Significant evidence for linkage of mite-sensitive childhood asthma to chromosome 5q31-q33 near the interleukin 12 B locus by a genome-wide search in Japanese families

Asthma/Rhinitis (The United Airway) and Allergy: Chicken or Egg; Which Comes First?

While allergy, asthma and rhinitis do not inevitably co-exist, there are strong associations. Not all those with asthma are allergic, rhinitis may exist without asthma, and allergy commonly exists in the absence of asthma and/or rhinitis. This is likely due to the separate gene/environment interactions which influence susceptibility to allergic sensitization and allergic airway diseases. Allergic sensitization, particularly to foods, and eczema commonly manifest early in infancy, and not infrequently are followed by the development of allergic rhinitis and ultimately asthma. This has become known as the "allergic march". However, many infants with eczema never develop asthma or rhinitis, and both the latter conditions can evolve without prior eczema or food allergy. Understanding the mechanisms underlying the ontogeny of allergic sensitization and allergic disease will facilitate rational approaches to the prevention and management of asthma and allergic rhinitis. Furthermore, a range of new, so-called biological, therapeutic approaches, targeting specific allergy-promoting and pro-inflammatory molecules, are now in clinical trials or have been recently approved for use by regulatory authorities and could have a major impact on disease prevention and control in the future. Understanding basic mechanisms will be essential to the employment of such medications. This review will explain the concept of the united airway (rhinitis/asthma) and associations with allergy. It will incorporate understanding of the role of genes and environment in relation to the distinct but interacting origins of allergy and rhinitis/asthma. Understanding the patho-physiological differences and varying therapeutic requirements in patients with asthma, with or without rhinitis, and with or without associated allergy, will aid the planning of a personalized evidence-based management strategy.

IRAK-M Associates with Susceptibility to Adult-Onset Asthma and Promotes Chronic Airway Inflammation

IL-1R-associated kinase (IRAK)-M regulates lung immunity during asthmatic airway inflammation. However, the regulatory effect of IRAK-M differs when airway inflammation persists. A positive association between IRAK-M polymorphisms with childhood asthma has been reported. In this study, we investigated the role of IRAK-M in the susceptibility to adult-onset asthma and in chronic airway inflammation using an animal model. Through genetic analysis of IRAK-M polymorphisms in a cohort of adult-onset asthma patients of Chinese Han ethnicity, we identified two IRAK-M single nucleotide polymorphisms, rs1624395 and rs1370128, genetically associated with adult-onset asthma. Functionally, the top-associated rs1624395, with an enhanced affinity to the transcription factor c-Jun, was associated with a higher expression of IRAK-M mRNA in blood monocytes. In contrast to the protective effect of IRAK-M in acute asthmatic inflammation, we found a provoking impact of IRAK-M on chronic asthmatic inflammation. Following chronic OVA stimulation, IRAK-M knockout (KO) mice presented with significantly less inflammatory cells, a lower Th2 cytokine level, a higher IFN-γ concentration, and increased percentage of Th1 cells in the lung tissue than wild type mice. Moreover, lung dendritic cells (DC) from OVA-treated IRAK-M KO mice expressed a higher percentage of costimulatory molecules PD-L1 and PD-L2. Mechanistically, in vitro TLR ligation led to a greater IFN-γ production by IRAK-M KO DCs than wild type DCs. These findings demonstrated a distinctive role of IRAK-M in maintaining chronic Th2 airway inflammation via inhibiting the DC-mediated Th1 activation and indicated a complex role for IRAK-M in the initiation and progression of experimental allergic asthma.

Functional annotation of the T-cell immunoglobulin mucin family in birds

T‐cell immunoglobulin and mucin (TIM) family molecules are cell membrane proteins, preferentially expressed on various immune cells and implicated in recognition and clearance of apoptotic cells. Little is known of their function outside human and mouse, and nothing outside mammals. We identified only two TIM genes (chTIM) in the chicken genome, putative orthologues of mammalian TIM1 and TIM4, and cloned the respective cDNAs. Like mammalian TIM1, chTIM1 expression was restricted to lymphoid tissues and immune cells. The gene chTIM4 encodes at least five splice variants with distinct expression profiles that also varied between strains of chicken. Expression of chTIM4 was detected in myeloid antigen‐presenting cells, and in γδ T cells, whereas mammalian TIM4 is not expressed in T cells. Like the mammalian proteins, chTIM1 and chTIM4 fusion proteins bind to phosphatidylserine, and are thereby implicated in recognition of apoptotic cells. The chTIM4–immunoglobulin fusion protein also had co‐stimulatory activity on chicken T cells, suggesting a function in antigen presentation.

Interleukin-12B gene polymorphisms and bronchial asthma risk: A meta-analysis

OBJECTIVE

This meta-analysis aims to investigate whether interleukin-12B (IL-12B) -1188A/C or the promoter polymorphisms may be a risk factor for asthma.

DATA SOURCES

Web of Science, PubMed, China National Knowledge Infrastructure (CNKI) and Wanfang databases were searched (updated August 20, 2015).

STUDY SELECTIONS

Articles evaluating the association between IL-12B genetic polymorphisms and asthma risk were selected.

RESULTS

13 eligible studies with a total of 5092 subjects were finally included in this meta-analysis. For IL-12B -1188A/C, analysis by ethnicity indicated that there was a markedly reduced risk for asthma in East Asian (CC + AC vs. AA: OR = 0.64, 95% CI = 0.50-0.81, P < 0.001). For IL-12B promoter, analysis by ethnicity indicated there was a markedly increased risk in East Asian (MM vs. WM + WW: OR = 1.57, 95% CI = 1.18-2.10, P = 0.002). Analysis by allergic state revealed the similar results in atopic subgroup.

CONCLUSIONS

IL-12B -1188 C allele may be a protective factor against asthma in East Asian. In addition, promoter MM genotype may be a risk factor for asthma in East Asian and allergic people.

Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases

Genome-wide association studies (GWASs) have identified loci that are robustly associated with asthma and related phenotypes; however, the molecular mechanisms underlying these associations need to be explored. The most relevant tissues to study the functional consequences of asthma are the airways. We used publically available data to derive expression quantitative trait loci (eQTLs) for human epithelial cells from small and large airways and applied the eQTLs in the interpretation of GWAS results of asthma and related phenotypes. For the small airways (n = 105), we discovered 660 eQTLs at a 10% false discovery rate (FDR), among which 315 eQTLs were not previously reported in a large-scale eQTL study of whole lung tissue. A large fraction of the identified eQTLs is supported by data from Encyclopedia of DNA Elements (ENCODE) showing that the eQTLs reside in regulatory elements (57.5 and 67.6% of cis- and trans-eQTLs, respectively). Published pulmonary GWAS hits were enriched as airway epithelial eQTLs (9.2-fold). Further, genes regulated by asthma GWAS loci in epithelium are significantly enriched in immune response pathways, such as IL-4 signaling (FDR, 5.2 × 10(-4)). The airway epithelial eQTLs described in this study are complementary to previously reported lung eQTLs and represent a powerful resource to link GWAS-associated variants to their regulatory function and thus elucidate the molecular mechanisms underlying asthma and airway-related conditions.

Polymorphisms of RAD50, IL33 and IL1RL1 are associated with atopic asthma in Chinese population

Genetic architecture of asthma remains obscure. This study aimed to investigate whether the genetic polymorphisms of CDHR3 (rs6967330), GSDMB (rs2305480), IL33 rs928413, RAD50 (rs6871536) and IL1RL1 (rs1558641) are associated with the development of atopic asthma in Chinese population. Genotype and allele frequencies were compared between 516 patients and 552 controls by Chi-square test. Patients were found to have significantly higher allele G of rs928413 and allele C of rs6871536 (9.5% vs 6.2%, P = 0.004 for rs928413; 26.1% vs 19.9%, P < 0.001 for rs6871536). Besides, patients were found to have significantly lower frequency of allele A of rs1558641 (17.2% vs 21.7%, P = 0.007). This is the first study validating that IL33, IL1R1, and RAD50 genes are associated with the risk of asthma in Chinese population.

Naturally Occurring Missense Mutation in Plasma PAF-AH Among the Japanese Population

A single nucleotide polymorphism in the plasma PAF-AH enzyme, i.e., G994T, which causes the substitution of Val at amino acid 279 with Phe (V279F), has been found in the Japanese population. This enzyme preferentially degrades oxidatively modulated or truncated phospholipids; therefore, it has been suggested that this enzyme may prevent the accumulation of proinflammatory and proatherogenic oxidized phospholipids. This hypothesis is supported by the higher prevalence of the V279F mutation in patients with asthmatic and atherosclerotic diseases, as compared with healthy controls. This mutation is rare in the Caucasian population. The plasma PAF-AH mass and enzyme activity are distributed over a wide range in the plasma and they are positively correlated with low-density lipoprotein (LDL) cholesterol. However, several clinical studies in the Caucasian population have suggested that this enzyme has the opposite role. This enzyme plays an active role in the development and progression of atherosclerosis via proinflammatory and proatherogenic lysophosphatidylcholine and oxidized fatty acids produced through the oxidation of LDL by this enzyme. Thus, plasma PAF-AH is a unique enzyme with dual roles in human inflammatory diseases. In this chapter, on the basis of recent findings we describe the association between a naturally occurring missense mutation in plasma PAF-AH and human diseases especially including atherosclerosis and asthma.

Genetics of allergic diseases

Genome-wide association studies (GWAS) have been employed in the field of allergic disease, and significant associations have been published for nearly 100 asthma genes/loci. An outcome of GWAS in allergic disease has been the formation of national and international collaborations leading to consortia meta-analyses, and an appreciation for the specificity of genetic associations to sub-phenotypes of allergic disease. Molecular genetics has undergone a technological revolution, leading to next-generation sequencing strategies that are increasingly employed to hone in on the causal variants associated with allergic diseases. Unmet needs include the inclusion of diverse cohorts and strategies for managing big data.

IFNG+874A/T polymorphisms and IFNG CA repeat polymorphism associated with asthma in Asian--a meta-analysis

INTRODUCTION

Asthma is an etiologically complex disease and develops by the interaction of multiple genes and environmental factors. Previous studies suggested a linkage between the interferon-gamma (INFG) gene cluster in the chromosome 12q region and susceptibility to asthma.

METHODS

This meta-analysis was undertaken to examine the relationship between +874A/T and CA-repeat polymorphisms in INFG gene and asthma. Eligible articles were accumulated via online databases in October 2013. A total of nine articles were included that were associated with the +874A/T polymorphism, involving 470 cases and 574 controls, as well as articles involving CA-repeat polymorphisms, which included 365 cases and 517 controls. The meta-analysis was performed for heterogeneity and calculation of pooled odds ratio and evaluation of publication bias by Egger's linear regression test.

RESULTS

The differences between IFNG polymorphism and the susceptibility to asthma may vary across ethnicities and ages, and also that the allelic frequencies of the AA genotypes in IFNG at +874 is associated with an increased risk of asthma in the Chinese Han adult population; additionally, CA14 occurrence in the first intron can increase the risk of asthma in the Japanese population.

CONCLUSION

Our findings suggested that some polymorphisms in the IFNG gene could act as high prevalence-susceptibility markers of asthma. Larger scale studies are warranted to address these associations among different ethnic populations, ages and the severity of asthma prognosis.

Introduction to genetics and genomics in asthma: genetics of asthma

While asthma is a heterogeneous disease, a strong genetic basis has been firmly established. Rather than being a single disease entity, asthma consists of related, overlapping syndromes [Barnes (Proc Am Thor Soc 8:143-148, 2011)] including three general domains: variable airway obstruction, airway hyper-responsiveness, and airway inflammation with a considerable proportion, but not all, of asthma being IgE-mediated further adding to its heterogeneity. This chapter reviews the approaches to the elucidation of genetics of asthma from the early evidence of familial clustering to the current state of knowledge with genome-wide approaches. The conclusion is that research efforts have led to a tremendous repository of genetic determinants of asthma, most of which fall into the above phenotypic domains of the syndrome. We now look to future integrative approaches of genetics, genomics (Chap. 10), and epigenetics (Chap. 11) to better understand the causal mechanism through which, these genetic loci act in manifesting asthma.

Gene polymorphisms of Interleukin-4 in allergic rhinitis and its association with clinical phenotypes

BACKGROUND

Allergic rhinitis (AR) is an inflammatory disorder of the upper airway. T-helper (Th)2 cytokines seems to have major roles behind the scene of unpleasant symptoms resulted from AR. Expression of interleukin (IL)-4 and its receptor could be affected by single nucleotide polymorphisms (SNPs). This study assessed the effect of 4 genetic variants within genes of IL-4 and IL-4R in AR.

METHODS

Allele frequencies of one IL-4R variant (rs1801275) and three SNPs of IL-4 (rs2243248, rs2243250, and rs2070874) were investigated in 98 patients with AR, compared to a group of controls, using PCR sequence-specific-primers (PCR-SSP) method.

RESULTS

Homozygosity for the C allele of rs2243250 in IL-4 was significantly overrepresented in the patient group. CC genotype in rs2070874 significantly was correlated with AR. GG/CC/CC and TT/TT/TT (rs2243248, rs2243250, and rs2070874) haplotypes in the IL-4 gene had a significant negative correlation with AR.

CONCLUSION

SNPs in IL-4 are associated with AR and could change the clinical picture of the disease in patients.

Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene

Asthma is a common chronic respiratory disease characterized by airway hyperresponsiveness (AHR). The genetics of asthma have been widely studied in mouse and human, and homologous genomic regions have been associated with mouse AHR and human asthma-related phenotypes. Our goal was to identify asthma-related genes by integrating AHR associations in mouse with human genome-wide association study (GWAS) data. We used Efficient Mixed Model Association (EMMA) analysis to conduct a GWAS of baseline AHR measures from males and females of 31 mouse strains. Genes near or containing SNPs with EMMA p-values <0.001 were selected for further study in human GWAS. The results of the previously reported EVE consortium asthma GWAS meta-analysis consisting of 12,958 diverse North American subjects from 9 study centers were used to select a subset of homologous genes with evidence of association with asthma in humans. Following validation attempts in three human asthma GWAS (i.e., Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG) and two human AHR GWAS (i.e., SHARP, DAG), the Kv channel interacting protein 4 (KCNIP4) gene was identified as nominally associated with both asthma and AHR at a gene- and SNP-level. In EVE, the smallest KCNIP4 association was at rs6833065 (P-value 2.9e-04), while the strongest associations for Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG were 1.5e-03, 1.0e-03, 3.1e-03 at rs7664617, rs4697177, rs4696975, respectively. At a SNP level, the strongest association across all asthma GWAS was at rs4697177 (P-value 1.1e-04). The smallest P-values for association with AHR were 2.3e-03 at rs11947661 in SHARP and 2.1e-03 at rs402802 in DAG. Functional studies are required to validate the potential involvement of KCNIP4 in modulating asthma susceptibility and/or AHR. Our results suggest that a useful approach to identify genes associated with human asthma is to leverage mouse AHR association data.

CD14 gene polymorphism is not associated with asthma but rather with bronchial obstruction and hyperreactivity in Slovenian children with non-atopic asthma

BACKGROUND

Though the associations of CD14 with asthma have already been studied, the results of different independent studies are in conflict, mostly due to differences in the pathogenesis of varying asthma sub-phenotypes. The aim of our study was to perform an association analysis of promoter single nucleotide polymorphism (SNP) -159C/T (rs2569190) in the CD14 gene for Slovenian children with asthma.

METHODS

We analyzed SNP -159C/T in a group of all asthmatics, and separately in a group of atopic and non-atopic asthmatics. We also analyzed the influence of SNP -159C/T on clinical parameters and the response to therapy with inhaled corticosteroids. We have genotyped 247 children with asthma and a median age of 11 years (interquartile range, 5 years), and 158 healthy controls with a median age of 13 years (interquartile range, 5 years). We performed genotyping using a polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis.

RESULTS

We found that SNP -159C/T in CD14 is not associated with asthma in Slovenian children. However, non-atopic asthmatics with CT or TT genotypes have a lower FEV1/FVC ratio as a measure of bronchial obstruction (87.4%, compared to 91.8% in patients with the CC genotype, p = 0.017). Non-atopic asthmatics with CC or CT genotypes also have increased bronchial hyperreactivity measured by PC20 of methacholine (0.41 mg/ml, compared to 1.50 mg/ml in patients with a TT genotype, p = 0.018).

CONCLUSIONS

Our results suggest that CD14 is associated with asthma severity in Slovenian children with non-atopic asthma.

Association of ADAM33 polymorphisms with childhood asthma in a northern Chinese population

BACKGROUND

Genetic factors contribute to the increasing incidence of childhood asthma. The ADAM33 (a disintegrin and metalloprotease domain-containing protein 33) gene, discovered through positional cloning, is the first to be associated with asthma and bronchial hyperresponsiveness. This case-control study conducted in a Han Chinese population in northern China compared the genotypes of child asthmatic patients to healthy controls for the presence of 6 single nucleotide polymorphisms (SNPs) in the ADAM33 gene.

METHODS

The study population was composed of 412 children with asthma and 397 healthy controls. We genotyped 6 SNPs (F+1, T+1, T2, T1, V4, and Q-1) of ADAM33 with the PCR-restriction fragment length polymorphism (PCR-RFLP) method. Data were statistically analyzed to determine if an association existed between these genotypes and childhood asthma morbidity.

RESULTS

Three SNPs (T+1, T1, and V4) and 4 haplotypes (H1, H3, H5, and H8) were strongly associated with childhood asthma in children of northern China compared to healthy controls (P<0.05), whereas the other tested SNPs and haplotypes demonstrated no significant relationship.

CONCLUSION

The ADAM33 gene plays an important role in facilitating susceptibility to childhood asthma in this Han Chinese population.

Association of 5-hydroxytryptamine (serotonin) receptor 4 (5-HTR4) gene polymorphisms with asthma

BACKGROUND AND OBJECTIVE

The neurotransmitter, 5-hydroxytryptamine, acts as an immunomodulator by stimulating the release of inflammatory cytokines and regulating the function of dendritic cells and monocytes. The 5-hydroxytryptamine receptor 4 (HTR4) gene is located in a region previously linked to an increased risk of asthma and atopy. The aim of this study was to investigate the association between HTR4 and asthma.

METHODS

Thirty-two single nucleotide polymorphisms (SNP) in HTR4 were investigated by direct sequencing of 24 DNA samples from unrelated Korean subjects.

RESULTS

The 32 genetic variants comprised 22 intronic SNP, two SNP in the 3'-untranslated region (exon 7) and eight SNP in the 3'-downstream region. Logistic regression analysis showed that two intronic polymorphisms were significantly associated with the risk of asthma. Two minor HTR4 alleles, +142828G>A and +122769G>A, occurred at significantly higher frequencies in the asthmatic group than in the healthy control group (49.59% vs 42.29%, P=0.003, and 47.99% vs 40.35%, P=0.008, respectively), and these differences remained significant after correction for multiple testing (P=0.05, dominant mode of inheritance; and P=0.03, dominant mode, respectively). Haplotype analysis revealed three haplotype blocks. The frequency of haplotype 1 in block 2 was significantly higher in asthmatics (P=0.003, dominant mode), whereas the frequency of haplotype 4 in block 3 was significantly lower in asthmatics (P=0.0009, dominant mode).

CONCLUSIONS

SNP and haplotypes of the HTR4 gene were associated with the asthma phenotype and genetic variation of HTR4 may affect susceptibility to the development of asthma.

The association of a single-nucleotide polymorphism of the IL-2 inducible T-cell Kinase gene with asthma

Asthma manifests as TH2-dominant airway inflammation regulated by inducible T-cell kinase (ITK). To investigate associations between genetic variants of the ITK gene and asthma, 31 single-nucleotide polymorphisms (SNPs) were genotyped in 303 normal controls and 498 asthmatics and the two groups were compared using logistic regression models. The functional effects of the ITK promoter SNP were assessed using pGL3 luciferase reporter systems and gel-shift assays. The minor allele-196C>T in the promoter region of the ITK gene was significantly more frequent in asthmatics than in controls. The luciferase activity of the PGL3-ITK-196T allele construct was higher than that of the -196C allele. In the gel-shift assay, -196T double-stranded oligonucleotides bound more strongly to Jurkat cell nuclear protein compared to the -196C double-stranded oligonucleotides. People with the -rare allele 196C>T may be more susceptible to asthma via transcriptional regulation of the ITK gene.

Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1)

BACKGROUND

Asthma is a common, chronic inflammatory airway disease of major public health importance with multiple genetic determinants. Previously, we found by positional cloning that PHD finger protein 11 (PHF11) on chromosome 13q14 modifies serum immunoglobulin E (IgE) concentrations and asthma susceptibility. No coding variants in PHF11 were identified.

OBJECTIVE

Here we investigate the 3 single nucleotide polymorphisms (SNPs) in this gene most significantly associated with total serum IgE levels--rs3765526, rs9526569, and rs1046295--for a role in transcription factor binding.

METHODS

We used electrophoretic mobility shift assays to examine the effect of the 3 SNPs on transcription factor binding in 3 cell lines relevant to asthma pathogenesis. Relative preferential expression of alleles was investigated by using the allelotyping method.

RESULTS

Electrophoretic mobility shift assays show that rs1046295 modulates allele-specific binding by the octamer-binding transcription factor 1 (Oct-1). Analysis of the relative expression levels of the 2 alleles of this SNP in heterozygous individuals showed a modest, but highly significant (P = 6.5 × 10(-16)), preferential expression of the A allele consistent with a functional role for rs1046295.

CONCLUSION

These results suggest a mechanism by which rs1046295 may act as a regulatory variant modulating transcription at this locus and altering asthma susceptibility.

The -112G>A polymorphism of the secretoglobin 3A2 (SCGB3A2) gene encoding uteroglobin-related protein 1 (UGRP1) increases risk for the development of Graves' disease in subsets of patients with elevated levels of immunoglobulin E

The human secretoglobin 3A2 (SCGB3A2) gene encoding secretory uteroglobin-related protein 1 (UGRP1) resides on the chromosome region 5q31-33 that harbors a susceptibility locus to several autoimmune and inflammatory diseases, including asthma and Graves' disease (GD). Recently, association between the marker rs1368408 (-112G >A), located in the promoter region of the SCGB3A2 gene, and susceptibility to GD was found in Chinese and UK Caucasians. The study aim was to evaluate whether this polymorphism confers GD susceptibility in a large population cohort comprising 1,474 Russian GD patients and 1,619 controls. The marker rs1368408 was studied using a TaqMan allele discrimination assay. Serum levels of UGRP1 and immunoglobulin E (IgE) were assessed using enzyme-linked immunosorbent assay (ELISA) analyses. Association between the allele A of SCGB3A2 and a higher risk of GD (odds ratio [OR] = 1.33, P = 2.9 × 10(-5)) was shown. Both affected and non-affected carriers of the higher risk genotype A/A had significantly decreased levels of serum UGRP1 compared to the subjects homozygous for G/G (93 ± 37 pg/ml vs. 132 ± 45 pg/ml, P = 0.0011 for GD patients; 77 ± 28 pg/ml vs. 119 ± 33 pg/ml, P = 0.0019 for controls). Serum IgE levels were significantly higher in non-affected subjects homozygous for A/A compared to control individuals homozygous for G/G (153 ± 46 IU/ml vs. 122 ± 40 IU/ml, P = 0.0095). Our data suggest that the carriage of the SCGB3A2 -112A/A variant increases the risk for GD in subsets of patients with elevated levels of IgE, a hallmark of allergic asthma. Therefore, the SCGB3A2 -112G >A polymorphism may be considered as a likely marker linking susceptibility to allergy/asthma and GD on chromosome 5q31-33.

Genomewide association studies in allergy and the influence of ethnicity

PURPOSE OF REVIEW

Asthma and allergic diseases are common and disproportionately affect racial and ethnic minorities. Large-scale research efforts and the expense committed to multiple genomewide association studies (GWAS) have led to the identification of numerous susceptibility loci for the allergic diseases, but few successes have been reported in populations that are not of European ancestry.

RECENT FINDINGS

Of the more than two dozen GWAS for asthma and allergic disease performed to date, very few have included racial/ethnic minorities. Lessons learned from the studies conducted so far suggest that the GWAS approach must include considerations unique to the ancestral populations represented in the sample, population stratification due to admixture, and recognition that the current coverage of common variants both in the public database and on commercially available single-nucleotide polymorphism chips is inadequate to detect true genetic associations among ethnic/racial groups.

SUMMARY

Advancements in the GWAS technology for identifying genes relevant to asthma and allergic disease among under-represented ethnic and racial minorities who suffer most will facilitate the identification and confirmation of validated genetic risk factors that are both unique to minority groups as well as confirm risk factors that are generic to the population at large.

Two polymorphisms in the TIM-4 gene are associated with asthma in a Chinese Han population

The gene family of the T cell immunoglobulin and mucin domain (TIM) proteins encodes cell surface receptors that are involved in the regulation of Th1- and Th2-cell-mediated immunity. TIM-1 gene has been found to be associated with asthma in several populations. TIM-4, the natural ligand for TIM-1, may influence the susceptility to asthma.To investigate the association of the TIM-4 gene polymorphisms with asthma in a Chinese Han population. Three single nucleotide polymorphisms (SNPs) in TIM-4 gene, rs6882076, rs12658558 and rs4702747, were genotyped in 551 unrelated asthma patients and 549 healthy controls. We found that two SNPs of the TIM-4 gene, rs6882076 and rs4702747, were associated with asthma susceptibility in our study population (with P-values = 0.009 and 0.005 respectively). No association was observed between asthma and rs12658558. Our results suggest that TIM-4 gene polymorphisms are associated with asthma in a Chinese Han population.

Association between colony-stimulating factor 1 receptor gene polymorphisms and asthma risk

Colony-stimulating factor 1 receptor (CSF1R) is expressed in monocytes/macrophages and dendritic cells. These cells play important roles in the innate immune response, which is regarded as an important aspect of asthma development. Genetic alterations in the CSF1R gene may contribute to the development of asthma. We investigated whether CSF1R gene polymorphisms were associated with the risk of asthma. Through direct DNA sequencing of the CSF1R gene, we identified 28 single nucleotide polymorphisms (SNPs) and genotyped them in 303 normal controls and 498 asthmatic patients. Expression of CSF1R protein and mRNA were measured on CD14-positive monocytes and neutrophils in peripheral blood of asthmatic patients using flow cytometry and real-time PCR. Among the 28 polymorphisms, two intronic polymorphism (+20511C>T and +22693T>C) were associated with the risk of asthma by logistic regression analysis. The frequencies of the minor allele at CSF1R +20511C>T and +22693T>C were higher in asthmatic subjects than in normal controls (4.6 vs. 7.7%, p = 0.001 in co-dominant and dominant models; 16.4 vs. 25.8%, p = 0.0006 in a recessive model). CSF1R mRNA levels in neutrophils of the asthmatic patients having the +22693CC allele were higher than in those having the +22693TT allele (p = 0.026). Asthmatic patients with the +22693CC allele also showed significantly higher CSF1R expression on CD14-positive monocytes and neutrophils than did those with the +22693TT allele (p = 0.045 and p = 0.044). The +20511C>T SNP had no association with CSF1R mRNA or protein expression. In conclusion, the minor allele at CSF1R +22693T>C may have a susceptibility effect in the development of asthma, via increased CSF1R protein and mRNA expression in inflammatory cells.

Association and gene-gene interactions of eight common single-nucleotide polymorphisms with pediatric asthma in middle china

BACKGROUND

Asthma is a common polygenic disease, caused by complex interactions between multiple genes and environmental factors. Study of the gene-gene interactions would contribute to a new insight into the pathogenesis and therapeutics of asthma.

OBJECTIVE

To evaluate the single and combined associations of eight single-nucleotide polymorphisms loci in five candidate genes with the development of asthma in Chinese children.

METHODS

We examined eight single-nucleotide polymorphisms (SNPs) in five key asthma susceptibility genes and performed single SNP association study, haplotype analysis, and gene-gene interactions analysis in 479 Chinese children, including 252 asthmatic subjects and 227 healthy controls. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Haplotype analysis was detected by SHEsis software. Gene-gene interactions were tested using the multifactor dimensionality reduction (MDR) method.

RESULTS

There were significant differences of interleukin (IL)-13 R130Q and IL-13 C1923T in genotype and allele frequency distributions between the asthmatic group and control group. Furthermore, the A allele of IL-13 R130Q and the T allele of IL-13 C1923T were significantly associated with increased risk of asthma (odds ratio [OR] = 1.59, 95% confidence interval [CI] 1.20-2.09, p = .0010; OR = 1.57, 95% CI 1.19-2.08, p = .0014, respectively). By haplotype analysis, the C-G and T-A haplotypes consisting of IL-13 C1923T and IL-13 R130Q and the G-A and A-A haplotypes consisting of IL-4Ralpha I75V and IL-4Ralpha Q576R were significantly associated with asthma (p < .05). Using MDR, the authors detected significant gene-gene interactions with a best six-locus model among IL-4 -C33T, IL-13 R130Q, IL-4Ralpha I75V, IL-4Ralpha Q576R, STAT6 C2892T, and CD14 -C159T on the risk of asthma (OR = 4.43, 95% CI 1.30-15.04, p < .001, by 1000-fold permutation test).

CONCLUSIONS

These data suggest that genetic variants in the IL-13 gene may play an important role in the development of pediatric asthma in Middle China. In addition, the significant gene-gene interactions among IL-4 -C33T, IL-13 R130Q, IL-4Ralpha I75V, IL-4Ralpha Q576R, STAT6 C2892T, and CD14 -C159T may increase an individual's susceptibility to asthma and contribute to the pathogenesis of asthma.

A new association between polymorphisms of the SLC6A7 gene in the chromosome 5q31-32 region and asthma

The human chromosomal 5q31-33 region has been implicated as a susceptibility locus for several immune-mediated diseases including asthma in several populations. Recently, the extraneuronal GABAergic system has been implicated as a new link to airway obstruction in asthma. In addition, the SLC6A7 gene, which is positioned at 5q31-32 and encodes the transporter for an excitatory neurotransmitter of L-proline, has never been studied for its association with asthma. In this study, resequencing of all exon, promoter region (2 kb), and exon-intron boundary regions in the SLC6A7 gene found a total of 33 single nucleotide polymorphisms (SNPs) in 24 Korean asthmatic patients. After the initial SNP survey, a total of 17 common SNPs with minor allele frequency (MAF) over 10% were genotyped in 498 asthmatic patients and 303 normal controls. Logistic analyses revealed significant associations between genetic variants of the SLC6A7 gene and asthma (P-value up to 6.0 x 10(-4); P(corr) value up to 0.009). In further regression analyses, minor alleles of intronic +11431T>C, +12213C>T and +12927A>G in linkage disequilibrium block 2 and +20113T>C in 3'UTR significantly increased the bronchodilator response in asthmatics (P-value of recessive model up to 0.008; which are not significant after multiple correction). Therefore, our findings suggest that SLC6A7 could be a susceptible gene for asthma.

Meta-analysis of 20 genome-wide linkage studies evidenced new regions linked to asthma and atopy

Asthma is caused by a heterogeneous combination of environmental and genetic factors. In the context of GA2LEN (Global Allergy and Asthma European Network), we carried out meta-analyses of almost all genome-wide linkage screens conducted to date in 20 independent populations from different ethnic origins (>or=3024 families with >or=10 027 subjects) for asthma, atopic asthma, bronchial hyper-responsiveness and five atopy-related traits (total immunoglobulin E level, positive skin test response (SPT) to at least one allergen or to House Dust Mite, quantitative score of SPT (SPTQ) and eosinophils (EOS)). We used the genome scan meta-analysis method to assess evidence for linkage within bins of traditionally 30-cM width, and explored the manner in which these results were affected by bin definition. Meta-analyses were conducted in all studies and repeated in families of European ancestry. Genome-wide evidence for linkage was detected for asthma in two regions (2p21-p14 and 6p21) in European families ascertained through two asthmatic sibs. With regard to atopy phenotypes, four regions reached genome-wide significance: 3p25.3-q24 in all families for SPT and three other regions in European families (2q32-q34 for EOS, 5q23-q33 for SPTQ and 17q12-q24 for SPT). Tests of heterogeneity showed consistent evidence of linkage of SPTQ to 3p11-3q21, whereas between-study heterogeneity was detected for asthma in 2p22-p13 and 6p21, and for atopic asthma in 1q23-q25. This large-scale meta-analysis provides an important resource of information that can be used to prioritize further fine-mapping studies and also be integrated with genome-wide association studies to increase power and better interpret the outcomes of these studies.

A genome-wide association study on African-ancestry populations for asthma

BACKGROUND

Asthma is a complex disease characterized by striking ethnic disparities not explained entirely by environmental, social, cultural, or economic factors. Of the limited genetic studies performed on populations of African descent, notable differences in susceptibility allele frequencies have been observed.

OBJECTIVES

We sought to test the hypothesis that some genes might contribute to the profound disparities in asthma.

METHODS

We performed a genome-wide association study in 2 independent populations of African ancestry (935 African American asthmatic cases and control subjects from the Baltimore-Washington, DC, area and 929 African Caribbean asthmatic subjects and their family members from Barbados) to identify single-nucleotide polymorphisms (SNPs) associated with asthma.

RESULTS

A meta-analysis combining these 2 African-ancestry populations yielded 3 SNPs with a combined P value of less than 10(-5) in genes of potential biologic relevance to asthma and allergic disease: rs10515807, mapping to the alpha-1B-adrenergic receptor (ADRA1B) gene on chromosome 5q33 (3.57 x 10(-6)); rs6052761, mapping to the prion-related protein (PRNP) gene on chromosome 20pter-p12 (2.27 x 10(-6)); and rs1435879, mapping to the dipeptidyl peptidase 10 (DPP10) gene on chromosome 2q12.3-q14.2. The generalizability of these findings was tested in family and case-control panels of United Kingdom and German origin, respectively, but none of the associations observed in the African groups were replicated in these European studies. Evidence for association was also examined in 4 additional case-control studies of African Americans; however, none of the SNPs implicated in the discovery population were replicated.

CONCLUSIONS

This study illustrates the complexity of identifying true associations for a complex and heterogeneous disease, such as asthma, in admixed populations, especially populations of African descent.

Identification of PCDH1 as a novel susceptibility gene for bronchial hyperresponsiveness

RATIONALE

Asthma is a chronic inflammatory airway disease that affects more than 300 million individuals worldwide. Asthma is caused by interaction of genetic and environmental factors. Bronchial hyperresponsiveness (BHR) is a hallmark of asthma and results from increased sensitivity of the airways to physical or chemical stimulants. BHR and asthma are linked to chromosome 5q31-q33.

OBJECTIVES

To identify a gene for BHR on chromosome 5q31-q33.

METHODS

In 200 Dutch families with asthma, linkage analysis and fine mapping were performed, and the Protocadherin 1 gene (PCDH1) was identified. PCDH1 was resequenced in 96 subjects from ethnically diverse populations to identify novel sequence variants. Subsequent replication studies were undertaken in seven populations from The Netherlands, the United Kingdom, and the United States, including two general population samples, two family samples, and three case-control samples. PCDH1 mRNA and protein expression was investigated using polymerase chain reaction, Western blotting, and immunohistochemistry.

MEASUREMENTS AND MAIN RESULTS

In seven out of eight populations (n = 6,168) from The Netherlands, United Kingdom, and United States, PCHD1 gene variants were significantly associated with BHR (P values, 0.005-0.05) This association was present in both families with asthma and general populations. PCDH1 mRNA and protein were expressed in airway epithelial cells and in macrophages.

CONCLUSIONS

PCDH1 is a novel gene for BHR in adults and children. The identification of PCDH1 as a BHR susceptibility gene may suggest that a structural defect in the integrity of the airway epithelium, the first line of defense against inhaled substances, contributes to the development of BHR.

Association between genotypes and phenotypes in coeliac disease

BACKGROUND

Coeliac disease (CD) is a genetically driven immunological intolerance to dietary gluten with a wide range of clinical presentations. The aim of this study was to investigate the heritability of the phenotype in CD and the influence on the phenotype of different genes associated with the disease.

PATIENTS AND METHODS

One hundred and seven families with at least 2 siblings with CD were collected. The patients were grouped in symptom grades on the basis of the clinical presentation, the age at diagnosis, and sex. Stratification analyses of the human leucocyte antigen-DQA1 and human leucocyte antigen-DQB1 genotypes, the CTLA4 +49A/G polymorphism, the CTLA4 haplotype MH30*G:-1147*T:+49*A:CT60*G:CT61*A, and the 5q31-33 loci were done.

RESULTS

The heritability of the phenotype was estimated to be 0.45. Significant association and linkage was found between the clinical presentation and the CTLA4 +49A/G polymorphism but not for the other genotypes. No correlation was found between genotypes and age at diagnosis or sex.

CONCLUSIONS

Our results indicate that the heritability is determiner of the phenotype in CD. The CTLA4 +49A/G polymorphism is correlated to the clinical presentation: the AA genotype is associated with clinically silent disease.

A multiple splitting approach to linkage analysis in large pedigrees identifies a linkage to asthma on chromosome 12

Large genealogies are potentially very informative for linkage analysis. However, the software available for exact non-parametric multipoint linkage analysis is limited with respect to the complexity of the families it can handle. A solution is to split the large pedigrees into sub-families meeting complexity constraints. Different methods have been proposed to "best" split large genealogies. Here, we propose a new procedure in which linkage is performed on several carefully chosen sub-pedigree sets from the genealogy instead of using just a single sub-pedigree set. Our multiple splitting procedure capitalizes on the sensitivity of linkage results to family structure and has been designed to control computational feasibility and global type I error. We describe and apply this procedure to the extreme case of the highly complex Hutterite pedigree and use it to perform a genome-wide linkage analysis on asthma. The detection of a genome-wide significant linkage for asthma on chromosome 12q21 illustrates the potential of this multiple splitting approach.

A functional polymorphism in the SPINK5 gene is associated with asthma in a Chinese Han Population

BACKGROUND

Mutation in SPINK5 causes Netherton syndrome, a rare recessive skin disease that is accompanied by severe atopic manifestations including atopic dermatitis, allergic rhinitis, asthma, high serum IgE and hypereosinophilia. Recently, single nucleotide polymorphism (SNP) of the SPINK5 was shown to be significantly associated with atopy, atopic dermatitis, asthma, and total serum IgE. In order to determine the role of the SPINK5 in the development of asthma, a case-control study including 669 asthma patients and 711 healthy controls in Han Chinese was conducted.

METHODS

Using PCR-RFLP assay, we genotyped one promoter SNP, -206G>A, and four nonsynonymous SNPs, 1103A>G (Asn368Ser), 1156G>A (Asp386Asn), 1258G>A (Glu420Lys), and 2475G>T (Glu825Asp). Also, we analyzed the functional significance of -206G>A using the luciferase reporter assay and electrophoresis mobility shift assay.

RESULTS

we found that the G allele at SNP -206G>A was associated with increased asthma susceptibility in our study population (p = 0.002, odds ratio 1.34, 95% confidence interval 1.11-1.60). There was no significant association between any of four nonsynonymous SNPs and asthma. The A allele at -206G>A has a significantly higher transcriptional activity than the G allele. Electrophoresis mobility shift assay also showed a significantly higher binding efficiency of nuclear protein to the A allele compared with the G allele.

CONCLUSION

Our findings indicate that the -206G>A polymorphism in the SPINK5 is associated with asthma susceptibility in a Chinese Han population.

Beta 2-adrenergic polymorphisms and total serum IgE levels in children with asthma from Argentina

BACKGROUND

Beta 2-Adrenergic receptor polymorphisms occurring at amino acid positions 16 (arginine/glycine) and 27 (glutamine/glutamic acid) are known to be functionally relevant. Associations with several asthma-related phenotypes, such as total serum IgE, have been investigated with different results.

OBJECTIVE

To determine the contribution of polymorphisms and haplotypes of beta 2-adrenergic receptor with serum IgE levels in children from Argentina with mild, moderate, and severe asthma.

METHODS

Beta 2-Adrenergic receptor polymorphisms were analyzed in 124 white asthmatic children using polymerase chain reaction during a 3-year period (January 1, 2005, through December 31, 2007). Total serum IgE level was measured by standard methods in all study participants, and age-adjusted values were determined for each individual.

RESULTS

Serum levels of IgE were 4.3-fold higher than age-adjusted normal values in the study population. No association was found in regard to asthma severity. A significant difference of IgE serum levels was observed among polymorphisms at position 16, with the highest IgE level in the arginine/arginine group (P = .04). At position 27, even though median levels of IgE in homozygous glutamine were 2.2 times higher than homozygous glutamic acid, this increase did not reach statistical significance. When the population was stratified according to the most common homozygous haplotypes (arginine-arginine 16/glutamine-glutamine 27, glycine-glycine 16/glutamine-glutamine 27, and glycine-glycine 16/glutamic acid-glutamic acid 27), no association was found in relation to the serum levels of IgE.

CONCLUSIONS

Beta 2-Adrenergic receptor polymorphisms, especially homozygous arginine 16, were associated with higher serum IgE levels in children with asthma. These genetic variants appear to contribute to the IgE level in asthmatic children from Argentina.

Linkage of atopic dermatitis to chromosomes 4q22, 3p24 and 3q21

Atopic dermatitis (AD) is a common, itchy skin disease of complex inheritance characterized by dermal and epidermal inflammation. The heritability is considerable and well documented. To date, four genome scans have examined the AD phenotype, showing replicated linkage at 3p26-22, 3q13-21 and 18q11-21. Our previous AD scan showed evidence of linkage to loci at 3p and 18q, and furthermore at 4p15-14. In order to further investigate the genetic basis of AD, we collected and analysed a new Danish family sample consisting of 130 AD sib pair families (555 individuals including 295 children with AD). AD was diagnosed after clinical examination, AD severity was scored and specific IgE was determined. A linkage scan of chromosome 3, 4 and 18 was performed using 91 microsatellite markers. Linkage analyses were performed of dichotomous phenotypes and semi-quantitative traits including the AD severity score. We analysed the novel AD sample alone and together with the previously examined sample. AD severity showed a maximum Z-score of 3.7 at 4q22.1 suggesting the localization of a novel gene for AD severity. A maximum MOD score of 4.6 was obtained at 3p24 for the AD phenotype, providing the first significant linkage of AD at this locus. A maximum MLS score of 3.3 was obtained at 3q21 for IgE-associated AD, and evidence of linkage was also obtained at 3p22.2-21.31, 3q13, 4q35, and 18q12. The results presented should provide a firm basis for gene-targeting studies of AD and related disorders.

Chromosome 12q24.3 controls sensitization to cat allergen in patients with asthma from Siberia, Russia

In Russian population of Siberia asthma is usually concomitant with high sensitization to indoor allergens (cat, dog and house dust mites), overproduction of total immunoglobulin E (IgE) and airway hyperreactivity. Definition of genes that predispose to development of various sub-components of the asthma phenotype is important for understanding of etiology of this disease. To map genes predisposing to asthma, we tested 21 microsatellite markers from candidate chromosomal regions in 136 Russian nuclear families with asthma from Siberia. We performed non-parametric analysis for linkage with asthma, total IgE, specific IgE to cat, dog, and dust mites, and spirometric indices (FEV1 (%) - percentage of predicted forced expiratory volume in 1s, FVC (%) - percentage of predicted forced vital capacity, and FEV1/FVC (%) - Tiffenau index). The most significant linkage was to the candidate region on chromosome 12. Locus controlling cat-specific IgE, which is the most abundant in asthma patients from Siberian population, mapped within the interval between 136 and 140 cM on chromosome 12q24.3, with the suggestive linkage at the marker D12S1611 (LOD=2.23, P=0.0007). Total IgE was also linked to this region (D12S1611 - LOD=1.12, P=0.012). FEV1 (%) exceeded LOD>1 threshold for significance with the same locus 12q24.3, but with the peak at a more proximal region at 111.87 cM (D12S338 - LOD=1.21, P=0.009). Some evidence of linkage (LOD>1.0) was also detected for asthma at 6p21.31 (D6S291) and total IgE at 13q14.2 (D13S165). These data indicate that the locus 12q24.3 is the most promising candidate for identification of asthma genes in Russian population of Siberia.

Significant evidence for linkage to chromosome 5q13 in a genome-wide scan for asthma in an extended pedigree resource

Asthma is a multifactorial disease with undetermined genetic factors. We performed a genome-wide scan to identify predisposition loci for asthma. The asthma phenotype consisted of physician-confirmed presence or absence of asthma symptoms. We analyzed 81 extended Utah pedigrees ranging from three to six generations, including 742 affected individuals, ranging from 2 to 40 per pedigree. We performed parametric multipoint linkage analyses with dominant and recessive models. Our analysis revealed genome-wide significant evidence of linkage to region 5q13 (log of the odds ratio (LOD)=3.8, recessive model), and suggestive evidence for linkage to region 6p21 (LOD=2.1, dominant model). Both the 5q13 and 6p21 regions indicated in these analyses have been previously identified as regions of interest in other genome-wide scans for asthma-related phenotypes. The evidence of linkage at the 5q13 region represents the first significant evidence for linkage on a genome-wide basis for this locus. Linked pedigrees localize the region to approximately between 92.3-105.5 Mb.

Association of TIM4 promoter polymorphism -1419G>A with childhood asthma in a Chinese Han population

TIM4, which is expressed on dendritic cells and macrophages, plays an important role in the proliferation of T helper type 2 (Th2) cells. Asthma, as a complex genetic disease, is thought to arise from the development of a Th2-lymphocyte-predominant immune response. To evaluate the effects of the promoter polymorphisms (-1419G>A and -1609G>A) in TIM4 on asthma susceptibility, case-control and family-based association studies were conducted by polymerase chain reaction and restriction fragment length polymorphism. Our results showed that TIM4 -1419G>A polymorphism was associated with asthma susceptibility in our study population (chi(2)= 9.88, P < 0.001, OR = 1.91, 95% CI 1.37-2.64). The -1419A/A and -1419A/G genotypes were observed more common in asthmatic group (6.3%, 41.8%) than in control group (1.7%, 29.3%). No significant difference was found in genotype and allele frequencies of TIM4 -1619G>A polymorphism between asthmatic and control groups. No association between the two SNPs and total serum IgE levels, lung function was observed. In conclusion, the present findings suggest that TIM4 -1419G>A polymorphism might be the genetic factor for the risk of childhood asthma in Chinese Han population.

Linkage analysis with dense SNP maps in isolated populations

OBJECTIVE

SNP maps are becoming the gold standard for genetic markers, even for linkage analyses. However, because of the density of SNPs on most high throughput platforms, the resulting significant linkage disequilibrium (LD) can bias classical nonparametric multipoint linkage analyses. This problem may be even stronger in population isolates where LD can extend over larger distances and with a more stochastic pattern. We investigate the issue of linkage analysis with SNPs from the Affymetrix 500K GeneChip array in extended families from the isolated Hutterite population.

METHODS

We minimized LD between SNPs by two methods based on a LD block pattern (Merlin and SNPLINK) and by MASEL, a new algorithm that we proposed to select SNP subsets with minimum LD and with no prior hypothesis about the LD pattern.

RESULTS

Simulations, performed using the real LD pattern observed in the Hutterite population, show that sizeable inflation of linkage statistics persist when LD between SNPs is minimized by Merlin and SNPLINK. Inflation of linkage statistics is better controlled with MASEL.

CONCLUSION

In this population, it may be difficult to extract from standard GeneChip arrays a SNP map without LD-driven bias that is more informative than a dense microsatellite map.

Gene-environment interactions and airway disease in children

Asthma is the most common chronic disease of childhood in the United States, affecting nearly 6.5 million children. The prevalence and severity of childhood asthma have continued to increase over the past 2 decades, despite major advances in the recognition and treatment of this condition. Representing a heterogeneous collection of airway diseases, asthma has multiple pathologic processes resulting from the interactions of genetic susceptibility and environmental exposures. Preventing and treating airway disease in children will require new research approaches to understanding these complex interactions.

Mouse to human comparative genetics reveals a novel immunoglobulin E-controlling locus on Hsa8q12

Atopy is a predisposition to hyperproduction of immunoglobulin E (IgE) against common environmental allergens. It is often associated with development of allergic diseases such as asthma, rhinitis, and dermatitis. Production of IgE is influenced by genetic and environmental factors. In spite of progress in the study of heredity of atopy, the genetic mechanisms of IgE regulation have not yet been completely elucidated. The analysis of complex traits can benefit considerably from integration of human and mouse genetics. Previously, we mapped a mouse IgE-controlling locus Lmr9 on chromosome 4 to a segment of <9 Mb. In this study, we tested levels of total IgE and 25 specific IgEs against inhalant and food allergens in 67 Czech atopic families. In the position homologous to Lmr9 on chromosome 8q12 marked by D8S285, we demonstrated a novel human IgE-controlling locus exhibiting suggestive linkage to composite inhalant allergic sensitization (limit of detection, LOD = 2.11, P = 0.0009) and to nine specific IgEs, with maximum LOD (LOD = 2.42, P = 0.0004) to plantain. We also tested 16 markers at previously reported chromosomal regions of atopy. Linkage to plant allergens exceeding the LOD > 2.0 was detected at 5q33 (D5S1507, LOD = 2.11, P = 0.0009) and 13q14 (D13S165, LOD = 2.74, P = 0.0002). The significant association with plant allergens (quantitative and discrete traits) was found at 7p14 (D7S2250, corrected P = 0.026) and 12q13 (D12S1298, corrected P = 0.043). Thus, the finding of linkage on chromosome 8q12 shows precision and predictive power of mouse models in the investigation of complex traits in humans. Our results also confirm the role of loci at 5q33, 7p14, 12q14, and 13q13 in control of IgE.

Evidence for an asthma risk locus on chromosome Xp: a replication linkage study

BACKGROUND

Asthma is a complex genetic disorder characterized by chronic inflammation in the airways. Identification of genetic risk factors for asthma has been complicated due to genetic heterogeneity and influence from environmental risk factors. Despite the fact that multiple genetic linkage studies have been carried out the results are still conflicting and call for replication experiments. A Danish genome-wide scan has prior reported evidence for candidate regions for asthma susceptibility genes on chromosomes 1p, 5q, 6p, 12q and Xp. Linkage to chromosome 12q was later confirmed in the same replication sample as used in the present study. The aim of the study was to replicate linkage to candidate regions for asthma in an independent Danish sample.

METHODS

We performed a replication study investigating linkage to candidate regions for asthma on chromosomes 1p36.31-p36.21, 5q15-q23.2, 6p24.3-p22.3, and Xp22.31-p11.4 using additional markers in an independent set of 136 Danish asthmatic sib pair families.

RESULTS

Nonparametric multipoint linkage analyses yielded suggestive evidence for linkage to asthma to chromosome Xp21.2 (MLS 2.92) but failed to replicate linkage to chromosomes 1p36.31-p36.21, 5q15-q23.2 and 6p24.3-p22.3.

CONCLUSIONS

The replication results provide evidence for chromosome Xp21 to harbour a susceptibility gene for asthma in the Danish population. To our knowledge, the study is the first to replicate evidence for linkage to chromosome X. A susceptibility gene for asthma on chromosome X could potentially explain observed gender differences in asthma prevalence.

Distribution characteristics and linkage disequilibrium of TIM4 promoter polymorphisms in asthma patients of Chinese Han population

To investigate the distribution characteristics and linkage disequilibrium of T cell immunoglobulin domain and mucin domain protein 4 (TIM4) promoter polymorphisms in asthma patients of Chinese Han population, the promoter region of TIM4 was re-sequenced by PCR-sequencing, and linkage disequilibrium was analyzed by SHEsis software. Four single nucleotide polymorphisms (SNPs) in the promoter region of TIM4 were detected, including two new SNPs (at positions-1609,-153) and two reported SNPs (rs6874202, rs6882076). The frequency distribution of rs6882076 was different among different races (P<0.05). In addition, linkage disequilibrium among the SNPs of the promoter region of TIM4 was found and GGTG was the predominant haplotype. There were four SNPs in the promoter region of TIM4 in asthma patients of Chinese Han population, which were in linkage disequilibrium.

Integrating genomic and clinical medicine: searching for susceptibility genes in complex lung diseases

The integration of molecular, genomic, and clinical medicine in the post-genome era provides the promise of novel information on genetic variation and pathophysiologic cascades. The current challenge is to translate these discoveries rapidly into viable biomarkers that identify susceptible populations and into the development of precisely targeted therapies. In this article, we describe the application of comparative genomics, microarray platforms, genetic epidemiology, statistical genetics, and bioinformatic approaches within examples of complex pulmonary pathobiology. Our search for candidate genes, which are gene variations that drive susceptibility to and severity of enigmatic acute and chronic lung disorders, provides a logical framework to understand better the evolution of genomic medicine. The dissection of the genetic basis of complex diseases and the development of highly individualized therapies remain lofty but achievable goals.

Sex-stratified linkage analysis identifies a female-specific locus for IgE to cockroach in Costa Ricans

RATIONALE

The basis for gender influences on allergen-specific IgEs is unclear.

OBJECTIVES

To perform regular and sex-stratified genomewide linkage analyses of IgE to each of three allergens (Ascaris lumbricoides, Blatella germanica [German cockroach]), and Dermatophagoides pteronyssinus [dust mite]) and to conduct an association study of a candidate gene in a linked genomic region.

METHODS

Genomewide linkage analyses of allergen-specific IgEs were conducted in 653 members of eight large families of Costa Rican children with asthma. An analysis of the association between single-nucleotide polymorphisms in thymic stromal lymphopoietin (TSLP) and IgE measurements was conducted in 417 parent-child trios in Costa Rica. Significant results were replicated in 470 families of white children in the Childhood Asthma Management Program (CAMP).

MEASUREMENTS AND MAIN RESULTS

Among all subjects, there was suggestive evidence of linkage (LOD >/= 2.72) to IgE to Ascaris (on chromosome 7q) and IgE to dust mite (on chromosomes 7p and 12q). In a sex-stratified analysis, there was significant evidence of linkage to IgE to cockroach on chromosome 5q23 (peak LOD, 4.14 at 127 cM) in female subjects. TSLP is located within the 1.5 LOD-unit support interval for this linkage peak and has female-specific effects on lung disease in mice. In a sex-stratified analysis, the T allele of single-nucleotide polymorphism rs2289276 in TSLP was associated with reductions in IgE to cockroach (in Costa Rican girls) and total IgE (in girls in Costa Rica and in CAMP; P value for sex-by-genotype interaction, <0.01 in both studies).

CONCLUSIONS

Consistent with findings in murine models, a variant in TSLP may have female-specific effects on allergic phenotypes.

Genetics of asthma: potential implications for reducing asthma disparities

Although genetic factors may partly explain the differences in asthma prevalence, morbidity, and mortality among ethnic groups in the United States, few studies of the genetics of asthma have included members of ethnic minority groups. Only one genome-wide linkage analysis of asthma and/or asthma-related phenotypes (conducted by the Collaborative Study on the Genetics of Asthma) has included any members of ethnic minority populations. The interpretation of the findings of genetic association studies of asthma in ethnic minority groups is complicated by reduced statistical power due to small sample sizes; the failure to correct for multiple comparisons; a lack of homogeneity of the populations studied with regard to area of residence, ancestral background, and/or country of origin; a lack of measurement of relevant environmental exposures; and (for case-control studies of genetic association) a lack of detection and control of potential population stratification. Genetic studies may improve our understanding of asthma and lead to new methods to prevent, diagnose, and treat this disease. Limited study of asthma genetics in ethnic minority populations is unacceptable, as it may prevent these groups from benefiting from future developments in asthma management and thus widen existing disparities in asthma care. Future genetic association studies of asthma among ethnic minorities in the United States should include large samples of populations that have been adequately defined with regard to area of residence, self-designated ancestry, and country of origin. These studies should also include an adequate assessment of potentially relevant environmental exposures and (for case-control association studies) population stratification.

Gene mapping in asthma-related traits

In asthma, as in many other common multifactorial diseases, the identification of the susceptibility genes has been challenging because consistent results at the genome-wide significance level have been scarce. So far, genome-wide scans have been reported in 17 study populations. By means of genome-wide linkage and hierarchical association analysis, six positional candidate genes (ADAM33, PHF11, DPP10, GPR154, HLA-G, and CYFIP2) for asthma-related traits have been cloned. The interactions of the proteins encoded by these genes and the biological relevance of these signaling pathways in the development of asthma are still poorly understood. Also, the disease mechanisms resulting from the genetic variance in the genes identified remain largely unknown. Although this information is gradually accumulating, we can examine the statistical robustness of each genetic finding in combination with the limited data available on the functional properties of the corresponding proteins to estimate the strengths and weaknesses in the chains of evidence.

[Asthma genetic factors]

Asthma is a chronic inflammatory airways disease, with a rising prevalence, particularly in childhood, and is considered an important public health problem. Its familial transmission is recognised, while the description and identification of the genes implicated in this disease are a challenge. In this revision paper the authors give a comprehensive explanation of the associated genes as well as the laboratorial methods that allow their identification.

A functional polymorphism in the TIM-1 gene is associated with asthma in a Chinese Han population

BACKGROUND

TIM-1, a member of the T cell immunoglobulin and mucin domain (TIM) gene family was implicated as an asthma susceptibility gene in previous studies. TIM-1 is selectively expressed on activated CD4+ T cells and its expression is sustained preferentially on T helper type 2 (Th2) cells, which suggests that TIM-1 is associated with T cell differentiation and the development of Th2-biased immune response.

METHODS

In order to evaluate the effects of the promoter polymorphism in the TIM-1 gene on asthma susceptibility in a Chinese Han population, 2 promoter polymorphisms, -416G>C and -1454G>A, from 2 alternative promoter regions, were genotyped in 409 unrelated asthma patients and 305 healthy controls by using polymerase chain reaction and restriction fragment length polymorphism. Also, we analyzed the functional significance of -416G>C using the luciferase reporter gene assay.

RESULTS

We found that -416G>C was associated with asthma susceptibility in our study population (chi2 = 9.88, p = 0.002, odds ratio 1.41, 95% confidence interval 1.14-1.75). No statistically significant difference in the distribution of genotype and allele frequency of the -1454G>A site was observed. The -416G>C substitution increased the transcriptional activity of the TIM-1 gene.

CONCLUSION

Our findings suggest that the -416G>C variation site in the human TIM-1 promoter region is associated with asthma susceptibility in a Chinese Han population.

Absence of association between two insertion/deletion coding genetic polymorphisms of TIM-1 gene and asthma in Chinese Han population

TIM-1, a member of T-cell immunoglobulin domain and mucin domain (TIM) gene family, was implicated as an asthma susceptibility gene in previous studies. TIM-1 was expressed on CD4(+) T cells after activation and its expression was sustained preferentially in T-helper type 2 (T(H)2) but not in T(H)1 cells, therefore TIM-1 became a good candidate gene for atopic diseases. Recent studies indicated that two insertion/deletion (ins/del) coding genetic polymorphisms in exon 4 of TIM-1 were associated with asthma susceptibility in some but not in all populations. In order to investigate the relationship between TIM-1 genetic polymorphisms and asthma in Chinese Han population, we performed a case-control study for two insertion/deletion polymorphisms in TIM-1 exon 4 (5383_5397ins/del and 5509_5511delCAA) and a single nucleotide polymorphism (SNP) in intron 8 (IVS 8+9 G/A) between a healthy control group of 309 people and an asthma patient group of 352 people recruited from Chinese Han population. The polymorphisms were genotyped and the allele and genotype frequencies were analysed, but none of the three polymorphisms showed association with asthma susceptibility in single-locus association analyses. Linkage disequilibrium (LD) analyses demonstrated that the two insertion/deletion polymorphisms were in strong LD but the haplotypes constructed from these two polymorphisms showed no significant association with asthma. In conclusion, our findings suggest that 5383_5397ins/del, 5509_5511delCAA and SNP IVS 8+9 G/A polymorphisms are not associated with asthma susceptibility in Chinese Han population.

Interaction between allelic variation in IL12B and CCR5 affects the development of AIDS: IL12B/CCR5 interaction and HIV/AIDS

OBJECTIVE

IL-12 is involved in immune surveillance and response that links the innate and adaptive arms of the immune system. Among its many effects, IL-12 increases the cell surface expression of the CCR5 co-receptor for R5 strains of HIV-1, which are predominantly involved in HIV-1 transmission and spread. In the present study we investigated the effect of epistasis between allelic variants of CCR5 and IL12B on the susceptibility to HIV-1 infection and HIV-1 disease progression.

METHODS

HIV-1-positive patients were genotyped for IL12Bpro from two groups of HIV-1 seroincident patients from Western Australia (n = 101 and 200), longitudinal clinical data were available for one of the Western Australian cohorts for a period of over 12 years and a group of seroprevalent individuals from Sydney (n = 112). A group of ethnically matched healthy volunteers (n = 200) was also genotyped as controls. Comparison of allele frequencies between HIV-1 patients and controls was performed to determine the influence on susceptibility to HIV-1 infection, and regression analysis was used to determine the influence on disease progression.

RESULTS

Individuals positive for CCR5Delta32 and who carry the IL12Bpro1.1 genotype were underrepresented across all three independent HIV-1-positive cohorts [odds ratio 0.5; 95% confidence interval (CI) 0.28-0.97; P = 0.038]. CCR5wt/wt and IL12Bpro2.2 individuals progressed to AIDS at a significantly faster rate than other CCR5 and IL12Bpro groups (hazards ratio 3.24; 95% CI 1.9-15.1; P = 0.002).

CONCLUSION

Epistatic interaction between allelic variants of CCR5 and IL12Bpro exert a significant influence on the clinical outcome of HIV-1 infection.