicated in food allergy and tolerance. With a focus on PA, we review how genetic risk factors across 3 genes (FLG, MALT1, and HLA-DQA1) have helped delineate distinct allergic characteristics and outcomes in the context of environmental interventions in the Learning Early about Peanut Allergy (LEAP) study and other clinical trials. We specifically consider and present a framework for genetic risk prediction for the development of PA and discuss how genetics, age, and oral consumption intertwine to predict PA outcome. Although there is some promise in this proposed framework, a better understanding of the mechanistic pathways by which PA develops and persists is needed to develop targeted therapeutics for established disease. Only by understanding the mechanisms by which PA develops, persists, and resolves can we identify adjuvants to oral immunotherapy to make older children and adults immunologically similar to their younger, more malleable counterparts and thus more likely to achieve long-term tolerance.

Allergy: Mechanistic insights into new methods of prevention and therapy

In the past few decades, the prevalence of allergic diseases has increased worldwide. Here, we review the etiology and pathophysiology of allergic diseases, including the role of the epithelial barrier, the immune system, climate change, and pollutants. Our current understanding of the roles of early life and infancy; diverse diet; skin, respiratory, and gut barriers; and microbiome in building immune tolerance to common environmental allergens has led to changes in prevention guidelines. Recent developments on the mechanisms involved in allergic diseases have been translated to effective treatments, particularly in the past 5 years, with additional treatments now in advanced clinical trials.

Recent progress in the genetic and epigenetic underpinnings of atopy

In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.

IL-4 receptor alpha signaling alters oral food challenge and immunotherapy outcomes in mice

BACKGROUND

Food allergy diagnosis and management causes a number of social and emotional challenges for individuals with food allergies and their caregivers. This has led to increased interest in developing approaches to accurately predict food allergy diagnosis, severity of food allergic reactions, and treatment outcomes. However, the utility of these approaches is somewhat conflicting.

OBJECTIVE

We sought to develop and utilize a murine model that mimics the disease course of food allergy diagnosis and treatment in humans and to identify biomarkers that predict reactivity during food challenge (FC) and responsiveness during oral immunotherapy (OIT) and how these outcomes are modified by genetics.

METHODS

Skin-sensitized intestinal IL-9 transgenic (IL9Tg) and IL9Tg mice backcrossed onto the IL-4RαY709F background received a single intragastric exposure of egg antigen (ovalbumin), underwent oral FC and OIT; food allergy severity, mast cell activation, and ovalbumin-specific IgE levels were examined to determine the predictability of these outcomes in determining reactivity and treatment outcomes.

RESULTS

Subcutaneous sensitization and a single intragastric allergen challenge of egg antigen to BALB/c IL9Tg mice and Il4raY709F IL9Tg induced a food allergic reaction. Enhanced IL-4Rα signaling altered the symptoms induced by the first oral exposure, decreased the cumulative antigen dose, increased the severity of reaction during oral FC, and altered the frequency of adverse events and OIT outcomes. Biomarkers after first oral exposure indicated that only the severity of the initial reaction significantly correlated with cumulative dose of oral FC.

CONCLUSION

Collectively, these data indicate that single nucleotide polymorphisms in IL-4Rα can alter clinical symptoms of food allergic reactions, severity, and reactive dose during FC and OIT, and that severity of first reaction can predict the likelihood of reaction during FC in mice with IL-4Rα gain of function.

Microbiome Therapeutics for Food Allergy

The prevalence of food allergies continues to rise, and with limited existing therapeutic options there is a growing need for new and innovative treatments. Food allergies are, in a large part, related to environmental influences on immune tolerance in early life, and represent a significant therapeutic challenge. An expanding body of evidence on molecular mechanisms in murine models and microbiome associations in humans have highlighted the critical role of gut dysbiosis in the pathogenesis of food allergies. As such, the gut microbiome is a rational target for novel strategies aimed at preventing and treating food allergies, and new methods of modifying the gastrointestinal microbiome to combat immune dysregulation represent promising avenues for translation to future clinical practice. In this review, we discuss the intersection between the gut microbiome and the development of food allergies, with particular focus on microbiome therapeutic strategies. These emerging microbiome approaches to food allergies are subject to continued investigation and include dietary interventions, pre- and probiotics, microbiota metabolism-based interventions, and targeted live biotherapeutics. This exciting frontier may reveal disease-modifying food allergy treatments, and deserves careful study through ongoing clinical trials.

HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success

Rationale

Previous studies identified an interaction between HLA and oral peanut exposure. HLA-DQA1*01:02 had a protective role with the induction of Ara h 2 epitope-specific IgG4 associated with peanut consumption during the LEAP clinical trial for prevention of peanut allergy, while it was a risk allele for peanut allergy in the peanut avoidance group. We have now evaluated this gene-environment interaction in two subsequent peanut oral immunotherapy (OIT) trials - IMPACT and POISED - to better understand the potential for the HLA-DQA1*01:02 allele as an indicator of higher likelihood of desensitization, sustained unresponsiveness, and peanut allergy remission.

Methods

We determined HLA-DQA1*01:02 carrier status using genome sequencing from POISED (N=118, age: 7-55yr) and IMPACT (N=126, age: 12-<48mo). We tested for association with remission, sustained unresponsiveness (SU), and desensitization in the OIT groups, as well as peanut component specific IgG4 (psIgG4) using generalized linear models and adjusting for relevant covariates and ancestry.

Results

While not quite statistically significant, a higher proportion of HLA-DQA1*01:02 carriers receiving OIT in IMPACT were desensitized (93%) compared to non-carriers (78%); odds ratio (OR)=5.74 (p=0.06). In this sample we also observed that a higher proportion of carriers achieved remission (35%) compared to non-carriers (22%); OR=1.26 (p=0.80). In POISED, carriers more frequently attained continued desensitization (80% versus 61% among non-carriers; OR=1.28, p=0.86) and achieved SU (52% versus 31%; OR=2.32, p=0.19). psIgG4 associations with HLA-DQA1*01:02 in the OIT arm of IMPACT which included younger study subjects recapitulated patterns noted in LEAP, but no associations of note were observed in the older POISED study subjects.

Conclusions

Findings across three clinical trials show a pattern of a gene environment interaction between HLA and oral peanut exposure. Age, and prior sensitization contribute additional determinants of outcomes, consistent with a mechanism of restricted antigen recognition fundamental to driving protective immune responses to OIT.

The role of the CBM complex in allergic inflammation and disease

The caspase activation and recruitment domain-coiled-coil (CARD-CC) family of proteins-CARD9, CARD10, CARD11, and CARD14-is collectively expressed across nearly all tissues of the body and is a crucial mediator of immunologic signaling as part of the CARD-B-cell lymphoma/leukemia 10-mucosa-associated lymphoid tissue lymphoma translocation protein 1 (CBM) complex. Dysfunction or dysregulation of CBM proteins has been linked to numerous clinical manifestations known as "CBM-opathies." The CBM-opathy spectrum encompasses diseases ranging from mucocutaneous fungal infections and psoriasis to combined immunodeficiency and lymphoproliferative diseases; however, there is accumulating evidence that the CARD-CC family members also contribute to the pathogenesis and progression of allergic inflammation and allergic diseases. Here, we review the 4 CARD-CC paralogs, as well as B-cell lymphoma/leukemia 10 and mucosa-associated lymphoid tissue lymphoma translocation protein 1, and their individual and collective roles in the pathogenesis and progression of allergic inflammation and 4 major allergic diseases (allergic asthma, atopic dermatitis, food allergy, and allergic rhinitis).

A Methodology of Epidemiologic Study in the General Population Focusing on Food Allergy - China, 2020

Introduction

Adverse reactions to food (ARF) are a major worldwide public health and food safety problem. Among the various causes of ARF, food allergies (FA) are particularly serious as the immune response that is triggered can be fatal even at very low doses. However, the prevalence of ARF and FA in the general population in China is presently unclear. This study aims to determine the epidemiological characteristics and risk factors for ARF and FA, which can be a basis for estimating thresholds for major food allergens.

Methods

This is a multicenter, cross-sectional, epidemiologic survey with a case-control study nested among a selected population in China. Random individuals were recruited using stratified cluster random sampling; ARF and FA were comprehensively assessed using modified EuroPrevall FA Project questionnaires as well as structured interviews, sensitization testing, and double-blind placebo-controlled food challenges (DBPCFC).

Results

This method of epidemiologic study on ARF and FA was a pilot application in Jiangxi Province from January 2020; among the total 21,273 children and adults that completed the questionnaire, 5.8% reported ARF and 4.3% reported FA. ARF were determined to be associated with age, gender, and region. Animal-derived foods were the dominant offending foods, especially shrimp, and skin symptoms were the most commonly reported ARF.

Discussion

This is the first multi-center, large-scale, epidemiologic study on ARF and FA using standardized methods, including DBPCFC, in the Chinese general population. This study presents an important approach to assessing ARF and FA, provides significant insights about the prevalence of ARF and FA, and facilitates support for updating the list of allergenic food labels: which will be essential for improving ARF prevention and management in China.

Review article: Diagnosis of coeliac disease: a perspective on current and future approaches

Diagnostics will play a central role in addressing the ongoing dramatic rise in global prevalence of coeliac disease, and in deploying new non-dietary therapeutics. Clearer understanding of the immunopathogenesis of coeliac disease and the utility of serology has led to partial acceptance of non-biopsy diagnosis in selected cases. Non-biopsy diagnosis may expand further because research methods for measuring gluten-specific CD4+ T cells and the acute recall response to gluten ingestion in patients is now relatively straightforward. This perspective on diagnosis in the context of the immunopathogenesis of coeliac disease sets out to highlight current consensus, limitations of current practices, gluten food challenge for diagnosis and the potential for diagnostics that measure the underlying cause for coeliac disease, gluten-specific immunity.

Enhanced expression of endogenous retroviruses and of TRIM28 and SETDB1 in children with food allergy

Background

Human endogenous retroviruses (HERVs) represent 8% of our genome. They originate from ancestral infections and although no longer contagious they can regulate transcription of adjacent cellular genes, produce viral RNAs sensed as non‐self by pattern recognition receptors, and encode viral proteins, such as Syncytin (SYN) 1 and 2, that exhibit potent immunomodulatory properties. Based on this, HERVs have been studied and proposed as relevant cofactors in several chronic inflammatory and immune‐mediated diseases. HERV transcription is regulated by host TRIM28 and SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), which in turn exert crucial regulatory functions on the host immune system. No studies explored the expression of HERVs, TRIM28, and SETDB1 in allergic patients.

Methods

We assessed, through a polymerase chain reaction real time Taqman amplification assay, the transcription levels of pol genes of HERV‐H, HERV‐K, HERV‐W, and of env genes of SYN1 and SYN2, as well as of TRIM28 and SETDB1 in whole blood from 32 children with IgE‐mediated food allergy, 19 with food protein‐induced enterocolitis syndrome (FPIES), and in healthy control children.

Results

The expression levels of pol genes of HERV‐H, ‐K, and ‐W were significantly enhanced in patients with IgE‐mediated FA or FPIES as compared to control subjects, while the mRNA concentrations of SYN1 and SYN2 were comparable in each group of children. Both TRIM28 and SETDB1 mRNA levels were significantly higher in allergic patients.

Conclusions

Given the influence of HERVs and of TRIM28 and SETDB1 on innate and adaptive immune responses, their transcriptional activation in children with food allergies suggest that they might play important roles in the development of these diseases.

Food allergy and hypersensitivity reactions in children and adults-A review

Adverse reactions after food intake are commonly reported and a cause of concern and anxiety that can lead to a very strict diet. The severity of the reaction can vary depending on the type of food and mechanism, and it is not always easy to disentangle different hypersensitivity diagnoses, which sometimes can exist simultaneously. After a carefully taken medical history, hypersensitivity to food can often be ruled out or suspected. The most common type of allergic reaction is immunoglobulin E (IgE)-mediated food allergy (prevalence 5-10%). Symptoms vary from mild itching, stomach pain, and rash to severe anaphylaxis. The definition of IgE-mediated food allergy is allergic symptoms combined with specific IgE-antibodies, and therefore only IgE-antibodies to suspected allergens should be analyzed. Nowadays, methods of molecular allergology can help with the diagnostic process. The most common allergens are milk and egg in infants, peanut and tree nuts in children, and fish and shellfish in adults. In young children, milk/egg allergy has a good chance to remit, making it important to follow up and reintroduce the food when possible. Other diseases triggered by food are non-IgE-mediated food allergy, for example, eosinophilic esophagitis, celiac disease, food protein-induced enterocolitis syndrome, and hypersensitivity to milk and biogenic amines. Some of the food hypersensitivities dominate in childhood, others are more common in adults. Interesting studies are ongoing regarding the possibilities of treating food hypersensitivity, such as through oral immunotherapy. The purpose of this review was to provide an overview of the most common types of food hypersensitivity reactions.

Structural insights into the amino acid usage variations in the profilin gene family

Profilin protein is present ubiquitously in all forms of life and is allied with allergic responses among atopic individuals. In addition to this, profilins from various food sources are also associated with IgE cross-reactivity and are thus classified as pan-allergens. The present study unravels the physicochemical basis of differential amino acid usage patterns observed in the profilin gene family. Correspondence analysis based on amino acid usage of allergen and non-allergen profilins revealed discrete clusters among them, signifying differential patterns of amino acid usage. The amino acids, namely methionine, proline, histidine, glutamine, glutamic acid, tryptophan and glycine were found to be more frequently utilised by the allergen profilins compared to the non-allergens. Correlation analysis revealed that physicochemical features like protein disorder, trypsin digestion and solubility differed significantly among the allergen and non-allergen profilins, thus supporting the observations from correspondence analysis. In addition, comprehensive sequence analysis revealed that the allergen profilins possess conserved motifs which may correlate with their distinct physicochemical features. An in-depth structural analysis revealed that the over-represented amino acids in allergen profilins have a propensity of being exposed on the surface, which may be attributed to their distinct allergenic characteristics. The distinguished physicochemical features observed among allergens and non-allergens can be employed as descriptors to develop machine learning-based allergenicity prediction models.

The year in food allergy

Research into food allergy continues to rapidly evolve, accompanying and driving real changes in the clinical approach to these diseases. The past year has seen the rollout of the first treatment approved for active management of food allergy, more data on alternative methods of treatment, the continued evolution of strategies for prevention of food allergy, a renewed interest in phenotyping food allergy subtypes, and, importantly, key new insights into the pathophysiology of food allergy. We expect that in the coming years, the therapies that are in preclinical or early clinical evaluation now will make their way to the clinic, finally allowing the possibility of safe and effective treatments for food allergy.

HLA alleles and sustained peanut consumption promote IgG4 responses in subjects protected from peanut allergy

We investigated the interplay between genetics and oral peanut protein exposure in the determination of the immunological response to peanut using the targeted intervention in the LEAP clinical trial. We identified an association between peanut-specific IgG4 and HLA-DQA1*01:02 that was only observed in the presence of sustained oral peanut protein exposure. The association between IgG4 and HLA-DQA1*01:02 was driven by IgG4 specific for the Ara h 2 component. Once peanut consumption ceased, the association between IgG4-specific Ara h 2 and HLA-DQA1*01:02 was attenuated. The association was validated by observing expanded IgG4-specific epitopes in people who carried HLA-DQA1*01:02. Notably, we confirmed the previously reported associations with HLA-DQA1*01:02 and peanut allergy risk in the absence of oral peanut protein exposure. Interaction between HLA and presence or absence of exposure to peanut in an allergen- and epitope-specific manner implicates a mechanism of antigen recognition that is fundamental to driving immune responses related to allergy risk or protection.

Early peanut introduction wins over the HLA-DQA1*01:02 allele in the interplay between environment and genetics

The rising incidence of food allergy in children underscores the importance of environmental exposures; however, genetic factors play a major role. How the environment and genetics interact to cause food allergy remains unclear. The landmark Learning Early About Peanut Allergy (LEAP) clinical trial established that early peanut introduction protects high-risk infants, consistent with the tolerizing effects of gut exposure. In this issue of the JCI, Kanchan et al. leveraged the LEAP trial data to examine molecular genetic mechanisms of early sensitization. A previously identified HLA risk allele for peanut allergy (DQA1*01:02) was associated with peanut-specific IgG4 levels in consumers. Notably, IgG4 antibodies likely provide protection by reducing the binding of allergen to IgE. The association of the same allele with peanut allergy in avoiders while potentially conferring protection in consumers reinforces the need to integrate genetic information toward a personalized therapeutic strategy for the best outcome in addressing food allergies.

Polygenic prediction of atopic dermatitis improves with atopic training and filaggrin factors

BACKGROUND

While numerous genetic loci associated with atopic dermatitis (AD) have been discovered, to date, work leveraging the combined burden of AD risk variants across the genome to predict disease risk has been limited.

OBJECTIVES

This study aims to determine whether polygenic risk scores (PRSs) relying on genetic determinants for AD provide useful predictions for disease occurrence and severity. It also explicitly tests the value of including genome-wide association studies of related allergic phenotypes and known FLG loss-of-function (LOF) variants.

METHODS

AD PRSs were constructed for 1619 European American individuals from the Atopic Dermatitis Research Network using an AD training dataset and an atopic training dataset including AD, childhood onset asthma, and general allergy. Additionally, whole genome sequencing data were used to explore genetic scoring specific to FLG LOF mutations.

RESULTS

Genetic scores derived from the AD-only genome-wide association studies were predictive of AD cases (PRSAD: odds ratio [OR], 1.70; 95% CI, 1.49-1.93). Accuracy was first improved when PRSs were built off the larger atopy genome-wide association studies (PRSAD+: OR, 2.16; 95% CI, 1.89-2.47) and further improved when including FLG LOF mutations (PRSAD++: OR, 3.23; 95% CI, 2.57-4.07). Importantly, while all 3 PRSs correlated with AD severity, the best prediction was from PRSAD++, which distinguished individuals with severe AD from control subjects with OR of 3.86 (95% CI, 2.77-5.36).

CONCLUSIONS

This study demonstrates how PRSs for AD that include genetic determinants across atopic phenotypes and FLG LOF variants may be a promising tool for identifying individuals at high risk for developing disease and specifically severe disease.

Genome-wide association study of asthma, total IgE, and lung function in a cohort of Peruvian children

BACKGROUND

Genetic ancestry plays a role in asthma health disparities.

OBJECTIVE

Our aim was to evaluate the impact of ancestry on and identify genetic variants associated with asthma, total serum IgE level, and lung function.

METHODS

A total of 436 Peruvian children (aged 9-19 years) with asthma and 291 without asthma were genotyped by using the Illumina Multi-Ethnic Global Array. Genome-wide proportions of indigenous ancestry populations from continental America (NAT) and European ancestry from the Iberian populations in Spain (IBS) were estimated by using ADMIXTURE. We assessed the relationship between ancestry and the phenotypes and performed a genome-wide association study.

RESULTS

The mean ancestry proportions were 84.7% NAT (case patients, 84.2%; controls, 85.4%) and 15.3% IBS (15.8%; 14.6%). With adjustment for asthma, NAT was associated with higher total serum IgE levels (P < .001) and IBS was associated with lower total serum IgE levels (P < .001). NAT was associated with higher FEV1 percent predicted values (P < .001), whereas IBS was associated with lower FEV1 values in the controls but not in the case patients. The HLA-DR/DQ region on chromosome 6 (Chr6) was strongly associated with total serum IgE (rs3135348; P = 3.438 × 10-10) and was independent of an association with the haplotype HLA-DQA1∼HLA-DQB1:04.01∼04.02 (P = 1.55 × 10-05). For lung function, we identified a locus (rs4410198; P = 5.536 × 10-11) mapping to Chr19, near a cluster of zinc finger interacting genes that colocalizes to the long noncoding RNA CTD-2537I9.5. This novel locus was replicated in an independent sample of pediatric case patients with asthma with similar admixture from Brazil (P = .005).

CONCLUSION

This study confirms the role of HLA in atopy, and identifies a novel locus mapping to a long noncoding RNA for lung function that may be specific to children with NAT.

Advancing Food Allergy Through Omics Sciences

Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.