Bani Kaur Suri

Genome-wide association study for atopy and allergic rhinitis in a Singapore Chinese population.

Allergic rhinitis (AR) is an atopic disease which affects about 600 million people worldwide and results from a complex interplay between genetic and environmental factors. However genetic association studies on known candidate genes yielded variable results. The aim of this study is to identify the genetic variants that influence predisposition towards allergic rhinitis in an ethnic Chinese population in Singapore using a genome-wide association study (GWAS) approach. A total of 4461 ethnic Chinese volunteers were recruited in Singapore and classified according to their allergic disease status. The GWAS included a discovery stage comparing 515 atopic cases (including 456 AR cases) and 486 non-allergic non-rhinitis (NANR) controls. The top SNPs were then validated in a replication cohort consisting of a separate 2323 atopic cases (including 676 AR cases) and 511 NANR controls. Two SNPs showed consistent association in both discovery and replication phases; MRPL4 SNP rs8111930 on 19q13.2 (OR = 0.69, Pcombined = 4.46×10−05) and BCAP SNP rs505010 on chromosome 10q24.1 (OR = 0.64, Pcombined = 1.10×10−04). In addition, we also replicated multiple associations within known candidates regions such as HLA-DQ and NPSR1 locus in the discovery phase. Our study suggests that MRPL4 and BCAP, key components of the HIF-1α and PI3K/Akt signaling pathways respectively, are two novel candidate genes for atopy and allergic rhinitis. Further study on these molecules and their signaling pathways would help in understanding of the pathogenesis of allergic rhinitis and identification of targets for new therapeutic intervention.

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare.

Whole metagenome analysis has the potential to reveal functional triggers of skin diseases, but issues of cost, robustness and sampling efficacy have limited its application. Here, we have established an alternative, clinically practical and robust metagenomic analysis protocol and applied it to 80 skin microbiome samples epidemiologically stratified for atopic dermatitis (AD). We have identified distinct non-flare, baseline skin microbiome signatures enriched for Streptococcus and Gemella but depleted for Dermacoccus in AD-prone versus normal healthy skin. Bacterial challenge assays using keratinocytes and monocyte-derived dendritic cells established distinct IL-1-mediated, innate and Th1-mediated adaptive immune responses with Staphylococcus aureus and Staphylococcus epidermidis. Bacterial differences were complemented by perturbations in the eukaryotic community and functional shifts in the microbiome-wide gene repertoire, which could exacerbate a dry and alkaline phenotype primed for pathogen growth and inflammation in AD-susceptible skin. These findings provide insights into how the skin microbial community, skin surface microenvironment and immune system cross-modulate each other, escalating the destructive feedback cycle between them that leads to AD flare.

Genome-wide association study identifies PERLD1 as asthma candidate gene

BackgroundRecent genome-wide association studies (GWAS) for asthma have been successful in identifying novel associations which have been well replicated. The aim of this study is to identify the genetic variants that influence predisposition towards asthma in an ethnic Chinese population in Singapore using a GWAS approach.MethodsA two-stage GWAS was performed in case samples with allergic asthma, and in control samples without asthma and atopy. In the discovery stage, 490 case and 490 control samples were analysed by pooled genotyping. Significant associations from the first stage were evaluated in a replication cohort of 521 case and 524 control samples in the second stage. The same 980 samples used in the discovery phase were also individually genotyped for purposes of a combined analysis. An additional 1445 non-asthmatic atopic control samples were also genotyped.Results19 promising SNPs which passed our genome-wide P value threshold of 5.52 × 10-8 were individually genotyped. In the combined analysis of 1011 case and 1014 control samples, SNP rs2941504 in PERLD1 on chromosome 17q12 was found to be significantly associated with asthma at the genotypic level (P = 1.48 × 10-6, ORAG = 0.526 (0.369-0.700), ORAA = 0.480 (0.361-0.639)) and at the allelic level (P = 9.56 × 10-6, OR = 0.745 (0.654-0.848)). These findings were found to be replicated in 3 other asthma GWAS studies, thus validating our own results. Analysis against the atopy control samples suggested that the SNP was associated with allergic asthma and not to either the asthma or allergy components. Genotyping of additional SNPs in 100 kb flanking rs2941504 further confirmed that the association was indeed to PERLD1. PERLD1 is involved in the modification of the glycosylphosphatidylinositol anchors for cell surface markers such as CD48 and CD59 which are known to play multiple roles in T-cell activation and proliferation.ConclusionsThese findings reveal the association of a PERLD1 as a novel asthma candidate gene and reinforce the involvement of genes on the 17q12-21 chromosomal region in the etiology of asthma.

Genetic variation in BDNF is associated with allergic asthma and allergic rhinitis in an ethnic Chinese population in Singapore

Allergic diseases affect more than 25% of the world population and result from a complex interplay between genetic and environmental factors. Recent evidence has shown that BDNF (Brain Derived Neurotrophic Factor) could serve as an important marker of allergic disease. Increased levels of BDNF in blood, bronchoalveolar lavage fluid and nasal lavage fluid positively correlate with disease activity and severity in patients with allergic rhinitis (AR), asthma and atopic eczema. However, reports on the association between genetic variation in BDNF and allergic disease have been controversial. This study therefore aims to clarify the relationship between single nucleotide polymorphisms (SNPs) in BDNF and a genetic predisposition to AR and asthma in an ethnic Chinese population of Singapore. Volunteers with a self-reported history of asthma (718 subjects) or a history of AR as determined by a researcher-administered questionnaire (795 subjects) were used in this study, alongside controls with no personal or family history of allergy (717 subjects). The association results identified a significant association for the tagSNP rs10767664 with a significant PDominant=0.0007 and OR=1.3 for AR and PDominant=0.0005 and OR=1.3 for asthma (using a dominant model of association). The haplotype based analysis also identified a significant association further confirming the single SNP association. The SNP rs10767664 is strongly linked (r2=0.95) to the functional polymorphism rs6265 (Val66Met), which has previously been reported to be associated to allergic phenotypes and also shown to affect BDNF expression. BDNF is a therefore a key molecular player in allergy. Further studies on polymorphisms within BDNF may shed light on its role in the pathogenesis of allergic diseases and potentially serve as biomarkers for allergic disease.

Functional variants of 17q12-21 are associated with allergic asthma but not allergic rhinitis.

BACKGROUND Allergic rhinitis (AR) and asthma are common allergic conditions with a shared genetic component to their cause. The 17q12-21 locus includes several genes that have been linked to asthma susceptibility, but the role of this locus in AR is unclear. Asthma and AR in adults of Chinese ethnicity in Singapore are predominately caused by sensitization against house dust mites with a nearly complete penetrance of the allergen, which presents a unique opportunity for accurately identifying genetic associations with allergic diseases. OBJECTIVE We sought to define the functional role of 17q12-21 in patients with AR and allergic asthma. METHODS We asked whether single nucleotide polymorphisms (SNPs) in the 17q12-21 locus were associated with AR or asthma in a cohort of 3460 ethnic Chinese subjects residing in Singapore (1435 in the discovery phase and 2025 in the validation phase). Full-blood mRNA gene expression data, plasma IgE levels, and immune cell frequencies in peripheral blood were tested against the tag SNP genotypes. Luciferase assays were used to measure the effect of putative promoter SNPs on expression of the asthma-associated orosomucoid-like 3 gene (ORMDL3). RESULTS Within 17q12-21, only the tag SNP rs8076131 was significantly associated with asthma (P = 8.53 × 10(-10); odds ratio, 0.6715), and AR status was independent of SNPs in this region. C-A alleles at rs8076131 resulted in significantly increased ORMDL3 expression in HEK293 cells in vitro relative to T-G alleles. Moreover, subjects with the risk genotype AA exhibited significantly higher total IgE levels and higher blood eosinophil counts than those with the lower-risk genotypes. CONCLUSION The 17q12-21 locus has a strong genetic association with allergic asthma but not with AR. The polymorphic effect of this locus is attributed to the linkage set tagged by rs8076131, which affects the expression of ORMDL3, protein phosphatase 1, regulatory inhibitor subunit 1B (PPP1R1B), zona pellucida binding protein 2 (ZPBP2), and gasdermin B (GSDMB) and is correlated with high IgE levels and eosinophil counts in subjects bearing the risk genotype.

Variation in Uteroglobin-Related Protein 1 (UGRP1) gene is associated with Allergic Rhinitis in Singapore Chinese

BackgroundUteroglobin-Related Protein 1 (UGRP1) is a secretoglobulin protein which has been suggested to play a role in lung inflammation and allergic diseases. UGRP1 has also been shown to be an important pneumoprotein, with diagnostic potential as a biomarker of lung damage. Previous genetic studies evaluating the association between variations on UGRP1 and allergic phenotypes have yielded mixed results. The aim of this present study was to identify genetic polymorphisms in UGRP1 and investigate if they were associated with asthma and allergic rhinitis in the Singapore Chinese population.MethodsResequencing of the UGRP1 gene was conducted on 40 randomly selected individuals from Singapore of ethnic Chinese origin. The polymorphisms identified were then tagged and genotyped in a population of 1893 Singapore Chinese individuals. Genetic associations were evaluated in this population comparing 795 individuals with allergic rhinitis, 718 with asthma (of which 337 had both asthma and allergic rhinitis) and 717 healthy controls with no history of allergy or allergic diseases.ResultsBy resequencing the UGRP1 gene within our population, we identified 11 novel and 16 known single nucleotide polymorphisms (SNPs). TagSNPs were then genotyped, revealing a significant association between rs7726552 and allergic rhinitis (Odds Ratio: 0.81, 95% Confidence Interval: 0.66-0.98, P = 0.039). This association remained statistically significant when it was analyzed genotypically or when stratified according to haplotypes. When variations on UGRP1 were evaluated against asthma, no association was observed.ConclusionThis study documents the association between polymorphisms in UGRP1 and allergic rhinitis, suggesting a potential role in its pathogenesis.

Validation of GWAS Loci for Atopic Dermatitis in a Singapore Chinese Population

TO THE EDITOR Atopic dermatitis (AD) is a complex trait resulting from an interaction between a large variety of environmental and genetic factors (Irvine and McLean, 2006; Rodrı́guez et al., 2009; van den Oord and Sheikh, 2009). Research on the filaggrin gene (FLG) in Asian populations including Singapore has confirmed that allelic variants in this gene influence risk to AD (Akiyama, 2010), as in Europe, while also strengthening the evidence for other factors involved in the disease etiology (Chen et al., 2011). Recently, Sun et al. (2011) reported a genome-wide association study on AD in which they identified two new susceptibility loci at 5q22.1 (rs7701890) and 20q13.33 (rs6010620), and one suggestive locus at 10q21.2 (rs2393903) in the Chinese population. The previously unreported associations were validated in Northern and Southern Chinese, but only the 20q13.33 (rs6010620) locus was validated in a German population, supporting the presence of ethnic differences or environmental influences on the observed genetic associations. Here, we analyzed these three loci in 827 AD cases and 1,104 controls (Supplementary Information online), all of which were Singaporean Chinese (Andiappan et al., 2011). All three single-nucleotide polymorphisms (SNPs) were directly assayed by Taqman genotyping and were found to be in Hardy– Weinberg equilibrium in controls (P40.05). The chromosome (chr)10 and chr20 SNPs showed significant association in our population (odds ratio (OR)1⁄4 1.26 (95% confidence interval (CI) 1.11–1.44), P1⁄40.0004; and OR1⁄4 1.18 (95% CI 1.02–1.36), P1⁄40.024, respectively). The effect sizes of these associations are similar to that reported in Sun et al. (Table 1). However, the chr5 SNP rs7701890 showed no evidence of association (OR1⁄40.96 (95% CI 0.81–1.13), P1⁄40.59). With our current sample size and the minor allele frequency of 20% in Singaporean Chinese, we estimate that we had close to 80% power to detect the effect observed by Sun et al. (OR 1.24; Purcell et al., 2003). The well-known association of atopy with allergic phenotypes (Bousquet et al., 2001, 2008) prompted us to investigate the association of the three SNPs with positive skin prick test (SPT) results in our cohort. We analyzed a total of 2,627 SPT-positive and 389 SPT-negative individuals, which included both AD cases and controls. There was no association with positive SPT status (Supplementary Table S1 online), and adjustment for this SPT status had little or no impact on the AD association results for the chr10 and chr20 SNPs. We then tested the three above-mentioned SNPs (rs7701890, rs2393903, and rs6010620) for association with allergic rhinitis (AR; 472 cases) and asthma (323 cases), in the absence of AD. The rs6010620 SNP on 20q13.33 was associated with AR (P1⁄40.008), although further validation of this result is required. Although the 5q22.1 locus has recently been reported to be associated with AR (Ramasamy et al., 2011), the SNP we tested was not in linkage disequilibrium with any of the reported SNPs (r1⁄4 0 with rs17513503 and rs1898671). The AD cases were separated into two groups (i) AD only and (ii) AD with other associated atopic conditions (asthma, AR, or both). We found the risk C allele of the chr10 locus showed a significantly stronger association with the group with AD only compared with the group with AD and other atopic conditions (OR1⁄4 1.45 (95% CI 1.21–1.79) vs 1.19 (1.03–1.38), P1⁄4 0.038; Table 1). We then performed a quantitative trait analysis in a subset of 397 AD cases whose disease severities were determined by the SCORing Atopic Dermatitis (SCORAD) index (Oranje et al., 2007). Consistently, we found the CC genotype of rs2393903 at chr10 was significantly associated with a lower SCORAD score (mean 33.99±1.568; n1⁄494), compared with Abbreviations: AD, atopic dermatitis; AR, allergic rhinitis; CI, confidence interval; OR, odds ratio; SCORAD, SCORing Atopic Dermatitis; SNP, single-nucleotide polymorphism; SPT, skin prick test