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1.  Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease 
Nature genetics  2014;46(8):895-900.
Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder associated with allergic hypersensitivity to food. We interrogated >1.5 million genetic variants in European EoE cases and subsequently in a multi-site cohort with local and out-of-study control subjects. In addition to replication of the 5q22 locus (meta-analysis p = 1.9×10−16), we identified association at 2p23 (encoding CAPN14, p = 2.5×10−10). CAPN14 was specifically expressed in the esophagus, dynamically upregulated as a function of disease activity and genetic haplotype and after exposure of epithelial cells to IL-13, and located in an epigenetic hotspot modified by IL-13. There was enriched esophageal expression for the genes neighboring the top 208 EoE sequence variants. Multiple allergic sensitization loci were associated with EoE susceptibility (4.8×10−2 < p < 5.1×10−11). We propose a model that elucidates the tissue specific nature of EoE that involves the interplay of allergic sensitization with an EoE-specific, IL-13–inducible esophageal response involving CAPN14.
doi:10.1038/ng.3033
PMCID: PMC4121957  PMID: 25017104
2.  Molecular Diagnosis of Eosinophilic Esophagitis by Gene Expression Profiling 
Gastroenterology  2013;145(6):1289-1299.
Background & Aims
Gene expression profiling provides an opportunity for definitive diagnosis but has not yet been well applied to inflammatory diseases. Herein, we describe an approach for diagnosis of an emerging form of esophagitis, eosinophilic esophagitis (EoE), currently diagnosed by histology and clinical symptoms.
Methods
We developed an EoE diagnostic panel (EDP), comprising a 96-gene quantitative PCR array and an associated dual-algorithm that uses cluster analysis and dimensionality reduction, using a cohort of randomly selected esophageal biopsy samples from pediatric patients with EoE (n = 15) or without EoE (non-EoE controls, n = 14), subsequently vetted using a separate cohort of 194 pediatric and adult patient samples derived from both fresh or formalin-fixed paraffin embedded (FFPE) tissue: active EoE (n = 91), control (non-EoE and EoE remission, n = 57), histologically ambiguous (n = 34), and reflux (n = 12) samples.
Results
The EDP identified adult and pediatric patients with EoE with ~96% sensitivity and ~98% specificity, and distinguished patients with EoE in remission from controls, as well as identified patients exposed to swallowed glucorticoids. The EDP could be used with FFPE tissue RNA and distinguished patients with EoE from those with reflux esophagitis, identified by pH-impedance testing. Preliminary evidence showed that the EDP could identify patients likely to have disease relapse following treatment.
Conclusions
We developed a molecular diagnostic test (referred as the EDP) that identifies patients with esophagitis in a fast, objective, and mechanistic manner, offering an opportunity to improve diagnosis and treatment, and a platform approach for other inflammatory diseases.
doi:10.1053/j.gastro.2013.08.046
PMCID: PMC4070519  PMID: 23978633
EoE; GERD; NERD; diagnostic panel; signature; eosinophil; EoE transcriptome; fluidic card; genomics; transcriptome; esophagus
3.  IL-33 markedly activates murine eosinophils by an NFκB-dependent mechanism differentially dependent upon an IL-4-driven autoinflammatory loop 
Journal of immunology (Baltimore, Md. : 1950)  2013;191(8):10.4049/jimmunol.1301465.
Eosinophils are major effector cells in type 2 inflammatory responses and become activated in response to IL-4 and IL-33, yet the molecular mechanisms and cooperative interaction between these cytokines remain unclear. Our objective was to investigate the molecular mechanism and cooperation of IL-4 and IL-33 in eosinophil activation. Eosinophils derived from bone marrow or isolated from Il5-transgenic mice were activated in the presence of IL-4 or IL-33 for 1 or 4h and the transcriptome was analysed by RNA-sequencing. The candidate genes were validated by qPCR and ELISA. We first demonstrated that murine cultured eosinophils respond to IL-4 and IL-33 by phosphorylation of STAT-6 and NFκB, respectively. RNA sequence analysis of murine cultured eosinophils indicated that IL-33 induced 519 genes; whereas, IL-4 induced only 28 genes, including 19 IL-33-regulated genes. Interestingly, IL-33 induced eosinophil activation via two distinct mechanisms, IL-4 independent and IL-4 secretion/auto-stimulation dependent. Anti-IL-4 or anti-IL-4Rα antibody-treated cultured and mature eosinophils, as well as Il4- or Stat6-deficient cultured eosinophils, had attenuated protein secretion of a subset of IL-33-induced genes, including Retnla and Ccl17. Additionally, IL-33 induced the rapid release of pre-formed IL-4 protein from eosinophils by an NFκB-dependent mechanism. However, the induction of most IL-33-regulated transcripts (e.g. Il6 and Il13) was IL-4 independent and blocked by NFκB inhibition. In conclusion, we have identified a novel activation pathway in murine eosinophils that is induced by IL-33 and differentially dependent upon an IL-4 auto-amplification loop.
doi:10.4049/jimmunol.1301465
PMCID: PMC3807853  PMID: 24043894
4.  MiR-375 is down-regulated in epithelial cells after IL-13 stimulation and regulates an IL-13 induced epithelial transcriptome 
Mucosal immunology  2012;5(4):388-396.
IL-13-induced epithelial gene and protein expression changes are central to the pathogenesis of multiple allergic diseases. Herein, using human esophageal squamous and bronchial columnar epithelial cells, we identified miRNAs that were differentially regulated after IL-13 stimulation. Among the IL-13-regulated miRNAs, miR-375 showed a conserved pattern of down-regulation. Furthermore, miR-375 was down regulated in the lung of IL-13 lung transgenic mice. We subsequently analyzed miR-375 levels in a human disease characterized by IL-13 overproduction – the allergic disorder eosinophilic esophagitis (EE), and observed down-regulation of miR-375 in EE patient samples compared to control patients. MiR-375 expression levels reflected disease activity, normalized with remission, and inversely correlated to the degree of allergic inflammation. Using a lentiviral strategy and whole-transcriptome analysis in epithelial cells, miR-375 over-expression was sufficient to markedly modify IL-13-associated immunoinflammatory pathways in epithelial cells in vitro, further substantiating interactions between miR-375 and IL-13. Taken together, our results support a key role of miRNAs, particularly miR-375, in regulating and fine-tuning IL-13 mediated responses.
doi:10.1038/mi.2012.16
PMCID: PMC4154234  PMID: 22453679
5.  Natural or engineered mutations in Surfactant Protein-D alter allergic asthmatic responses in mice and man 
Background
Surfactant protein D (SP-D) has been proposed to be protective in allergic airway responses.
Objective
We aimed to determine the effect of SP-D deficiency on murine and human airway allergy.
Methods
Immunological responses of SP-D gene deficient mice (Sftpd−/−) at baseline and following four Aspergillus fumigatus exposures were assessed. In addition, the significance of a single nucleotide polymorphism (Met11Thr) in the human SP-D gene (known to decrease SP-D function) on asthma susceptibility was investigated.
Results
Macrophage BALF levels and lung CD-4+ T-cells were increased in naive Sftpd−/− mice in association with increased lung CCL17 levels. Th2-associated antibody levels (IgG1 and IgE) were significantly lower in 4–6 week old Sftpd−/− mice (p<0.05). Accordingly, naive Sftpd−/− splenocytes released significantly less IL-4 and IL-13 upon anti-CD3/CD28 stimulation (p<0.01). Following intranasal allergen exposures, a modest decrease in BALF eosinophilia was observed in Sftpd−/− mice compared to wild type mice (p<0.01). Translational studies in a pediatric population of Caucasians with asthma revealed that a single nucleotide polymorphism in the SFTPD gene, affecting SP-D levels and pathogen binding, was associated with lower asthma susceptibility (p<0.05).
Conclusion
Sftpd−/− mice have an impaired systemic Th2 response at baseline and modestly reduced pulmonary eosinophilia following allergen exposure. Translational studies revealed that a mutation in the SFTPD gene was associated with lower asthma susceptibility in Caucasians. Taken together, these results support the hypothesis that SP-D-dependent innate immunity influences atopy and asthma.
Clinical implications
SP-D deficiency results in increased pulmonary inflammation and decreased susceptibility to asthma, perhaps related to impaired endotoxin and pathogen clearance.
doi:10.1016/j.jaci.2008.02.011
PMCID: PMC4145593  PMID: 18355911
allergy; lung; surfactant protein D; polymorphism; eosinophil; IL-13; Aspergillus; endotoxin
6.  Targeting IL-4/IL-13 signaling to alleviate oral allergen-induced diarrhea 
Rationale
Intestinal anaphylaxis (manifested by acute diarrhea) is dependent on IgE and mast cells.
Objective
We aimed to define the respective roles of IL-4 and IL-13 and their receptors in disease pathogenesis.
Methods
Wild-type mice and mice deficient in IL-4, IL-13, and IL-13Rα1 (part of the type 2 IL-4R) were sensitized with ovalbumin (OVA)/alum and subsequently given repeated intragastric OVA exposures. IL-4Rα chain was targeted with anti-IL-4Rα mAb prior to or after intragastric OVA exposures.
Results
IL-4−/− (and IL-4/13−/−) mice produced almost no IgE and were highly resistant to OVA-induced diarrhea, whereas allergic diarrhea was only partially impaired in IL-13−/− and IL-13Rα1−/− mice. IL-13Rα1-deficient mice developed decreased IgE despite having normal baseline IL-4 levels. Intestinal mast cell accumulation and activation also depended mainly on IL-4 and to a lesser extent on IL-13. Prophylactic anti-IL-4Rα mAb treatment, which blocks all IL-4 and IL-13 signaling, suppressed development of allergic diarrhea. However, treatment with anti-IL-4Rα mAb for 7 days only partially suppressed IgE and did not prevent intestinal diarrhea.
Conclusion
Endogenously-produced IL-13 supplements the ability of IL-4 to induce allergic diarrhea by promoting oral allergen sensitization rather than the effector phase of intestinal anaphylaxis.
doi:10.1016/j.jaci.2008.10.001
PMCID: PMC4121593  PMID: 18996576
allergy; anaphylaxis; IL-4; IL-13; IL-13Ralpha1; intestine; mast cell
7.  Chemotactic factors associated with eosinophilic gastrointestinal diseases 
The gastrointestinal (GI) tract is in constant “negotiation” with the microbial flora present in the lumen. Resident hematopoietic cells (i.e. lymphocytes, mast cells and eosinophils) are part of this ongoing and silent homeostatic battle. Eosinophilic GI diseases (EGID) are characterized by an increased number of eosinophil infiltrates with no identified cause. In this review, we describe the past and present knowledge regarding the chemotactic factors involved in GI eosinophilia.
doi:10.1016/j.iac.2008.10.002
PMCID: PMC4122321  PMID: 19141349
Eosinophil; gastrointestinal; chemokine; cytokine; pathogenesis
8.  High prevalence of eosinophilic esophagitis in patients with inherited connective tissue disorders 
The Journal of allergy and clinical immunology  2013;132(2):10.1016/j.jaci.2013.02.030.
Background
Eosinophilic esophagitis (EoE) is an emerging chronic inflammatory disease mediated by immune hypersensitization to multiple foods and strongly associated with atopy and esophageal remodeling.
Objective
We provide clinical and molecular evidence indicating a high prevalence of EoE in patients with inherited connective tissue disorders (CTDs).
Methods
We examined the rate of EoE among patients with CTDs and subsequently analyzed esophageal mRNA transcript profiles in patients with EoE with or without CTD features.
Results
We report a cohort of 42 patients with EoE with a CTD-like syndrome, representing 0.8% of patients with CTDs and 1.3% of patients with EoE within our hospital-wide electronic medical record database and our EoE research registry, respectively. An 8-fold risk of EoE in patients with CTDs (relative risk, 8.1; 95% confidence limit, 5.1-12.9; χ21 = 112.0; P < 10−3) was present compared with the general population. Esophageal transcript profiling identified a distinct subset of genes, including COL8A2, in patients with EoE and CTDs.
Conclusion
There is a remarkable association of EoE with CTDs and evidence for a differential expression of genes involved in connective tissue repair in this cohort. Thus, we propose stratification of patients with EoE and CTDs into a subset referred to as EoE-CTD.
doi:10.1016/j.jaci.2013.02.030
PMCID: PMC3807809  PMID: 23608731
Eosinophilic esophagitis; eosinophilic gastrointestinal disease; eosinophil; connective tissue disorders; Ehlers-Danlos syndrome; Marfan syndrome; hypermobility syndrome
9.  Identification, Epidemiology and Chronicity of Pediatric Esophageal Eosinophilia from 1982–1999 
Background
Eosinophilic Esophagitis (EE) is now a commonly encountered disorder that was rarely diagnosed a decade ago.
Objective
We aimed to determine the epidemiologic and histologic features of retrospective pediatric esophageal eosinophilia before the first case of EE at our institution was recognized.
Methods
Esophageal biopsies obtained between 1982–1999 with reflux esophagitis were re-examined and re-organized into 2 groups based on peak esophageal eosinophil number (<15 eos/hpf, ≥ 15 eos/hpf). The epidemiology and histology of the entire cohort and a population based cohort were evaluated.
Results
807 biopsies from 666 patients were re-examined; 198 patients had ≥ 15 eos/hpf. Among a population-based cohort of patients with ≥ 15 eos/hpf, there was a modest increase in incidence (p < 0.001; IRR 1.18; CI 1.09–1.28). After correcting for a 40-fold increase in the number of endoscopies during this time period, the proportion of biopsies with ≥ 15 eos/hpf did not change (0.08 in 1982 vs. 0.08 in 1996 (peak), (p = 0.9; IRR 1.02; CI 0.73 –1.44). Patients who had as few as 5 eos/hpf were more likely to have persistent esophageal eosinophilia on repeat EGD, evidence of basal layer hyperplasia and lamina propria fibrosis compared to patients with < 5 eos/hpf (p <0.001).
Conclusions
Esophageal Eosinophilia, at levels consistent with EE, was present among 30% of patients diagnosed with reflux esophagitis and the incidence of esophageal eosinophilia did not change over time. Patients with ≥ 5 eos/hpf had evidence of other histologic abnormalities and were likely to have persistent esophageal eosinophilia.
doi:10.1016/j.jaci.2010.05.027
PMCID: PMC4115587  PMID: 20620567
eosinophilic esophagitis; incidence; diagnosis; chronic esophagitis; eosinophil; esophagitis; epidemiology; retrospective
10.  Biology of the Eosinophil 
Advances in immunology  2009;101:81-121.
In this review, we aim to put in perspective the biology of a multifunctional leukocyte, the eosinophil, by placing it in the context of innate and adaptive immune responses. Eosinophils have a unique contribution in initiating inflammatory and adaptive responses due to their bidirectional interactions with dendritic cells and T cells, as well as their large panel of secreted cytokines and soluble mediators. The mechanisms and consequences of eosinophil responses in experimental inflammatory models are discussed.
doi:10.1016/S0065-2776(08)01003-1
PMCID: PMC4109275  PMID: 19231593
Eosinophil; chemokine; cytokine; pathogenesis; gastrointestinal; asthma
11.  Diagnostic, Functional and Therapeutic Roles of MicroRNA in Allergic Diseases 
Allergic inflammation is accompanied by the coordinated expression of a myriad of genes and proteins that initiate, sustain, and propagate immune responses and tissue remodeling. MicroRNAs (miRNAs) are a class of short single-stranded RNA molecules that post-transcriptionally silence gene expression and have been shown to fine-tune gene transcriptional networks as single miRNAs can target hundreds of genes. 7 Considerable attention has focused on the key role of miRNAs in regulating homeostatic immune architecture and acquired immunity. Recent studies have identified miRNA profiles in multiple allergic inflammatory diseases including asthma, eosinophilic esophagitis, allergic rhinitis, and atopic dermatitis. Specific miRNAs have been found to have critical roles in regulating key pathogenic mechanisms in allergic inflammation including polarization of adaptive immune responses and activation of T cells (e.g. miR-21 and miR-146), regulation of eosinophil development (e.g. miR-21 and miR-223), and modulation of interleukin (IL)-13-driven epithelial responses (e.g. miR-375). This review discusses recent advances in our understanding of the expression and function of miRNAs in allergic inflammation, their role as disease biomarkers, and perspectives for future investigation and clinical utility.
doi:10.1016/j.jaci.2013.04.039
PMCID: PMC3737592  PMID: 23735656
Allergy; microRNA; miRNA; non-coding RNA; asthma; eosinophilic esophagitis; atopic dermatitis; allergic rhinitis; eosinophils; inflammation; biomarkers
12.  Demethylation of the human eotaxin-3 gene promoter leads to the elevated expression of eotaxin-3 
DNA demethylation has been primarily studied in the context of development biology, cell fate, and cancer, with less attention on inflammation. Herein, we investigate the association between DNA methylation and production of the chemoattractant cytokine eotaxin-3 in the tissue of patients with allergic disease. Regions of the human eotaxin-3 promoter were found to be hypomethylated in primary epithelial cells obtained from allergic tissue compared with normal control tissue (CTL). The demethylation of a specific CpG site (designated CpG 2), which is juxtaposed to a key cyclic AMP-responsive element (CRE) site, was significantly demethylated in patient-derived compared to CTL-derived epithelial cells. Levels of methylation at CpG 2 inversely correlated with basal and IL-13–induced eotaxin-3 gene expression. Conversely, global inhibition of methylation with 5-azacytidine (5-AzaC) promoted eotaxin-3 production in association with decreasing CpG 2 methylation. In addition, the basal and IL-13-induced eotaxin-3 transcriptional activity was suppressed by promoter methylation using a methylation-free in vitro system. Further, electrophoretic mobility shift assays (EMSA) demonstrated that the attachment of CREB binding protein (CBP) and activating transcription factor 2 (ATF-2) to the CRE site was methylation dependent. Taken together, these data identify a contributory role for DNA methylation in regulating eotaxin-3 production in human allergic inflammation.
doi:10.4049/jimmunol.1302454
PMCID: PMC3902544  PMID: 24323578
13.  MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression1 
Allergic airway inflammation is characterized by marked in situ changes in gene and protein expression, yet the role of microRNAs (miRNAs), a new family of key mRNA regulatory molecules, in this process has not yet been reported. Using a highly sensitive microarray based approach, we identified 21 miRNAs with differential expression between doxycycline-induced lung-specific IL-13 transgenic mice (with allergic airway inflammation) and control mice. In particular, we observed over-expression of miR-21 and under-expression of miR-1 in the induced IL-13 transgenic mice compared to control mice. These findings were validated in two independent models of allergen-induced allergic airway inflammation and in IL-4 lung transgenic mice. While IL-13 induced miR-21 expression was IL-13 receptor alpha 1 dependent, allergen induced miR-21 expression was mediated mainly independent of IL-13 receptor alpha 1 and STAT6. Notably, predictive algorithms identified potential direct miR-21 targets among IL-13-regulated lung transcripts such as IL-12p35 mRNA that was decreased in IL-13 transgenic mice. Introduction of pre-miR-21 dose-dependently inhibited cellular expression of a reporter vector harboring the 3’UTR of IL-12p35. Moreover, mutating miR-21 binding sites in IL-12p35 3’UTR abrogated miR-21 mediated repression. In summary, we have identified a miRNA signature in allergic airway inflammation, which includes miR-21 that modulates IL-12, a molecule germane to T helper cell polarization.
doi:10.4049/jimmunol.0803560
PMCID: PMC4280862  PMID: 19342679
Allergy; lung; inflammation; gene regulation
14.  MiR-223 deficiency increases eosinophil progenitor proliferation 
Recently, microRNAs (miRNAs) have been shown to be involved in hematopoietic cell development but their role in eosinophilopoeisis has not yet been described. Here we show that miR-223 is up-regulated during eosinophil differentiation in an ex vivo bone marrow derived eosinophil culture system. Targeted ablation of miR-223 leads to an increased proliferation of eosinophil progenitors. We found up-regulation of a miR-223 target gene – IGF1R in the eosinophil progenitor cultures derived from miR-223-/- mice compared to miR-223+/+ littermate controls. The increased proliferation of miR-223-/- eosinophil progenitors was reversed by treatment with the IGF1R inhibitor (picropodophyllin). Whole genome microarray analysis of differentially regulated genes between miR-223+/+ and miR-223-/- eosinophil progenitor cultures identified a specific enrichment in genes that regulate hematologic cell development. Indeed, miR-223-/- eosinophil progenitors had a delay in differentiation. Our results demonstrate that miRNAs regulate the development of eosinophils by influencing eosinophil progenitor growth and differentiation and identify a contributory role for miR-223 in this process.
doi:10.4049/jimmunol.1202897
PMCID: PMC3563857  PMID: 23325891
15.  IL-13Rα2 Has a Protective Role in a Mouse Model of Cutaneous Inflammation 
IL-13 is expressed in lesions of atopic dermatitis (AD) and has been associated with increased disease severity. IL-13 has two cognate receptors: IL-13Rα1 and IL-13Rα2. Although IL-13Rα2 expression is known to be induced in response to IL-13 in keratinocytes, its function in AD has never been evaluated. We characterized the loss of skin barrier function and the development of cutaneous inflammation in IL-13Rα2–null versus wild-type BALB/c mice following an epicutaneous allergen-sensitization/challenge model that shares similarities with human AD. Mice lacking IL-13Rα2 had significantly increased transepidermal water loss, cutaneous inflammation, peripheral eosinophilia, and IgG1 and IgE levels compared with wild-type mice. The rate of resolution of the cutaneous inflammation was not significantly altered in the IL-13Rα2–null mice. IL-13 induced expression of IL-13Rα2 in keratinocyte cell lines and primary human keratinocytes. Depletion of IL-13Rα2 in a keratinocyte cell line resulted in increased STAT6 signaling in response to IL-13. In conclusion, IL-13Rα2 serves a protective role in the pathogenesis of allergic inflammation and loss of skin barrier function in a mouse model of AD, suggesting that it may be an important endogenous regulator of IL-13–induced cutaneous inflammation in humans.
doi:10.4049/jimmunol.1002118
PMCID: PMC4251801  PMID: 20971924
16.  Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis 
Frontiers in Genetics  2014;5:401.
Objective: We report the first pediatric specific Phenome-Wide Association Study (PheWAS) using electronic medical records (EMRs). Given the early success of PheWAS in adult populations, we investigated the feasibility of this approach in pediatric cohorts in which associations between a previously known genetic variant and a wide range of clinical or physiological traits were evaluated. Although computationally intensive, this approach has potential to reveal disease mechanistic relationships between a variant and a network of phenotypes.
Method: Data on 5049 samples of European ancestry were obtained from the EMRs of two large academic centers in five different genotyped cohorts. Recently, these samples have undergone whole genome imputation. After standard quality controls, removing missing data and outliers based on principal components analyses (PCA), 4268 samples were used for the PheWAS study. We scanned for associations between 2476 single-nucleotide polymorphisms (SNP) with available genotyping data from previously published GWAS studies and 539 EMR-derived phenotypes. The false discovery rate was calculated and, for any new PheWAS findings, a permutation approach (with up to 1,000,000 trials) was implemented.
Results: This PheWAS found a variety of common variants (MAF > 10%) with prior GWAS associations in our pediatric cohorts including Juvenile Rheumatoid Arthritis (JRA), Asthma, Autism and Pervasive Developmental Disorder (PDD) and Type 1 Diabetes with a false discovery rate < 0.05 and power of study above 80%. In addition, several new PheWAS findings were identified including a cluster of association near the NDFIP1 gene for mental retardation (best SNP rs10057309, p = 4.33 × 10−7, OR = 1.70, 95%CI = 1.38 − 2.09); association near PLCL1 gene for developmental delays and speech disorder [best SNP rs1595825, p = 1.13 × 10−8, OR = 0.65(0.57 − 0.76)]; a cluster of associations in the IL5-IL13 region with Eosinophilic Esophagitis (EoE) [best at rs12653750, p = 3.03 × 10−9, OR = 1.73 95%CI = (1.44 − 2.07)], previously implicated in asthma, allergy, and eosinophilia; and association of variants in GCKR and JAZF1 with allergic rhinitis in our pediatric cohorts [best SNP rs780093, p = 2.18 × 10−5, OR = 1.39, 95%CI = (1.19 − 1.61)], previously demonstrated in metabolic disease and diabetes in adults.
Conclusion: The PheWAS approach with re-mapping ICD-9 structured codes for our European-origin pediatric cohorts, as with the previous adult studies, finds many previously reported associations as well as presents the discovery of associations with potentially important clinical implications.
doi:10.3389/fgene.2014.00401
PMCID: PMC4235428  PMID: 25477900
PheWAS; ICD-9 code; genetic polymorphism
19.  Comparative Dietary Therapy Effectiveness in Remission of Pediatric Eosinophilic Esophagitis 
Background
Eosinophilic esophagitis is a chronic, immune-mediated inflammatory disorder that responds to dietary therapy; however, data evaluating the effectiveness of dietary therapeutic strategies is limited.
Objective
This study compared the effectiveness of three frequently prescribed dietary therapies [elemental, six-food elimination, and skin prick and atopy patch-directed elimination] and assessed the remission predictability of skin tests and their utility in directing dietary planning.
Methods
A retrospective cohort of proton-pump inhibitor-unresponsive, non-glucocorticoid-treated eosinophilic esophagitis patients who had two consecutive endoscopic biopsies associated with dietary intervention was identified. Biopsy histology and remissions (< 15 eosinophils/high-power field) following dietary therapy and food reintroductions were evaluated.
Results
Ninety-eight of 513 patients met eligibility criteria. Of these 98, 50% (49), 27% (26), and 23% (23) received elemental, six-food elimination, and directed diets, respectively. Remission occurred in 96%, 81%, and 65% of patients on elemental, six-food elimination, and directed diets, respectively. The odds of post-diet remission vs. non-remission were 5.6-fold higher (P=0.05) on elemental vs. six-food elimination, 12.5-fold higher (P=0.003) on elemental vs. directed, and were not significantly different (P=0.22) on six-food elimination vs. directed diets. Following 116 single-food reintroductions, the negative predictive value of skin testing for remission was 40%–67% (milk 40%, egg 56%, soy 64%, and wheat 67%).
Conclusion
All three dietary therapies are effective; however, an elemental diet is superior at inducing histologic remission compared with six-food elimination and skin test-directed diets. Notably, an empiric six-food elimination diet is as effective as a skin test-directed diet. The negative predictive values of foods most commonly reintroduced in single-food challenges are not sufficient to support the development of dietary advancement plans solely based on skin tests.
doi:10.1016/j.jaci.2012.03.023
PMCID: PMC3367096  PMID: 22541246
Eosinophilic esophagitis; eosinophils; histologic remission; pediatric; dietary therapy; food allergy; negative predictive values; elemental diet; six-food elimination diet; skin test-directed elimination diet
20.  MicroRNA signature in patients with eosinophilic esophagitis, reversibility with glucocorticoids, and assessment as disease biomarkers 
Background
The role of microRNAs (miRNAs), a key class of regulators of mRNA expression and translation, in patients with eosinophilic esophagitis (EoE) has not been explored.
Objective
We aimed to identify miRNAs dysregulated in patients with EoE and assess the potential of these miRNAs as disease biomarkers.
Methods
Esophageal miRNA expression was profiled in patients with active EoE and those with glucocorticoid-induced disease remission. Expression profiles were compared with those of healthy control subjects and patients with chronic (noneosinophilic) esophagitis. Expression levels of the top differentially expressed miRNAs from the plasma of patients with active EoE and patients with EoE remission were compared with those of healthy control subjects.
Results
EoE was associated with 32 differentially regulated miRNAs and was distinguished from noneosinophilic forms of esophagitis. The expression levels of the most upregulated miRNAs (miR-21 and miR-223) and the most downregulated miRNA (miR-375) strongly correlated with esophageal eosinophil levels. Bioinformatic analysis predicted interplay of miR-21 and miR-223 with key roles in the polarization of adaptive immunity and regulation of eosinophilia, and indeed, these miRNAs correlated with key elements of the EoE transcriptome. The differentially expressed miRNAs were largely reversible in patients who responded to glucocorticoid treatment. EoE remission induced a single miRNA (miR-675) likely to be involved in DNA methylation. Plasma analysis of the most upregulated esophageal miRNAs identified miR-146a, miR-146b, and miR-223 as the most differentially expressed miRNAs in the plasma.
Conclusions
We have identified a marked dysregulated expression of a select group of miRNAs in patients with EoE and defined their reversibility with glucocorticoid treatment and their potential value as invasive and noninvasive biomarkers.
doi:10.1016/j.jaci.2012.01.060
PMCID: PMC3466056  PMID: 22391115
Eosinophilic esophagitis; microRNA; glucocorticoid; biomarkers
21.  The pan-B cell marker CD22 is expressed on gastrointestinal eosinophils and negatively regulates tissue eosinophilia¶ 
CD22 is currently recognized as a B cell-specific Siglec and has been exploited therapeutically with humanized anti-CD22 monoclonal antibody having been used against B cell leukemia. Herein, tissue-specific eosinophil mRNA microarray analysis identified that CD22 transcript levels of murine gastrointestinal (GI) eosinophils are 10-fold higher than those of lung eosinophils. In order to confirm the mRNA data at the protein level, we developed a FACS-based protocol designed to phenotype live GI eosinophils isolated from the murine lamina propria. Indeed, we found that jejunum eosinophils expressed remarkably high levels of surface CD22, similar to levels found in B cells across multiple mouse strains. In contrast, CD22 was undetectable on eosinophils from the colon, blood, thymus, spleen, uterus, peritoneal cavity and allergen-challenged lung. Eosinophils isolated from newborn mice did not express CD22 but subsequently upregulated CD22 expression to adult levels within the first 10 days after birth. The GI lamina propria from CD22 gene-targeted mice harbored more eosinophils than wild-type control mice, while the GI eosinophil turnover rate was unaltered in the absence of CD22. Our findings identify a novel expression pattern and tissue eosinophilia-regulating function for the “B cell-specific” inhibitory molecule CD22 on GI eosinophils.
doi:10.4049/jimmunol.1102222
PMCID: PMC3262961  PMID: 22190185
Eosinophils; mucosa; Siglec; CD22
22.  Importance of Cytokines in Murine Allergic Airway Disease and Human Asthma1 
Asthma is a common, disabling inflammatory respiratory disease that has increased in frequency and severity in developed nations. We review studies of murine allergic airway disease (MAAD2) and human asthma that evaluate the importance of Th2 cytokines, Th2 response-promoting cytokines, IL-17 and pro- and anti-inflammatory cytokines in MAAD and human asthma. We discuss murine studies that directly stimulate airways with specific cytokines or delete, inactivate, neutralize or block specific cytokines or their receptors, as well as controversial issues, including the roles of IL-5, IL-17 and IL-13Rα2 in MAAD and IL-4Rα expression by specific cell types. Studies of human asthmatic cytokine gene and protein expression, linkage of cytokine polymorphisms to asthma, cytokine responses to allergen stimulation and clinical responses to cytokine antagonists are discussed as well. Results of these analyses establish the importance of specific cytokines in MAAD and human asthma and have therapeutic implications.
doi:10.4049/jimmunol.0902185
PMCID: PMC4122090  PMID: 20130218
23.  PedsQL™ Eosinophilic Esophagitis Module: Feasibility, Reliability and Validity 
Objective
Eosinophilic esophagitis (EoE) is a chronic esophageal inflammatory condition with a paucity of information on health-related quality of life (HRQOL). The objective of the study was to report on the measurement properties of the PedsQL™ EoE Module.
Methods
The PedsQL™ EoE Module was completed in a multisite study by 196 pediatric EoE patients and 262 EoE parents.
Results
The PedsQL™ EoE Module scales evidenced excellent feasibility (0.6%–3.1% missing), excellent group comparison reliability across total scale scores (patient α = 0.93; parent proxy α = 0.94), good reliability for the seven individual scales (patient α = 0.75–0.87; parent proxy α = 0.81–0.92), excellent test-retest reliability (patient ICC = 0.88; parent ICC= 0.82), demonstrated no floor effects and low ceiling effects, and demonstrated a high percentage of scaling success for most scales. Intercorrelations with the PedsQL™ Generic Core Scales were in the medium (0.30) to large (0.50) range. PedsQL™ EoE Module scores were worse among patients with active histologic disease (> 5 eos/hpf) compared to those in remission (patient self-report: 63.3 vs. 69.9 [p<0.05]; parent proxy-report: 65.1 vs. 72.3 [p<0.01]), and those treated with dietary restrictions compared to those with no restrictions (patient self-report: 61.6 vs. 74.3 [p< 0.01]; parent proxy-report: 65.5 vs. 74.7 [p<0.01]).
Conclusions
The results demonstrate excellent measurement properties of the PedsQL™ EoE Module. Patients with active histologic disease and those treated with dietary restrictions demonstrated worse PedsQL™ scores. The PedsQL™ EoE Module may be utilized in evaluation of pediatric EoE disease-specific HRQOL in clinical research and practice.
doi:10.1097/MPG.0b013e31828f1fd2
PMCID: PMC4115583  PMID: 23478422
Eosinophilic Esophagitis; PedsQL; pediatrics; children; health-related quality of life; patient-reported outcomes
24.  Interleukin-15 expression is increased in human eosinophilic esophagitis and mediates pathogenesis in mice 
Gastroenterology  2010;139(1):182-93.e7.
Background & Aims
Quantitative microarray analyses have shown increased expression of IL-15 mRNA in the esophagus of patients with eosinophilic esophagitis (EoE), a recently recognized allergic disorder with poorly understood pathogenesis.
Methods
Quantitative PCR and ELISA analyses were performed to examine protein and transcript levels in tissue samples from patients with EoE. Tissues from IL-15Ra-deficient and wild-type (control) mice were also examined. Tissue eosinophilia was determined by immunostaining for major basic protein (MBP) and flow cytometry for cell-surface receptors.
Results
Quantitative PCR analyses demonstrated that levels of IL-15 and its receptor IL-15Ra were increased ~6- and ~10-fold, respectively, in tissues from patients with EoE and ~3- and ~4-fold, respectively, in mice with allergen-induced EoE. A >2-fold increase in serum IL-15 protein was also detected in human EoE samples compared with those from healthy individuals. Human IL-15 mRNA levels correlated with esophageal eosinophilia (p<0.001). IL-15Ra-deficient mice were protected from allergen-induced esophageal eosinophilia compared with controls (p<0.001), even though similar levels of airway eosinophilia were observed in all mice. IL-15 activated STAT5 and CD4+ T cells to produce cytokines that act on eosinophils. Incubation of primary esophageal epithelial cells from mice and humans with IL-15 caused a dose-dependent increase in the mRNA expression and protein levels of eotaxins-1, -2 and -3.
Conclusion
IL-15 mediates in the pathogenesis of EoE. IL-15 activates CD4+ T cells to produce cytokines that act on eosinophils.
doi:10.1053/j.gastro.2010.03.057
PMCID: PMC4116278  PMID: 20381491
Eosinophils; Esophagus; Interleukin (IL)-15; IL-15Ra; T cells; EoE Patients
25.  Expanding the paradigm of eosinophilic esophagitis: mast cells and IL-9 
doi:10.1016/j.jaci.2013.04.010
PMCID: PMC4115361  PMID: 23726533
Eosinophilic Esophagitis; Immunology; Mast cells; IL-9

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