Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis

Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.

Peanut oral immunotherapy in a pediatric allergy clinic: Patient factors associated with clinical outcomes

BACKGROUND

Additional information is needed to inform optimal patient selection, expected outcomes, and treatment end points for clinical peanut oral immunotherapy (OIT).

OBJECTIVE

To provide insight into the optimal patient selection, expected outcomes, and treatment end points for clinical peanut oral immunotherapy by analyzing a real-world peanut OIT cohort.

METHODS

Records were reviewed for 174 children undergoing peanut OIT at a pediatric allergy clinic. Patient age, peanut skin prick test results, and peanut-specific immunoglobulin E (sIgE) results, with inclusion of additional foods in OIT, were analyzed for correlations with OIT outcomes.

RESULTS

To date, 144 patients have achieved maintenance dosing, 50 of whom transitioned to ad lib twice-weekly peanut ingestion. A total of 30 discontinued OIT. In addition, 47 patients who underwent multifood OIT had no significant difference in reactions (FDR-adjusted P = .48) or time-to-reach maintenance (FDR-adjusted P = .48) compared with those on peanut OIT alone. Age at initiation inversely correlated with achievement of maintenance: 92% of patients 0.5 to less than 5 years, 81% of those 5 to less than 11 years, and 70% of those 11 to less than 18 years reached and continued maintenance (P = .01). Baseline peanut-sIgE level positively correlated with number of reactions during updosing (P < .001) and maintenance (P = .005), though it was not significantly different in patients achieving successful maintenance vs those who discontinued OIT (P = .09). Furthermore, 66% of patients experienced greater than or equal to 1 adverse reaction during OIT. Of those on ad lib peanut ingestion, 2 reported mild reactions after lapses in peanut consumption.

CONCLUSION

Clinical peanut OIT has similar outcomes to research protocols. OIT can be successful in older children and those with high peanut-sIgE levels, though these factors affect outcomes. Clinical and laboratory criteria can guide successful transition to intermittent ad lib peanut consumption.

The Phenotype of the Food-Allergic Patient

Food allergy's increasing prevalence across the globe has initiated research into risk factors associated with the disease and coexistence with other allergic diseases. Longitudinal birth cohorts have identified food allergy phenotypes of patients based on genetic background, racial diversity, and environmental factors. Identifying food sensitization patterns and coexistence of other allergic diseases allows physicians to provide appropriate care for food allergy and personalized anticipatory guidance for the appearance of other allergic diseases. The authors seek to detail key findings of 4 longitudinal allergy birth cohorts that investigate food allergy and other allergic diseases to further characterize food allergy phenotypes.

Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes

BACKGROUND

Eosinophilic esophagitis (EoE) is an emerging, chronic, rare allergic disease associated with marked eosinophil accumulation in the esophagus. Previous genome-wide association studies have provided strong evidence for 3 genome-wide susceptibility loci.

OBJECTIVE

We sought to replicate known and suggestive EoE genetic risk loci and conduct a meta-analysis of previously reported data sets.

METHODS

An EoE-Custom single-nucleotide polymophism (SNP) Chip containing 956 candidate EoE risk single-nucleotide polymorphisms was used to genotype 627 cases and 365 controls. Statistical power was enhanced by adding 1959 external controls and performing meta-analyses with 2 independent EoE genome-wide association studies.

RESULTS

Meta-analysis identified replicated association and genome-wide significance at 6 loci: 2p23 (2 independent genetic effects) and 5q22, 10p14, 11q13, and 16p13. Seven additional loci were identified at suggestive significance (P < 10-6): 1q31, 5q23, 6q15, 6q21, 8p21, 17q12, and 22q13. From these risk loci, 13 protein-coding EoE candidate risk genes were expressed in a genotype-dependent manner. EoE risk genes were expressed in disease-relevant cell types, including esophageal epithelia, fibroblasts, and immune cells, with some expressed as a function of disease activity. The genetic risk burden of EoE-associated genetic variants was markedly larger in cases relative to controls (P < 10-38); individuals with the highest decile of genetic burden had greater than 12-fold risk of EoE compared with those within the lowest decile.

CONCLUSIONS

This study extends the genetic underpinnings of EoE, highlighting 13 genes whose genotype-dependent expression expands our etiologic understanding of EoE and provides a framework for a polygenic risk score to be validated in future studies.

Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk

Introduction

The etiology of steroid-sensitive nephrotic syndrome (SSNS) is not well understood. Genetic studies have established common single nucleotide polymorphisms (SNPs) that are associated with increased SSNS disease risk. We review previous genetic association studies of SSNS and nominate particular transcriptional regulators and immune cells as potential key players in the etiology of this disease.

Methods

A list of SNPs associated with SSNS was compiled from published genome wide association and candidate gene studies. The Regulatory Element Locus Intersection (RELI) tool was used to calculate the enrichment of the overlap between disease risk SNPs and the genomic coordinates of data from a collection of >10,000 chromatin immunoprecipitation sequencing experiments.

Results

After linkage disequilibrium expansion of the previously reported tag associated SNPs, we identified 192 genetic variants at 8 independent risk loci. Using the Regulatory Element Locus Intersection algorithm, we identified transcriptional regulators with enriched binding at SSNS risk loci (10^-05 < P_corrected < 10^-124), including ZNF530, CIITA, CD74, RFX5, and ZNF425. Many of these regulators have well-described roles in the immune response. RNA polymerase II binding in B cells also demonstrated enriched binding at SSNS risk loci (10^-37<P_corrected<10^-5).

Conclusion

SSNS is a complex disease, and immune dysregulation has been previously implicated as a potential underlying cause. This assessment of established SSNS risk loci and analysis of possible function implicates transcriptional dysregulation, and specifically particular transcriptional regulators with known roles in the immune response, as important in the genetic etiology of SSNS.

Oral immunotherapy for multiple foods in a pediatric allergy clinic setting

BACKGROUND

The increasing incidence of pediatric food allergy results in significant health care burden and family stress. Oral immunotherapy (OIT) can induce tolerance to peanut, milk, and egg. OIT for other foods, particularly multiple foods simultaneously, has not been thoroughly studied.

OBJECTIVE

To summarize our experience with OIT for multiple foods in a pediatric allergy clinic setting.

METHODS

Medical records were reviewed for patients undergoing OIT for multiple foods. Methods and outcomes of OIT were summarized. Outcomes were analyzed for correlation with baseline food allergen skin prick tests (SPTs) and specific IgE (sIgE) test results.

RESULTS

Forty-five patients aged 1.5 to 18 years undertook OIT for up to 12 foods, including peanut, tree nuts, seeds, legumes, and egg. At the time of review, 35 patients were receiving daily maintenance dosing, 4 had completed OIT and were continuing to eat their foods 3 times weekly, and 6 had stopped OIT because of anxiety, inconvenience, or allergy symptoms. A total of 49% of patients had reactions during the up-dosing process, mostly oral itching (33%), perioral hives (40%), and abdominal pain (35%). There was no correlation of baseline skin prick test (SPT) and sIgE test results with reaction threshold for baseline food challenge, lowest dose causing reactions during up-dosing, or time to reach maintenance. Higher baseline sIgE level but not baseline SPT result was associated with an increased number of allergic reactions during OIT. Baseline SPT correlated with stopping OIT.

CONCLUSION

A similar approach to that used for peanut OIT can be taken for nonpeanut foods and for multiple foods simultaneously. High baseline allergy test results are not a contraindication to OIT.

Oral food challenge failures among foods restricted because of atopic dermatitis

BACKGROUND

Recent studies have suggested that removing foods from the diet to manage atopic dermatitis (AD), based on positive allergy test results, may lead to immediate allergic reactions on reintroduction of that food.

OBJECTIVE

To examine the frequency of oral food challenge (OFC) failures among foods removed from the diet as suspected AD triggers, focusing on the 5 major food allergens in the United States.

METHODS

OFCs to egg, milk, peanut, soy, and wheat, performed from 2008 to 2014, at a children's hospital's allergy clinics, were reviewed. OFCs were offered based on history and laboratory values. Reasons for food avoidance were classified as food allergy (IgE-mediated reaction occurring within 2 hours); sensitization only (lack of introduction because of positive test results); and removal because of test results during AD evaluation.

RESULTS

There were 442 OFCs performed, with 89 failures (20.1%). Reasons for OFCs included a history of food allergy (320 of 442 [72.4%]), food sensitization without any introduction (77 of 442 [17.4%]), and AD (45 of 442 [10.2%]). OFC failures among those who had food allergy (70 of 320 [21.9%]), sensitization only (13 of 77 [16.9%]), and suspected AD trigger (6 of 45 [13.3%]) did not significantly differ (P = .63). Wheat was more likely to be avoided than the other 4 foods for AD concerns (P < .001).

CONCLUSION

The frequency of OFC failure among those who removed foods suspected as AD triggers was 13.3%, indicating a loss of tolerance. Restriction of foods to manage AD must be done with caution and close monitoring.