Upregulation of miR-155 regulates group 2 innate lymphoid cells by targeting c-maf in allergic rhinitis.

Group 2 innate lymphoid cells (ILC2s) and Th2 type immune response are critically involved in the pathogenesis of allergic rhinitis (AR), and this pathological process is influenced by microRNAs-mediated post-transcriptional regulation. The present study investigated the adaptation and function of miR-155 in AR patients and mouse model. We found that significantly increased miR-155 expression (1.63 ± 0.12 vs. 0.92 ± 0.11 in human, and 1.68 ± 0.15 vs. 1.06 ± 0.06 in mice) and ILC2s activity in nasal mucosa and serum in AR patients and mice. Administration of miR-155 antagomir significantly reduced the activity of ILC2s in nasal mucosa, suppressed the production of Th2 cytokines in serum and nasal mucosa, and alleviated the airway inflammation and allergic symptoms in AR mice, while miR-155 agomir increased ILC2s activity and production of Th2 cytokines and induced airway inflammation and allergic symptoms in control mice. Meanwhile, the expression of transcriptional factor c-Maf (0.57 ± 0.05 vs. 0.37 ± 0.04) in nasal mucosa in AR mice, which was significantly recovered by miR-155 antagomir (0.56 ± 0.04). Treatment with miR-155 agomir decreased c-Maf expression in nasal mucosa in control mice. This synchronized with the similar pattern in the current observations that miR-155 regulated Th2 cytokine (IL-4, IL-5, IL-9 and IL-13) production, airway inflammation and allergic symptoms in AR mice. Together, upregulation miR-155 suppressed the expression of transcriptional factor c-Maf and was critically involved in the ILC2s activation, which contributed to the airway inflammation and allergic symptoms in AR.

Genome-wide association analysis of 350 000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema.

Even though heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors, previous studies have not explained a large part of the genetics behind these diseases. In this genome-wide association study, we include 346 545 Caucasians from the UK Biobank to identify novel loci for asthma, hay fever and eczema and replicate novel loci in three independent cohorts. We further investigate if associated lead single nucleotide polymorphisms (SNPs) have a significantly larger effect for one disease compared to the other diseases, to highlight possible disease-specific effects. We identified 141 loci, of which 41 are novel, to be associated (P ≤ 3 × 10-8) with asthma, hay fever or eczema, analyzed separately or as disease phenotypes that includes the presence of different combinations of these diseases. The largest number of loci was associated with the combined phenotype (asthma/hay fever/eczema). However, as many as 20 loci had a significantly larger effect on hay fever/eczema only compared to their effects on asthma, while 26 loci exhibited larger effects on asthma compared with their effects on hay fever/eczema. At four of the novel loci, TNFRSF8, MYRF, TSPAN8, and BHMG1, the lead SNPs were in Linkage Disequilibrium (LD) (>0.8) with potentially casual missense variants. Our study shows that a large amount of the genetic contribution is shared between the diseases. Nonetheless, a number of SNPs have a significantly larger effect on one of the phenotypes, suggesting that part of the genetic contribution is more phenotype specific.

Analysis of the Serum Cytokine Profile in Allergic Patients Opens a Way to Personalized Treatment of Allergy.

Plant lipid transfer proteins and homologues of the main birch pollen allergen Bet v 1 are involved in the development of allergic reactions of varying severity to plant foods and pollen. In this study, the sera from patients with tree and weed pollen allergies in the Moscow region were examined. The levels of IL-4, IL-5, IL-9, IL-10, IL-13, IL-17A, IFNγ, TNFα, and TNFß cytokines were determined in the sera of patients with specific IgE antibodies to Bet v 1 and Pru p 3 allergens. It was confirmed that patients with pollen allergy are often characterized by Th2 response of the immune system, though other mechanisms of allergy development occurred in some cases. The data obtained demonstrate the necessity of detailed analysis of the individual mechanism of allergic reactions and patient-centered approach to the personalized allergy treatment.

Distinct Gene Expression Patterns between Nasal Mucosal Cells and Blood Collected from Allergic Rhinitis Sufferers.

BACKGROUND: Investigations of gene expression in allergic rhinitis (AR) typically rely on invasive nasal biopsies (site of inflammation) or blood samples (systemic immunity) to obtain sufficient genetic material for analysis. New methodologies to circumvent the need for invasive sample collection offer promise to further the understanding of local immune mechanisms relevant in AR. METHODS: A within-subject design was employed to compare immune gene expression profiles obtained from nasal washing/brushing and whole blood samples collected during peak pollen season. Twelve adults (age: 46.3 ± 12.3 years) with more than a 2-year history of AR and a confirmed grass pollen allergy participated in the study. Gene expression analysis was performed using a panel of 760 immune genes with the NanoString nCounter platform on nasal lavage/brushing cell lysates and compared to RNA extracted from blood. RESULTS: A total of 355 genes were significantly differentially expressed between sample types (9.87 to -9.71 log2 fold change). The top 3 genes significantly upregulated in nasal lysate samples were Mucin 1 (MUC1), Tight Junction Protein 1 (TJP1), and Lipocalin-2 (LCN2). The top 3 genes significantly upregulated in blood samples were cluster of differentiation 3e (CD3E), FYN Proto-Oncogene Src Family Tyrosine Kinase (FYN) and cluster of differentiation 3d (CD3D). CONCLUSIONS: Overall, the blood and nasal lavage samples showed vastly distinct gene expression profiles and functional gene pathways which reflect their anatomical and functional origins. Evaluating immune gene expression of the nasal mucosa in addition to blood samples may be beneficial in understanding AR pathophysiology and response to allergen challenge.

Genome-wide association study for pollinosis identified two novel loci in interleukin (IL)-1B in a Japanese population.

The number of pollinosis patients in Japan has significantly increased over the past 20 years. The majority of genome-wide association studies (GWAS) on pollinosis have been conducted in subjects of European descent, with few studies in Japanese populations. The aim of our GWAS was to identify genetic loci associated with self-reported pollinosis in a Japanese population and to understand its molecular background using a combination of single nucleotide polymorphisms (SNPs) and gene- and pathway-based analyses. A total of 731 and 560 individuals who were recruited as participants of the Japan Multi-Institutional Collaborative Cohort Study participated in the discovery and replication phases, respectively. The phenotype of pollinosis was based on the information from a self-administered questionnaire. In the single-SNP analysis, four SNPs (rs11975199, rs11979076, rs11979422, and rs12669708) reached suggestive significance level (P < 1 × 10-4) and had effects in the same direction in both phases of the study. The pathway-based analysis identified two suggestive pathways (nucleotide-binding oligomerization domain -like receptor and tumor necrosis factor signaling pathways). Both rs1143633 and rs3917368 in the interleukin-1B gene showed associations in the retrace (from pathway to gene and SNP) analysis. We performed single-SNP, gene, and pathway analysis and shed light on the molecular mechanisms underlying pollinosis in a Japanese population.

Identification of potential crucial gene network related to seasonal allergic rhinitis using microarray data.

The aim of this study was to reveal a potential key gene network associated with seasonal allergic rhinitis (SAR). The microarray data GSE50101 downloaded from Gene Expression Omnibus were used to screen differentially expressed genes (DEGs) between SAR patients and healthy controls. Then, functional enrichment analysis was conducted using Database for Annotation, Visualization, and Integrated Discovery. Afterwards, the protein-protein interactions (PPIs) of DEGs were obtained from STRING, and the PPI network was constructed. In addition, the PPI network module was analyzed. In total, 98 up-regulated and 63 down-regulated DEGs were identified from the SAR samples, comparing the healthy controls. The up-regulated DEGs were mainly enriched in the Gene Ontology terms about cell death (e.g., DUSP1 and JUN) and pathways related to immune (e.g., FOS and JUN). The down-regulated DEGs were mainly enriched in regulation of transcription (e.g., CEBPD and SCML1). In the PPI network, a set of genes was predicted to interact with each other, such as FOS, JUN, and CEBPD. Furthermore, genes in the network module (e.g., FOS, JUN and CEBPD) was mainly enriched in regulation of transcription, and pathways about immune, such as mitogen-activated protein kinase signaling pathway, B cell receptor signaling pathway, and toll-like receptor signaling pathway. Several genes related to immunity and regulation of transcription, such as FOS, JUN, and CEBPD, may play crucial roles during the process of SAR through the interactions with each other.

Immunodominance in allergic T-cell reactivity to Japanese cedar in different geographic cohorts.

BACKGROUND: Japanese cedar (JC) pollen is a common trigger for allergic rhinitis in Japan. Pollen proteins targeted by IgE, including Cry j 1 and Cry j 2, and isoflavone reductase (IFR) have been identified. OBJECTIVE: To compare antigen-specific IgE titers and T-cell responses to JC pollen-derived extract and peptides in cohorts with high and low pollen exposure. METHODS: Peripheral blood mononuclear cells from JC pollen allergic or nonallergic patients who have lived in Japan for at least 1 year and JC pollen allergic patients who have never been to Japan were tested for T-cell responses against JC pollen extract and peptide pools derived from Cry j 1, Cry j 2, or IFR. T-cell reactivity was assessed by interleukin 5 and interferon γ production by ELISPOT. RESULTS: JC pollen-specific T-cell reactivity and IgE titers were significantly higher in the allergic compared with the nonallergic Japanese cohort, which was also associated with different patterns of polysensitization. Interestingly, a significant overlap was observed in the hierarchy of the T-cell epitopes in the allergic Japanese cohort compared with the allergic non-Japanese cohort. In all 3 cohorts, T-cell reactivity was dominantly directed against peptides from the major allergens Cry j 1 and 2, with few T-cell responses detected against IFR. CONCLUSION: Our studies identify common denominators of T-cell reactivity in patient populations with different sensitization patterns, suggesting that generally applicable immunotherapeutic approaches might be developed irrespective of exposure modality.

A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases.

Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.

Molecular evolution of hypoallergenic hybrid proteins for vaccination against grass pollen allergy.

More than 10% of the population in Europe and North America suffer from IgE-associated allergy to grass pollen. In this article, we describe the development of a vaccine for grass pollen allergen-specific immunotherapy based on two recombinant hypoallergenic mosaic molecules, designated P and Q, which were constructed out of elements derived from the four major timothy grass pollen allergens: Phl p 1, Phl p 2, Phl p 5, and Phl p 6. Seventeen recombinant mosaic molecules were expressed and purified in Escherichia coli using synthetic genes, characterized regarding biochemical properties, structural fold, and IgE reactivity. We found that depending on the arrangement of allergen fragments, mosaic molecules with strongly varying IgE reactivity were obtained. Based on an extensive screening with sera and basophils from allergic patients, two hypoallergenic mosaic molecules, P and Q, incorporating the primary sequence elements of the four grass pollen allergens were identified. As shown by lymphoproliferation experiments, they contained allergen-specific T cell epitopes required for tolerance induction, and upon immunization of animals induced higher allergen-specific IgG Abs than the wild-type allergens and a registered monophosphoryl lipid A-adjuvanted vaccine based on natural grass pollen allergen extract. Moreover, IgG Abs induced by immunization with P and Q inhibited the binding of patients' IgE to natural allergens from five grasses better than IgG induced with the wild-type allergens or an extract-based vaccine. Our results suggest that vaccines based on the hypoallergenic grass pollen mosaics can be used for immunotherapy of grass pollen allergy.

Polymorphisms of tumor necrosis factor-α, transforming growth factor-ß, and interleukin-10 in asthma associated with olive pollen sensitization.

Sensitization to specific olive pollen-allergens (Ole e 2 and 10) has been correlated with a clinical pattern of asthma. This study analyzes the association between several polymorphims of TNFA (G-308A, C-857T, and C-1031T), IL10 (C-571A and A-1117G), and TGFB (C-509-T) and these sensitizations. These polymorphisms were genotyped by allelic discrimination, in olive pollen-allergic patients (phenotyped for specific Ole e 2 and 10 sensitizations) and healthy controls. Levels of serum-soluble cytokines were correlated with specific genotypes and clinical phenotypes. The results showed that heterozygous TGFB C-509T genotype, besides having the lowest sera TGF- levels, was significantly increased in olive pollen-allergic patients compared with controls. According specific sensitizations, CC genotype of IL10 C-571A could be a protective factor for Ole e 2 sensitization and mainly for asthmatic Ole e 2 sensitized patients compared with asthmatic non-Ole e 2 sensitized patients (OR: 0.26, P = 0.008). In contrast, heterozygous CA genotype was increased in Ole e 2 asthmatic subjects compared to asthmatic non-Ole e 2 sensitized patients. Lastly, heterozygous TNFA G-308A genotype was associated with Ole e 10 sensitization (OR: 2.5, P = 0.04). In conclusion, these results suggest a role of TGF-ß1 in olive-pollen sensitization and TNF-α and IL-10 genotypes in the asthma induced by specific olive-pollen allergens.

C-type lectin receptors mRNA expression in patients with otitis media with effusion.

OBJECTIVE: The role of C-type lectin receptor, a type of pattern recognition receptor, in otitis media with effusion (OME) is unclear. We assayed the levels of expression of C-type lectin receptor mRNA in children with OME and evaluated its relationship to the presence of bacteria, accompanying diseases, and characteristics of exudates. SUBJECTS AND METHODS: The study population consisted of 73 children with OME who had undergone ventilating tube insertion. The levels of expression of Dectin-1, MR1, MR2, DC-SIGN, Syk, Card-9, Bcl-10, Malt-1, Src, Dec-205, Galectin-1, Tim-3, Trem-1, and DAP-12 mRNA in middle ear effusion were determined by real-time PCR. The level of expression of each mRNA was correlated with the presence of bacteria, accompanying diseases, and exudates characteristics. RESULTS: The levels of expression of C-type lectin receptor mRNAs were not associated with bacterial presence or exudates characteristics (p>0.05 each). Levels of expression, however, were significantly higher in patients with sinusitis, adenoid vegetation or adenoiditis, and allergic rhinitis (p<0.05 each). CONCLUSIONS: Levels of expression of C-type lectin receptor mRNA may be associated with the pathogenesis of OME, being significantly higher in patients with than without accompanying sinusitis, adenoid vegetation or adenoiditis, and allergic rhinitis.

MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases.

MicroRNAs (miRNAs) play a key role in regulating mRNA expression, and individual miRNAs have been proposed as diagnostic and therapeutic candidates. The identification of such candidates is complicated by the involvement of multiple miRNAs and mRNAs as well as unknown disease topology of the miRNAs. Here, we investigated if disease-associated miRNAs regulate modules of disease-associated mRNAs, if those miRNAs act complementarily or synergistically, and if single or combinations of miRNAs can be targeted to alter module functions. We first analyzed publicly available miRNA and mRNA expression data for five different diseases. Integrated target prediction and network-based analysis showed that the miRNAs regulated modules of disease-relevant genes. Most of the miRNAs acted complementarily to regulate multiple mRNAs. To functionally test these findings, we repeated the analysis using our own miRNA and mRNA expression data from CD4+ T cells from patients with seasonal allergic rhinitis. This is a good model of complex diseases because of its well-defined phenotype and pathogenesis. Combined computational and functional studies confirmed that miRNAs mainly acted complementarily and that a combination of two complementary miRNAs, miR-223 and miR-139-3p, could be targeted to alter disease-relevant module functions, namely, the release of type 2 helper T-cell (Th2) cytokines. Taken together, our findings indicate that miRNAs act complementarily to regulate modules of disease-related mRNAs and can be targeted to alter disease-relevant functions.

Cystatin SN upregulation in patients with seasonal allergic rhinitis.

Seasonal allergic rhinitis (SAR) to the Japanese cedar, Cryptomeria japonica (JC) pollen is an IgE-mediated type I allergy affecting nasal mucosa. However, the molecular events underlying its development remain unclear. We sought to identify SAR-associated altered gene expression in nasal epithelial cells during natural exposure to JC pollen. We recruited study participants in 2009 and 2010 and collected nasal epithelial cells between February and April, which is the period of natural pollen dispersion. Fifteen patients with SAR-JC and 13 control subjects were enrolled in 2009, and 17 SAR-JC patients, 13 sensitized asymptomatic subjects (Sensitized), and 15 control subjects were enrolled in 2010. Total RNA was extracted from nasal epithelial cells and 8 SAR-JC patients and 6 control subjects in 2009 were subjected to microarray analysis with the Illumina HumanRef-8 Expression BeadChip platform. Allergen-stimulated histamine release was examined in the peripheral blood basophils isolated from patients with SAR. We identified 32 genes with significantly altered expression during allergen exposure. One of these, CST1 encodes the cysteine protease inhibitor, cystatin SN. CST1 expression in nasal epithelial cells was significantly upregulated in both the 2009 and 2010 SAR-JC groups compared with the control groups. Immunohistochemical staining confirmed the increased expression of CST1 in the nasal epithelial cells of SAR patients. Addition of exogenous CST1 to basophils inhibited JC allergen-stimulated histamine release in vitro. We propose that CST1 may contribute to inactivation of protease allergens and help re-establish homeostasis of the nasal membranes.

MUC5AC and inflammatory mediators associated with respiratory outcomes in the British 1946 birth cohort.

BACKGROUND AND OBJECTIVE: Dysregulation of respiratory mucins, MUC5AC in particular, has been implicated in respiratory disease and MUC5AC expression is up-regulated in response to environmental challenges and inflammatory mediators. The aim of this study was to examine the effect of genetic variation on susceptibility to common respiratory conditions. METHODS: The association of MUC5AC and the closely linked genes MUC2 and MUC5B with respiratory outcomes was tested in the MRC National Survey of Health and Development, a longitudinal birth cohort of men and women born in 1946. Also examined were the functional variants of the genes encoding inflammatory mediators, IL13, IL1B, IL1RN, TNFA and ERBB1, for which there is a likely influence on MUC5AC expression and were explored potential gene-gene interactions with these inflammatory mediators. RESULTS: Statistically significant associations between the 3'ter MUC5AC simple nucleotide polymorphism (SNP) rs1132440 and various non-independent respiratory outcomes (bronchitis, wheeze, asthma, hay fever) were reported while the adjacent loci show slight (but largely non-statistically significant) differences, presumably reflective of linkage disequilibrium (allelic association) across the region. A novel association between bronchitis and a non-synonymous functional ERBB1 SNP, rs2227983 (aka epidermal growth factor receptor:R497K, R521K) is also reported and evidence presented of interaction between MUC5AC and ERBB1 and between MUC5AC and IL1RN with respect to bronchitis. The ERBB1 result suggests a clear mechanism for a biological interaction in which the allelic variants of epidermal growth factor receptor differentially affect mucin expression. CONCLUSIONS: The MUC5AC association and the interactions with inflammatory mediators suggest that genetically determined differences in MUC5AC expression alter susceptibility to respiratory disease.

Expressions of nuclear factor-kappa B p50 and p65 and their significance in the up-regulation of intercellular cell adhesion molecule-1 mRNA in the nasal mucosa of allergic rhinitis patients.

The purpose of the study was to investigate expressions of nuclear factor-kappa B (NF-κB) and intercellular cell adhesion molecule-1 mRNA (ICAM-1 mRNA) in the nasal mucosa of allergic rhinitis (AR) patients. Expressions of NF-κB and ICAM-1 mRNA were studied using immunohistochemistry and reverse transcription-PCR (RT-PCR) in AR tissues and corresponding normal nasal mucosa. The correlation between NF-κB and ICAM-1 mRNA was studied using linear correlation analysis. The results of immunohistochemistry showed that expression of NF-κB was significantly up-regulated in the nasal mucosa of AR compared with that in normal tissue (P < 0.01), over-expression of NF-κB p50 was found in the cytoplasm and nucleus (P < 0.01), and NF-κB p65 was mainly expressed in the cytoplasm (P < 0.01). ICAM-1 mRNA was strongly expressed in the nasal mucosa of AR compared with that in normal tissue as shown by RT-PCR (P < 0.01). Up-regulation of ICAM-1 mRNA was significantly correlated with over-expressions of NF-κB p50 and NF-κB p65 (r = 0.8995, P < 0.01; r = 0.7601, P < 0.01). In conclusion, NF-κB plays a key role in AR. Excessively activated NF-κB promotes the transcription of ICAM-1 mRNA. ICAM-1 is related to the pathogenesis and development of AR.

[Genetic study of allergic diseases].

Allergic diseases mentioned in this review is regarding to I type allergic inflammation induced by an IgE-mediated reaction, including asthma, allergic rhinitis, atopic dermatitis and food allergy. It is convinced that allergic diseases belong to multiple genes diseases and are controlled by both genetic and environmental factors. Meanwhile there exists gene-gene as well as gene-environment interactions during the development of the disease. The aim of this review is to summarize the toolkit, advance, inherent difficulties and future clinical application prospect in genetic studies of allergic disease.

Prevalence and risk factors of atopic diseases in German children and adolescents.

BACKGROUND: Atopic diseases became an important health problem in affluent Western societies. METHODS: To study the prevalence and factors associated with the risk of atopic diseases in Germany, data from the German Health Interview and Examination Survey for Children and Adolescents (KiGGS) were analysed (n = 17,450). Standardized, computer-assisted personal interviews with parents and parent-administered questionnaires provided physician diagnoses of allergic rhinoconjunctivitis, atopic dermatitis and asthma as well as data on demographic characteristics, migration background, birth order, age at the beginning of nursery, atopic diseases of parents, parents' smoking status, parents' occupation, breastfeeding and living environment. RESULTS: The life-time prevalence of atopic dermatitis was 13.2% (95% confidence limit: 12.5-13.9%), 10.7% (10.1-11.3%) for allergic rhinoconjunctivitis and 4.7% (4.3-5.1%) for asthma. At least one atopic disease in parents was the strongest factor associated with atopic diseases in the offspring, with a prevalence ratio of up to 2.6. High and middle socio-economic status (prevalence ratio, 95% confidence limit: 1.28, 1.12-1.46; 1.15, 1.01-1.32) were associated with the risk of atopic dermatitis, whereas a two-sided background of migration reduced the risk (0.76, 0.65-0.88). Factors that reduced the risk of allergic rhinoconjunctivitis were parents working as self-employed farmers (0.48, 0.30-0.76) and older siblings (0.80, 0.71-0.89), whereas the beginning of nursery school at older age was associated with an increased risk in children who were cared for outside the family before school age (1.05, 1.00-1.10). Living in mould-infested rooms (1.64, 1.23-2.19), an urban living environment (1.20, 1.02-1.42) and a smoking mother and/or father (1.20, 1.02-1.40) were associated with the risk of asthma. CONCLUSIONS: Our results are in line with the so-called 'hygiene hypothesis', which emphasizes the role of environmental factors in addition to a genetic predisposition in the development of atopic diseases. Research on factors associated with atopic diseases can facilitate decisions on preventive strategies. Further studies are needed to explore trends in prevalence and risk factors for atopic diseases.

[Association between single-nucleotide polymorphisms in the IRAK-4 gene and allergic rhinitis].

OBJECTIVE: To investigate the genetic association pattern between single-nucleotide polymorphisms (SNP) in the interleukin-1 receptor-associated kinase 4 (IRAK-4) gene and allergic rhinitis (AR). METHODS: A population of 379 patients with the diagnosis of AR and 333 healthy controls who lived in Beijing region was recruited. A total of 8 reprehensive marker SNP which were in IRAK-4 gene region were selected according to the Beijing people database from Hapmap website. The individual genotyping was performed by MassARRAY platform. SPSS 13.0 software was used for statistic analysis. RESULTS: Subgroup analysis for the presence of different allergen sensitivities displayed associations only in the house dust mite-allergic cohorts (rs3794262: P = 0.0034, OR = 1.7388; rs4251481: P = 0.0023, OR = 2.6593), but not in subjects who were allergic to pollens as well as mix allergens. CONCLUSION: The potential genetic contribution of the IRAK-4 gene to AR demonstrated an allergen-dependant association pattern in Chinese population.

Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms.

BACKGROUND: Complex diseases are associated with altered interactions between thousands of genes. We developed a novel method to identify and prioritize disease genes, which was generally applicable to complex diseases. RESULTS: We identified modules of highly interconnected genes in disease-specific networks derived from integrating gene-expression and protein interaction data. We examined if those modules were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies. First, we analyzed publicly available gene expression microarray and genome-wide association study (GWAS) data from 13, highly diverse, complex diseases. In each disease, highly interconnected genes formed modules, which were significantly enriched for genes harboring disease-associated SNPs. To test if such modules could be used to find novel genes for functional studies, we repeated the analyses using our own gene expression microarray and GWAS data from seasonal allergic rhinitis. We identified a novel gene, FGF2, whose relevance was supported by functional studies using combined small interfering RNA-mediated knock-down and gene expression microarrays. The modules in the 13 complex diseases analyzed here tended to overlap and were enriched for pathways related to oncological, metabolic and inflammatory diseases. This suggested that this union of the modules would be associated with a general increase in susceptibility for complex diseases. Indeed, we found that this union was enriched with GWAS genes for 145 other complex diseases. CONCLUSIONS: Modules of highly interconnected complex disease genes were enriched for disease-associated SNPs, and could be used to find novel genes for functional studies.

A prospective study in children with a severe form of atopic dermatitis: clinical outcome in relation to cytokine gene polymorphisms.

BACKGROUND AND OBJECTIVE: The course of atopic dermatitis (AD) in childhood is characterized by typical changes in phenotype, including a shift from skin involvement to respiratory allergy usually around the third year of age. We thus designed a prospective study to monitor the outcome of severe AD and to investigate the association between cytokine gene polymorphisms and clinical manifestations. METHODS: Clinical and laboratory follow-up of 94 patients with severe AD and 103 healthy controls was performed using routine methodology. Allele, genotype, and haplotype frequencies of single nucleotide polymorphisms of 13 selected cytokine/receptor genes were analyzed using PCR with sequence-specific primers. RESULTS: In our study, genotypes of 7 polymorphisms--LL-4 -1098G/T and -590C/T, IL-6 -174C/G and nt565A/G, and IL-10 -1082A/G, -819C/T, and -592A/C were significantly associated with atopic AD (P < .05). A significant association was also found for TNF-alpha AA and IL-4 GC haplotypes and AD. We confirm the progressive clinical improvement of AD together with a decrease in the severity index SCORAD (SCORing atopic dermatitis) during childhood (P < .05). We found significant differences between IL-4Ralpha +1902 A/G and positivity of tree pollen-specific IgE (P < .05) in the AD group. Moreover, a weak association was also found between IL-10 -819C/T and IL-10 -590A/C and the appearance of allergic rhinitis (P < 0.1). CONCLUSIONS: We confirmed a clinical shift in allergic phenotype in the first 3 years of life, and showed an association between IL-4, IL-6, and IL-10 polymorphisms and AD. Our data indicate that IL-4alpha and IL-10 polymorphisms may be considered predictive factors of respiratory allergy in children with AD.