Genome-wide search for asthma susceptibility loci in a founder population. The Collaborative Study on the Genetics of Asthma

A high-density genetic map of the chromosome 13q14 atopy locus

Atopy describes a syndrome of immunoglobulin E (IgE)-mediated allergy that underlies asthma and infantile eczema. We have previously identified a locus on chromosome 13q14 that is linked to atopy and to the total serum immunoglobulin A concentration. We have therefore made a saturation genetic map of the region by typing 59 polymorphic microsatellite loci on chromosome 13q. Multipoint linkage analysis identified a 1-LOD support unit for the location of the atopy locus with a 7.5-cM region flanked by the loci D13S328 and D13S1269. The peak of linkage was at locus D13S161 with a nonparametric -log of P score of approximately 4.5. Parent of origin effects were present, with linkage primarily observed to paternally derived alleles. The genetic map of this region provides a basis for the effective identification of the chromosome 13 atopy gene.

Exhaled nitric oxide in patients with asthma: association with NOS1 genotype

An increased concentration of nitric oxide (NO) in exhaled air (FENO) is now recognized as a critical component of the asthmatic phenotype. When we identified patients with asthma on the basis of a standard case definition alone, we found that they were remarkably heterogeneous with respect to their FENO. However, when we included genotype at a prominent asthma candidate gene (i.e., NOS1) in the case definition, and determined the number of AAT repeats in intron 20, we identified a remarkably homogeneous cohort of patients with respect to FENO. Both mean FENO (p = 0.00008) and variability around the mean (p = 0.000002) were significantly lower in asthmatic individuals with a high number (> or = 12) of AAT repeats at this locus than in those with fewer repeats. These data provide a biologically tenable link between genotype at a candidate gene in a region of linkage, NOS1, and an important component of the asthmatic phenotype, FENO. We show that addition of NOS1 genotype to the case definition of asthma allows the identification of a uniform cohort of patients, with respect to FENO, that would have been indistinguishable by other physiologic criteria. Our isolation of this homogeneous cohort of patients ties together the well-established associations among asthma, increased concentrations of NO in the exhaled air of asthmatic individuals, and variations of trinucleotide repeat sequences as identified in several neurologic conditions.

Lesion-associated accumulation of uPAR/CD87- expressing infiltrating granulocytes, activated microglial cells/macrophages and upregulation by endothelial cells following TBI and FCI in humans

Urokinase-type plasminogen activator receptor (uPAR/CD87) together with its ligand, urokinase-type plasminogen activator (uPA), constitutes a proteolytic system associated with tissue remodelling and leucocyte infiltration. uPAR is a member of the glycosyl phosphatidyl inositol (GPI) anchored protein family. The functional role of uPAR comprises fibrinolysis by conversion of plasminogen to plasmin. In addition, uPAR promotes cell adhesion, migration, proliferation, re-organization of the actin cytoskeleton, and angiogenesis. Furthermore, uPAR is involved in prevention of scar formation and is chemoattractant to macrophages and leucocytes. In order to investigate the pathophysiological role of uPAR following human CNS injury we examined necrotic brain lesions resulting from traumatic brain injury (TBI; n = 28) and focal cerebral infarctions (FCI; n = 17) by immunohistochemistry. Numbers of uPAR+ cells and uPAR+ blood vessels were counted. Following brain damage, uPAR+ cells increased significantly within 12 h, reached a maximum after 3-4 days and remained elevated until later stages. uPAR was expressed by infiltrating granulocytes, activated microglia/macrophages and endothelial cells. Numbers of uPAR+ vessels increased in parallel subsiding earlier following FCI than post TBI. The restricted, lesion-associated accumulation of uPAR+ cells in the brain parenchyma and upregulated expression by endothelial cells suggests a crucial role for the influx of inflammatory cells and blood-brain barrier (BBB) disturbance. Through a failure in BBB function, uPAR participates in formation of brain oedema and thus contributes to secondary brain damage. In conclusion, the study defines the localization, kinetic course and cellular source of uPAR as a potential pharmacological target following human TBI and FCI.

Use of population isolates for mapping complex traits

Geneticists have repeatedly turned to population isolates for mapping and cloning Mendelian disease genes. Population isolates possess many advantages in this regard. Foremost among these is the tendency for affected individuals to share ancestral haplotypes derived from a handful of founders. These haplotype signatures have guided scientists in the fine mapping of scores of rare disease genes. The past successes with Mendelian disorders using population isolates have prompted unprecedented interest among medical researchers in both the public and private sectors. Despite the obvious genetic and environmental complications, geneticists have targeted several population isolates for mapping genes for complex diseases.

A major susceptibility locus for atopic dermatitis maps to chromosome 3q21

Atopic dermatitis (eczema) is a chronic inflammatory skin disease with onset mainly in early childhood It is commonly the initial clinical manifestation of allergic disease, often preceding the onset of respiratory allergies. Along with asthma and allergic rhinitis, atopic dermatitis is an important manifestation of atopy that is characterized by the formation of allergy antibodies (IgE) to environmental allergens. In the developed countries, the prevalence of atopic dermatitis is approximately 15%, with a steady increase over the past decades. Genetic and environmental factors interact to determine disease susceptibility and expression, and twin studies indicate that the genetic contribution is substantial. To identify susceptibility loci for atopic dermatitis, we ascertained 199 families with at least two affected siblings based on established diagnostic criteria. A genome-wide linkage study revealed highly significant evidence for linkage on chromosome 3q21 (Zall=4.31, P= 8.42 10(-6)). Moreover, this locus provided significant evidence for linkage of allergic sensitization under the assumption of paternal imprinting (hlod=3.71,alpha=44%), further supporting the presence of an atopy gene in this region. Our findings indicate that distinct genetic factors contribute to susceptibility to atopic dermatitis and that the study of this disease opens new avenues to dissect the genetics of atopy.

Genome screen for asthma and related phenotypes in the French EGEA study

A genome-wide search was conducted in 107 nuclear families with at least two siblings with asthma, as part of the French EGEA study. A two-stage analysis strategy was applied to the 107 families divided into two independent subsets of 46 and 61 families, where all regions detected in the first set of families were tested for replication in the second set. In addition, all regions reported by published genome scans in different populations were examined in the total sample. A total of 254 markers were typed in the first set of families and 70% of them in the second set. Linkage was investigated by model-free methods for asthma and four asthma-related phenotypes: bronchial responsiveness (BR), skin test response, total immunoglobulin E (IgE) levels, and eosinophil count. The two-stage analysis led to the detection of three regions: 11p13 for IgE, 12q24 for eosinophils, and 17q12-21 for asthma and skin tests. Among the regions reported by published genome screens, seven were found in the 107 French EGEA families: three being already detected by the two-stage analysis, 11p13 (p = 0.005), 12q24 (p = 0.0008), and 17q12-21 (p = 0.001), and four additional ones, 1p31 (p = 0.005) for asthma, 11q13 (p = 0.006) for IgE, 13q31 (p = 0.001) for eosinophils, and 19q13 (p = 0.02) for BR.

A second-generation genomewide screen for asthma-susceptibility alleles in a founder population

A genomewide screen for asthma- and atopy-susceptibility loci was conducted, using 563 markers, in 693 Hutterites who are members of a single 15-generation pedigree, nearly doubling the sample size from the authors' earlier studies. The resulting increase in power led to the identification of 23 loci in 18 chromosomal regions showing evidence for linkage that is, in general, 10-fold more significant (P<.001 vs. P<.01) than the linkages reported previously in this population. Moreover, linkages to loci in 11 chromosomal regions were identified for the first time in the Hutterites in this report, including five regions (5p, 5q, 8p, 14q, and 16q) showing evidence both of linkage, by the likelihood ratio (LR) chi(2), and of disequilibrium, by the transmission/disequilibrium test. A region on chromosome 19 continues to show evidence for linkage, by both tests, in this study. Studies of 17 candidate genes provide evidence for association with variation in the IL4RA gene (16p12), the HLA class II genes (6p21), and the interferon-alpha gene cluster (9p22), but the lack of evidence for linkage in these regions by the LR chi(2) test suggests that these are minor susceptibility loci. A polymorphism in the CD14 gene is in linkage disequilibrium with an as yet unidentified susceptibility allele in the 5q cytokine cluster, a region showing evidence for linkage among the Hutterites. Finally, 10 of the regions showing evidence for linkage in the Hutterites have shown evidence of linkage to related phenotypes in other genome screens, suggesting that these regions may contain common alleles that have relatively large effects on asthma and atopy phenotypes in diverse populations.

A European study on the genetics of mite sensitization

BACKGROUND

Sensitization to mite allergens represents a prominent feature of atopy and an important predictor of bronchial asthma.

OBJECTIVE

It was the intention of this study to define genetic loci linked to mite sensitization because these could represent the genetic basis of the important atopic component of asthma.

METHODS

We studied a multiethnic white population of 99 families, including 224 sib pairs sensitized to Dermatophagoides pteronyssinus. A genome-wide candidate-region search was performed that covered potential asthma and atopy regions.

RESULTS

As for nonparametric linkage (NPL) analysis, 14 of the candidate regions showed evidence for linkage (NPL > 2.0), and 4 of them showed prominent linkage (NPL > 3.0). However, there were substantial ethnic differences. Maximizing the LOD score analysis identified candidate regions with suspected dominant and recessive mode of inheritance. Furthermore, genetic imprinting models provided significant evidence for linkage in the 8p23 region and revealed potential maternal imprinting. The regions found are distinct to those in asthma searches that have been found to be linked to asthma, as well to other inflammatory diseases. In addition, we could not find linkage to the HLA region. By different cutoff points of the phenotype definition, the IL cluster showed evidence of being linked to the degree of sensitization rather than to sensitization per se.

CONCLUSION

The results indicate that the genetic basis of the atopic component of asthma is different from that of the inflammatory component. Furthermore, it seems reasonable to assume that specific sensitizations are influenced by distinct genetic variants leading to their initiation versus those leading to their enhancement.

Evidence for common genetic elements in allergic disease

Genetic research in allergic disease has focused primarily on asthma and its associated phenotypes (eg, total IgE), with very little attention given to the presence or absence of concomitant allergic diseases, especially allergic rhinitis and atopic dermatitis. Because asthma, allergic rhinitis, and atopic dermatitis share common systemic characteristics, it is reasonable to propose that a number of susceptibility genes could contribute to the allergic process regardless of the specific clinical phenotype. Consequently, the many genetic linkages previously reported for asthma may not be specific for asthma per se but rather may reflect an overall predisposition for allergic disease. Finally, epidemiologic data suggest that asthma and allergic rhinitis represent a continuum of disease, whereby those individuals with less severe disease will express rhinitis without asthma and those individuals with more severe disease express more than 1 phenotype. Alternatively, it is plausible that, in addition to the "allergic disease genes," there are "phenotype-specific genes" or possibly certain combinations of susceptibility genes (eg, gene-gene interactions) that contribute to the expression of asthma, allergic rhinitis, or atopic dermatitis.

Application of an algorithm for the diagnosis of asthma in Chinese families: limitations and alternatives for the phenotypic assessment of asthma in family-based genetic studies

Phenotype assessment is a crucial issue in gene mapping studies of asthma. Recently, Panhuysen and coworkers proposed an algorithm to define the asthma phenotype in gene mapping family-based studies. We classified members of 2,756 Chinese families ascertained on the basis of the presence of two or more siblings and no more than one parent with asthma using a slightly modified version of the aforementioned algorithm. Among 4,097 Chinese parents, 404 (9.9%) were classified as having "definite asthma," 284 (6.9%) as "probable asthma," 1,193 (29.1%) as "unclassifiable obstructive airway disease, " 626 (15.3%) as "COPD," and 1,590 (38.8%) as "unaffected" (no obstructive airway disease). Among 6,424 Chinese offspring, 1,065 (16.6%) were classified as having "definite asthma," 820 (12.8%) as "probable asthma," 1,996 (31.1%) as "unclassifiable obstructive airway disease," 228 (3.5%) as "COPD," and 2,315 (36%) as "unaffected." The use of the algorithm proposed by Panhuysen and coworkers in a Chinese population with a high prevalence of smoking would result in the exclusion of subjects with asthma who smoke or who have severe airflow obstruction from linkage analysis, as well as in an inability to explore any potential interactions between genetic factors and cigarette smoking in the pathogenesis of asthma. In the absence of a "gold standard," definitions of asthma that incorporate a combination of respiratory symptoms, increased airway responsiveness or bronchodilator response, and a physician's diagnosis of asthma are reasonable. The choice of a particular diagnostic algorithm for family-based genetic studies of asthma should be made according to factors such as the prevalence of smoking in the study population. Genetic studies of intermediate phenotypes related to asthma, which are objectively defined and may be influenced by a smaller number of genes, continue to be of great importance.

Linkage analysis of chromosome 12 markers in Italian families with atopic asthmatic children

We investigated 116 Italian atopic families (560 individuals) for linkage with 13 DNA markers on chromosome 12. All the subjects were phenotyped for asthma, total serum IgE, bronchial hyperresponsiveness, skin-prick positivity to common aeroallergens, and atopy. A relative location map of the markers was prepared from Centre d'Etude du Polymorphisme Humain families. Affected sib pair multipoint linkage methods were used to perform the statistical analyses. We report suggestive linkage for asthma with markers on chromosome 12. The region of interest centers around marker D12S390 (maximum logarithm of odds [mlod] = 2.81; p = 0.003). These results provide additional support that asthma susceptibility factors are located on chromosome 12q.

Quantitative trait loci controlling allergen-induced airway hyperresponsiveness in inbred mice

Identification of the genetic loci underlying asthma in humans has been hampered by variability in clinical phenotype, uncontrolled environmental influences, and genetic heterogeneity. To circumvent these complications, the genetic regulation of asthma-associated phenotypes was studied in a murine model. We characterized the strain distribution patterns for the asthma-related phenotypes airway hyperresponsiveness (AHR), lung eosinophils, and ovalbumin (OVA)-specific serum immunoglobulin (Ig) E induced by allergen exposure protocols in A/J, AKR/J, BALB/cJ, C3H/HeJ, and C57BL/6J inbred strains and in (C3H/HeJ x A/J)F1 mice. Expression of AHR differed between strains and was sometimes discordant with lung eosinophils or serum IgE. Furthermore, we identified two distinct quantitative trait loci (QTL) for susceptibility to allergen-induced AHR, Abhr1 (allergen-induced bronchial hyperresponsiveness) (lod = 4. 2) and Abhr2 (lod = 3.7), on chromosome 2 in backcross progeny from A/J and C3H/HeJ mice. In addition, a QTL on chromosome 7 was suggestive of linkage to this trait. These QTL differ from those we have previously found to control noninflammatory AHR in the same crosses. Elucidation of the genes underlying these QTL will facilitate the identification of biochemical pathways regulating AHR in animal models of asthma and may provide insights into the pathogenesis of human disease.

A first trial of retrospective collaboration for positional cloning in complex inheritance: assay of the cytokine region on chromosome 5 by the consortium on asthma genetics (COAG)

The central problem of complex inheritance is to map oligogenes for disease susceptibility, integrating linkage and association over samples that differ in several ways. Combination of evidence over multiple samples with 1,037 families supports loci contributing to asthma susceptibility in the cytokine region on 5q [maximum logarithm of odds (lod) = 2.61 near IL-4], but no evidence for atopy. The principal problems with retrospective collaboration on linkage appear to have been solved, providing far more information than a single study. A multipoint lod table evaluated at commonly agreed reference loci is required for both collaboration and metaanalysis, but variations in ascertainment, pedigree structure, phenotype definition, and marker selection are tolerated. These methods are invariant with statistical methods that increase the power of lods and are applicable to all diseases, motivating collaboration rather than competition. In contrast to linkage, positional cloning by allelic association has yet to be extended to multiple samples, a prerequisite for efficient combination with linkage and the greatest current challenge to genetic epidemiology.

Genomic approaches to understanding asthma

Asthma is the most common chronic childhood disease in developed nations, and it is a complex disease that has high social and economic costs. Asthma and its associated intermediate phenotypes are under a substantial degree of genetic control. The genetic aetiology of asthma offers a means of better understanding its pathogenesis and, thus, improving preventive strategies, diagnostic tools, and therapies. Considerable effort and expense have been expended in attempts to detect genetic loci contributing to asthma susceptibility, and extensive candidate gene studies and a number of whole-genome screens have been undertaken. This article reviews the current state of knowledge of the genetics of asthma, with a focus on genomic approaches to understanding allergic diseases.

Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma

The prevalence and severity of allergic asthma continue to rise, lending urgency to the search for environmental triggers and genetic substrates. Using microarray analysis of pulmonary gene expression and single nucleotide polymorphism-based genotyping, combined with quantitative trait locus analysis, we identified the gene encoding complement factor 5 (C5) as a susceptibility locus for allergen-induced airway hyperresponsiveness in a murine model of asthma. A deletion in the coding sequence of C5 leads to C5-deficiency and susceptibility. Interleukin 12 (IL-12) is able to prevent or reverse experimental allergic asthma. Blockade of the C5a receptor rendered human monocytes unable to produce IL-12, mimicking blunted IL-12 production by macrophages from C5-deficient mice and providing a mechanism for the regulation of susceptibility to asthma by C5. The role of complement in modulating susceptibility to asthma highlights the importance of immunoregulatory events at the interface of innate and adaptive immunity in disease pathogenesis.

Human interleukin-10-related T cell-derived inducible factor: molecular cloning and functional characterization as an hepatocyte-stimulating factor

IL-10-related T cell-derived inducible factor (IL-TIF or IL-21) is a new cytokine structurally related to IL-10 and originally identified in the mouse as a gene induced by IL-9 in T cells and mast cells. Here, we report the cloning of the human IL-TIF cDNA, which shares 79% amino acid identity with mouse IL-TIF and 25% identity with human IL-10. Recombinant human IL-TIF was found to activate signal transducer and activator of transcription factors-1 and -3 in several hepatoma cell lines. IL-TIF stimulation of HepG2 human hepatoma cells up-regulated the production of acute phase reactants such as serum amyloid A, alpha1-antichymotrypsin, and haptoglobin. Although IL-10 and IL-TIF have distinct activities, antibodies directed against the beta chain of the IL-10 receptor blocked the induction of acute phase reactants by IL-TIF, indicating that this chain is a common component of the IL-10 and IL-TIF receptors. Similar acute phase reactant induction was observed in mouse liver upon IL-TIF injection, and IL-TIF expression was found to be rapidly increased after lipopolysaccharide (LPS) injection, suggesting that this cytokine contributes to the inflammatory response in vivo.

beta(2)-adrenergic receptor Arg16/Arg16 genotype is associated with reduced lung function, but not with asthma, in the Hutterites

In a genome-wide screen for asthma loci in the Hutterites, a marker locus on chromosome 5q23-31 showed evidence of linkage to asthma (C. Ober and colleagues, Hum. Molec. Genet. 1998;7:1393). To determine whether the beta(2)-adrenergic receptor (beta(2)AR) gene is the 5q-linked asthma locus in the Hutterites, we genotyped this sample for polymorphisms in the beta(2)AR gene. Neither the Arg16Gly nor Gln27Glu polymorphisms showed evidence of linkage to qualitative measures of asthma and bronchial hyperresponsiveness (BHR) (p > 0.10) or to quantitative measures of serum IgE and airway reactivity (p > 0.10). In contrast, FEV(1) percentage of predicted and FVC percentage of predicted were significantly lower among individuals homozygous for the Arg16 allele (FEV(1) %: 98.3 +/- 13.2% versus 103. 8 +/- 14.9%, p = 0.003; FVC %: 104.2 +/- 12.3% versus 108.3 +/- 13. 2%, p = 0.02 by t test). These findings held true for adolescents and adults, but not for children </= 12 yr of age. This study demonstrates that the observed linkage to asthma in the 5q23-31 region is unrelated to variation in the beta(2)AR gene. However, it is the first study to suggest that the beta(2)AR Arg16Gly polymorphism influences either lung growth or the rate of decline of lung function with age.

Molecular genetics of allergic diseases

Allergic diseases affect approximately one third of the general population. This class of disease, characterized by elevated serum IgE levels and hypersensitivity to normally innocuous antigen, can manifest in practically any mucosal tissue or as a systemic response. A few examples of serious allergic diseases include asthma, dermatitis, bee sting allergy, food allergy, conjunctivitis, and severe systemic anaphylaxis. Taken together, allergic diseases constitute one of the major problems of modern day medicine. A considerable portion of the healthcare budget is expended in the treatment of allergic disease, and morbidity rates of inner city asthmatics are rising steadily. Due to the enormity of the problem, there has been a worldwide effort to identify factors that contribute to the etiology of allergic diseases. Epidemiologic studies of multigeneration families and large numbers of twins clearly indicate a strong genetic component to atopic diseases. At least two independently segregating diseasesusceptibility genes are thought to come together with environmental factors to result in allergic inflammation in a particular tissue. On the basis of the strong genetic studies, multiple groups have attempted to identify disease-susceptibility genes via either a candidate gene approach or by genome-wide scans. Both of these approaches have implicated multiple regions in the human and mouse genomes, which are currently being evaluated as harboring putative atopy genes.

Lack of linkage between chromosome 5q23-33 markers and IgE/bronchial hyperreactivity in 67 Scottish families

BACKGROUND

Raised serum immunoglobulin E (IgE) and bronchial hyperreactivity (BHR) are risk factors for the expression of the asthma phenotype. Previous studies have reported evidence for linkage between these traits and markers on the 5q23-33 cytokine gene cluster.

OBJECTIVE

To test for linkage between total serum IgE/BHR and microsatellite markers which map to the 5q23-33 region in an ethnically distinct cohort of families from Aberdeen, Scotland.

METHODS

We performed a linkage study between five polymorphic markers (spanning the chromosome 5q23-33 region) and total serum IgE and BHR traits. A cohort of 67 families, who were recruited originally to study the natural history of wheeze, were clinically characterized and genotyped for D5S404, IL4, IRF-1, IL9, D5S436 markers. Linkage analyses were performed using the nonparametric Haseman-Elston algorithm for the quantitative trait log IgE, and the nonparametric LOD score (NPL-score) of the GENEHUNTER package for the qualitative traits serum IgE and BHR.

RESULTS

The results of the nonparametric linkage analysis using either the Haseman-Elston algorithm or NPL-score were consistent and showed no evidence for linkage with IgE. There was also no evidence for linkage between the BHR traits (at cut-off values of PD20FEV1 < 8 mmol and 16 mmol) and any of the tested five microsatellite markers.

CONCLUSIONS

This study presents evidence against the presence of a gene with a major effect on total serum IgE or BHR in the 5q23-33 region, in this ethnic group.

A neuronal NO synthase (NOS1) gene polymorphism is associated with asthma

Recent family-based studies have revealed evidence for linkage of chromosomal region 12q to both asthma and high total serum immunoglobulin E (IgE) levels. Among the candidate genes in this region for asthma is neuronal nitric oxide synthase (NOS1). We sought a genetic association between a polymorphism in the NOS1 gene and the diagnosis of asthma, using a case-control design. Frequencies for allele 17 and 18 of a CA repeat in exon 29 of the NOS1 gene were significantly different between 490 asthmatic and 350 control subjects. Allele 17 was more common in the asthmatics (0.83 vs 0.76, or 1.49 [95% CI 1.17-1.90], P = 0.013) while allele 18 was less common in the asthmatics (0.06 vs 0.12, or 0.49 [95% CI 0.34-0. 69], P = 0.0004). To confirm these results we genotyped an additional 1131 control subjects and found the frequencies of alleles 17 and 18 to be virtually identical to those ascertained in our original control subjects. Total serum IgE was not associated with any allele of the polymorphism. These findings provide support, from case-control association analysis, for NOS1 as a candidate gene for asthma.

Contributing factors to the pathobiology. The genetics of asthma

Markers in 19 chromosomal regions have shown some evidence of linkage to asthma, atopy, or related phenotypes in multiple independent genome-wide searches. Linkages to five of these regions (5q, 6p, 11q, 12q, and 13q) have also been reported in non-genome-wide screens. In addition, at least two independent studies have reported linkages to markers on 16p. Numerous candidate genes in these regions have shown varying levels of association to asthma or atopic phenotypes, potentially implicating them as disease susceptibility loci. These include the IL4, CD14, and B2ADR genes on 5q, the HLA-DRB1 and TNF genes on 6p, the FCERB1 and CC16 genes on 11q, and the IL4RA gene on 16p. It still remains to be determined whether polymorphisms in these genes account for the reported linkages in these regions. Studies are underway in laboratories around the world to identify the disease-causing variations in these genes that account for the linkages just discussed. Identifying specific genetic polymorphisms that influence asthma and atopic phenotypes will shed light on the molecular pathways involved in these complex disorders and provide a better understanding of the pathophysiology of asthma and atopy.

Common polymorphisms and alternative splicing in the ILT3 gene are not associated with atopy

Recently, a linkage of the chromosomal region 19q13.4 with bronchial asthma has been demonstrated. This region harbours the so-called leucocyte receptor cluster with the gene for immunoglobulin-like-transcript 3 (ILT3) as a member. ILT3 represents an inhibitory receptor bearing three immunoreceptor tyrosine inhibitory motifs (ITIM). The protein mediates downregulation of cell activation through recruitment of different SH2-containing protein tyrosine phosphatases. With regard to the negative immunoregulatory function particularly on B-cells, ILT3 represents a candidate gene for atopy and asthma. The aim of this study was to screen for common polymorphisms in the gene coding for ILT3 and to test for association with the atopic phenotype. Using single-stranded conformal polymorphism-analysis and direct genomic sequencing seven polymorphisms, three mutations, a common deletion of 7 bp in the third intron and evidence for further alternative splicing of the ILT3 gene were found. Although no association was found with atopy phenotypes, it might prove useful to test for association with bronchial asthma.

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

Childhood-onset asthma is frequently found in association with atopy. Although asthmatic children may develop IgE antibodies against variety of allergens, asthma is associated primarily with allergy to house-dust mites, molds, or other allergens. In this study, we conducted a genome-wide linkage search in 47 Japanese families (197 members) with more than two mite-sensitive atopic asthmatics (65 affected sib-pairs) using 398 markers. Multipoint linkage analysis was carried out for atopic asthma as a qualitative trait using the MAPMAKER/SIB program. We observed significant evidence for linkage with maximum lod scores (MLS) of 4.8 near the interleukin 12 B gene locus on chromosome 5q31-q33. In addition, suggestive evidence on 4q35 with MLS = 2.7 and on 13q11 with MLS = 2.4 was obtained. The other possible linkage regions included 6p22-p21.3 (MLS = 2.1), 12q21-q23 (MLS = 1.9), and 13q14.1-q14.3 (MLS = 2.0). Many of the linkage loci suggested in this study were at or close to those suggested by genome-wide studies for asthma in Caucasian populations. The present study suggests the contribution of the interleukin 12 B gene or nearby gene(s) to mite-sensitive atopic asthma and a considerable number of genetic variants common across Caucasians and Japanese populations contributing to asthma, although the relative importance of various variants may differ between the groups.

HLA-DRB1*01 alleles are associated with sensitization to cockroach allergens

BACKGROUND

Sensitization to cockroach allergens is an important epidemiologic risk factor for asthma, particularly among African Americans living in urban environments. A recent genome screen in the Hutterites, a white founder population, identified a linkage between an HLA-linked marker and sensitization to cockroach allergens.

OBJECTIVE

Our purpose was to determine whether alleles at one or more HLA loci are associated with sensitization to cockroach allergens in ethnically diverse populations.

METHODS

Alleles at 14 HLA region loci were studied in the Hutterites. On the basis of these results, selected loci were examined in 54 African Americans with cockroach sensitization (cases) and 65 African Americans without cockroach sensitization (controls). Sensitivity to cockroach allergens was assessed in both samples by skin prick test to purified cockroach allergens (Periplaneta americana and Blatella germanica).

RESULTS

Significant associations between cockroach allergies and DRB1*0101 (P(corrected) =.0066), DQA1*0101 (P(corrected) =.0012), and DQB1*0501 (P(corrected) =.00096) were detected in the Hutterites. In the African American sample, the most significant association was with the DRB1*0102 allele (P(corrected) =.0088, odds ratio 16.4, 95% confidence interval 2.0, 131). The DRB1*0101 allele was infrequent in the African American sample (frequency 0.06) and the DRB1*0102 allele was absent in the Hutterites. DRB1*0101 and DRB1*0102 are closely related alleles that differ from nearly all other DRB1 alleles at 3 amino acids in the 1 peptide binding domain of the HLA-DR molecule.

CONCLUSIONS

The DRB1*0101 allele in the Hutterites and the DRB1*0102 allele in African Americans confer risk for cockroach sensitization. Elucidating this interaction at the molecular level may allow for more targeted treatment and prevention of atopic asthma in inner-city populations.

The Ile198Thr and Ala379Val variants of plasmatic PAF-acetylhydrolase impair catalytical activities and are associated with atopy and asthma

The platelet-activating factor (PAF) represents a phospholipid with complex biological functions, including involvement in inflammatory processes. The degrading enzyme PAF acetylhydrolase (PAFAH) represents a candidate for asthma and other atopic diseases. Two loss-of-function mutations of PAFAH are associated with severe asthma in Japanese individuals. Our aim was to look for further PAFAH variants in white populations, their possible association with atopic and asthmatic phenotypes, and their functional importance. We picked up three common variants in the PAFAH gene: Arg92His (exon 4), Ile198Thr (exon 7), and Ala379Val (exon 11). The known loss-of-function mutations were not seen. The variant allele Thr198 was found to be highly associated with total IgE concentrations in an atopic population (P=.009) and with "atopic asthma" in an asthmatic population (P=.008). The variant allele Val379 was found to be highly associated with "specific sensitization" in the atopic population (P=.002) and with "asthma" in the asthmatic population (P=.003). By use of recombinant PAFAH enzymes, the variant Val379 showed increased (14 microM) and Thr198 markedly increased (42 microM) KM values compared to the wild type (7 microM); furthermore, Vmax of Val379 was highly increased (132%). Thr198 and Val379 influence plasmatic PAFAH toward lower substrate affinities and therefore are very likely to prolong the activities of PAF. At the same time, they are associated with an increased risk to develop asthma and atopy. Thus, two PAFAH variants seem to play a key role in atopic and asthmatic processes in Caucasian populations.

Variation in the interleukin 4-receptor alpha gene confers susceptibility to asthma and atopy in ethnically diverse populations

After a genomewide screen in the Hutterites was completed, the IL4RA gene was examined as the 16p-linked susceptibility locus for asthma and atopy. Seven known variants and one novel variant, representing all nonsynonymous substitutions in the mature protein, were examined in the Hutterites; on the basis of studies in the Hutterites, outbred white, black, and Hispanic families were genotyped for selected markers. All population samples showed evidence of association to atopy or to asthma (P values.039-.0044 for atopy and. 029-.0000061 for asthma), but the alleles or haplotypes showing the strongest evidence differed between the groups. Overall, these data suggest that the IL4RA gene is an atopy- and asthma-susceptibility locus but that variation outside the coding region of the gene influences susceptibility.

Mapping susceptibility genes for asthma and allergy

Allergy and asthma are related conditions caused by a complex interaction of genetic factors and environmental influences. With family data from several different populations, linkage analysis has been performed and used to identify regions of the genome that contain susceptibility genes for these conditions. To date, 4 genome screens have been completed and have successfully identified several chromosomal locations that are likely to contain asthma and allergy genes. Many of these regions contain potential biologic candidate genes that modulate immunologic responses or airways inflammation. By focusing on the common regions that have been replicated in these 4 genome screens, the major susceptibility genes for asthma and allergy should be identified. This will lead to an improved understanding of pathogenic factors that lead to development or progression of asthma and allergic diseases.

Variants of NOS1, NOS2, and NOS3 genes in asthmatics

Nitric oxide (NO) gas concentrations are higher in expired air in asthmatics. NO is synthesized by three isoforms of NO synthase (NOS) encoded by three distinct genes, NOS1, NOS2, and NOS3. Genome-wide searches have identified linkages to asthma on chromosomes 7, 12, and 17 where these three genes are localized. No association study, however, has been reported to date. To test whether variants of NOS1, NOS2, and NOS3 relate to asthma, a genetic association study was conducted in a British population (n = 300). Intragenic microsatellite variants of NOS1 were significantly associated with asthma [odds ratio (OR) = 2.08, 95% CI: 1.20-3.57 (95% CI), P = 0.008 (Pc = 0.048)], but not with IgE levels. Neither NOS2 nor NOS3 variants showed any association with asthma nor IgE levels. These findings suggest that NOS1 variants may be a significant contributor to asthma in a British population.

From genome to drug--optimising the drug discovery process

Current drug discovery and development practices are technologically sophisticated and highly efficient. At the same time the failure rate of compounds in both preclinical and clinical development is high. These failures can be attributed to many factors. Two predominant causes of failure are lack of efficacy and toxicity. Often lack of efficacy is only determined late in the clinical trial process and can be difficult if not impossible to explain, as well as being expensive. Toxicity accounts for many failures during preclinical development, which are less costly, but it also occurs in the clinic. Often the underlying cause of clinical toxicity is never identified. Studies of the structure and activity of the human and other genomes has over the last decade lead to a revolution in biological and medical research. Disease associated genes can now be identified through the application of human genetics, whole genomes have been sequenced and tools have been developed that allow the complete characterization of an organism's gene expression profile in a single experiment. These tools are now being applied to pharmaceutical research and development with the aim to increase the efficiency of the process and the quality of the product.

Interleukin-4 receptor alpha gene variants and allergic disease

The interleukin-4 (IL-4) signalling cascade has been identified as a pathway potentially important in the development of asthma. Genetic variants within this signalling pathway might contribute to the risk of developing asthma in a given individual. A number of polymorphisms have been described within the IL-4 receptor alpha (IL-4Ralpha) gene. In addition polymorphism occurs in the promoter for the IL-4 gene itself. This commentary accompanies a paper by C Ober et al describing the contribution of IL-4Ralpha polymorphism to susceptibility to asthma and atopy in the Hutterite population and other outbred populations collected during the collaborative studies on the genetics of asthma (CSGA) programme.

The gene encoding interleukin-13: a susceptibility locus for asthma and related traits

Asthma is a complex inflammatory disorder controlled by both genetic and environmental influences. Multiple genetic analyses have identified the T helper type 2 (Th2) cytokine gene cluster on chromosome 5q as a susceptibility locus for asthma. Recently, the Th2 cytokine interleukin-13 has been shown to be a critical mediator of the asthma phenotype in murine models. In this commentary we discuss several recent studies that have identified polymorphisms in the gene encoding interleukin-13. The consistent genetic associations of interleukin-13 with asthma and related traits across diverse ethnic populations in these studies provides strong support for the candidacy of this cytokine as a susceptibility locus for asthma and atopy on chromosome 5q31.

Genetics of asthma and inflammation: the status

Genome-wide screens are consistently finding linkage between asthma-associated traits and specific chromosomal loci. Several loci coincide with linkages to other inflammatory diseases, suggesting the presence of common pathways in their pathogenesis. Candidate-gene studies have found an association between a CD14 polymorphism and IgE levels, suggesting a mechanism for the increased prevalence of allergic disease. A polymorphism in Fc epsilon RI-beta shows parent-of-origin effects when associated with severe infantile eczema, further illustrating the complexity of gene-environment effects on the developing immune system.

Genetic and environmental interaction in allergy and asthma

Asthma is an inflammatory disorder of the airways involving coordinate up-regulation of T(H)2-type cytokines encoded in a cluster on chromosome 5q(31-33) on T cells and inflammatory cells. There is also a requirement for local airway susceptibility factors that, together with T(H)2 polarization, results in hyperresponsiveness, variable airflow obstruction, and, over time, remodeling of the airway wall. Asthma has strong genetic and environmental components that interact both in the induction and subsequent expression of the disease phenotypes. Multiple genes are involved and probably interact. Whole genome screens are beginning to identify gene-rich regions of special relevance to asthma and atopy, although a novel disease-related gene has yet to be discovered from these. By contrast, there are a plethora of candidate genes whose function in relation to disease pathophysiologic mechanisms and response to treatment are known. Two examples are polymorphisms involving IL-4 receptors and the enzymes controlling cysteinyl leukotriene production. Abnormal signaling between the epithelium, which is in contact with the environment, and the underlying (myo)fibroblasts and dendritic cells indicating reactivation of the epithelial mesenchymal trophic unit, which is involved in fetal lung development and branching, provide a basis for asthma that encapsulates both T(H)2 polarization and airway wall remodeling.

Missense mutations in the cystic fibrosis gene in adult patients with asthma

Asthma is a complex genetic disorder that affects 5% of adults and 10% of children worldwide. The complete characterization of the cystic fibrosis transmembrane conductance regulator (CFTR) gene identified missense mutations in 15% of 144 unrelated adult patients with asthma, but in none of 41 subjects from the general population. The four more common mutations were analyzed in an extended sample consisting of 184 individuals from the general population and did not show a significant difference in frequency. The hyperfunctional CFTR M470 allele was detected in 90% of patients with CFTR missense mutations, but in 63% of subjects from the general population and 63% of asthma patients without CFTR mutations. None of the patients with missense mutations had the 5T allele of intron 8 of CFTR, responsible for low CFTR levels, while it was detected in 8% of asthma patients without CFTR mutations and in 9% of subjects from the general population. These findings suggest a putative role for a combination of CFTR missense mutations, including the M470 allele, in the genetic variability of asthma.

The alliance of genes and environment in asthma and allergy

The diseases of asthma, eczema and hay fever are typified by reactions to common allergens, which are mediated by immunoglobulin E. These allergic diseases are increasing in prevalence, and are now a major source of disability throughout the developed world. They are the result of complex interactions between largely unknown genetic and environmental mechanisms. The identification of the environmental factors offers the real possibility of prevention of disease, and unravelling the genetics of allergic illnesses is likely to change their classification and treatment. Early life seems particularly important, when the initiation of allergic disease may result from genetic and environmental modification of the immune interaction between mother and child.

Definition of human interleukin-4 receptor alpha chain haplotypes and allelic association with atopy markers

Cumulative evidence indicates that the human interleukin-4 receptor alpha chain gene (IL-4Ralpha, CD124) is highly polymorphic in contrast to other cytokine receptor genes. Our group recently identified the IL-4Ralpha variant R551 as being strongly associated with decreased kidney allograft survival. Due to the key immunoregulatory role of IL-4 and controversial reports on the association of IL-4Ralpha variants with atopy, we present here the development of polymerase chain reaction-primer sets for sequence-specific amplification of all seven hitherto described amino acid polymorphisms, and we investigated 158 blood donors prospectively. By using an Expectation-Maximization algorithm, we calculated the presence of 11 putative human IL-4Ralpha haplotypes and identified 4 putative IL-4Ralpha haplotypes with a cumulative frequency of >90%. None of the polymorphisms showed a significant association with the phenotype atopy. All mutant alleles showed a trend toward decreased total IgE levels. This association was only significant (p < 0.05; Mann-Whitney U-test) for the A375, R406, and P478 variants in non-atopic blood-donors (n = 90), presumably due to the high variance of IgE levels among the smaller group of atopic individuals. We postulate that IL-4Ralpha mutations are associated to different extents with a decrease in function of the receptor but do not present a major atopy locus.

Nonpathogenic common variants of IFNGR1 and IFNGR2 in association with total serum IgE levels

Atopy is an immune disorder in which a Th2 dominant mechanism leads to high IgE levels and the clinical disorder asthma. It has been postulated that the Th1 cytokine IFNgamma, acting through its heterodimeric receptors, IFNgammaR1 and IFNgammaR2, in the induction/proliferation of Th1 cells, might suppress the Th2 responses that may underlie atopic asthma. However, neither murine nor human variants of IFNgamma associate with atopy. Several dysfunctional mutations have been identified in IFNgamma receptor genes (IFNGR1 and IFNGR2) in relation to severe and selective infections with poorly pathogenic organisms. However, little is known about common polymorphisms and their functional role in atopy. To test whether such variants of IFNGR1 and IFNGR2 relate to atopic asthma, we conducted a genetic association study in both British (n = 300) and Japanese (n = 200) populations. An intronic variant of IFNGR1 showed marginal association with total serum IgE levels in the British population compared with those with total IgE levels <30 IU/ml and those with >120-500 IU/ml [odds ratio = 2.00 (95% CI 1. 00-4.07), P = 0.048]. A coding variant, Gln64Arg of the IFNGR2, also associated with total serum IgE levels in the British population [chi(2) = 5.08, P = 0.024]. Further genetic and functional analyses are needed to clarify the role of variants of IFNgamma receptor genes in atopic immune disorder among different ethnic groups.

Population-based studies reveal differences in the allelic frequencies of two functionally significant human interleukin-4 receptor polymorphisms in several ethnic groups

PURPOSE

The presence of functionally significant human interleukin-4 receptor sequence variants, Gln551Arg and Ile50Val, was examined in four anonymous New York State populations defined by ethnic origin. These variants were studied because they are associated with atopy or atopic asthma whose prevalence varies in different populations.

METHODS

PCR/RFLP (Ile50Val) and PCR/allele-specific oligonucleotide hybridization (Gln551Arg) assays were developed to detect both polymorphisms in 855 newborn screening specimens.

RESULTS

Arg551 was most frequently found in Blacks (allele frequency of 68%). However, the Ile50 allele was most common in Whites (allele frequency, 87%). Significantly more Blacks had chromosomes bearing both of the "enhanced signaling" variants (Ile50/Arg551).

CONCLUSIONS

Enhanced IL-4R signaling is associated with increased IgE production (atopy). Therefore, our data suggest that the African American population may be at increased risk for diseases, including asthma, which are associated with atopy. These data also emphasize the importance of determining the frequencies of single nucleotide polymorphisms in different populations before drawing conclusions from allele association studies, since the background allele frequencies may be disparate between different populations.

Variants of endothelin-1 and its receptors in atopic asthma

Endothelin-1 (ET-1) is a 21 amino acid peptide released from several types of bronchial cells. It operates through two types of receptors, type A(ET-RA) and type B(ET-RB) and has various activities in the pathophysiology of atopic asthma. These genes are localised on different chromosomes where genome-wide searches have identified linkage for atopic asthma, thus supporting the candidacy of ET-1 and its receptors for atopic asthma. A genetic association study was performed with variants of these three genes in both British (n = 300) and Japanese populations (n = 200). No significant association was found between variants of EDN1 and EDNRB genes, and atopic asthma in either population. However, variants of EDNRA gene showed a marginal association with atopy [odds = 0.39(95% CI: 0.17-0.89), p = 0.022, Pc = 0.066], especially with antigen specific IgE levels [odds = 0.31 (95% CI: 0.20-0.77), p = 0.006, Pc = 0.018] in the British population. These findings suggest that EDNRA is a major candidate locus for atopy on chromosome 4.

Effect of inbreeding avoidance on Hardy-Weinberg expectations: examples of neutral and selected loci

Although all human populations avoid close inbreeding, the effect of inbreeding avoidance on genotype proportions has not been formally considered. This paper examines the expected proportions of genotype frequencies after adjusting the Hardy-Weinberg model for close inbreeding avoidance in an inbred population. This corrected model was used to evaluate genotype distributions for HLA haplotypes and haplotypes created from three microsatellite loci on human chromosome 13 in a sample of 315 married Hutterites. In this sample, there were five individuals who were homozygous for an HLA haplotype and 15 individuals who were homozygous for a chromosome 13 haplotype. The expected numbers of homozygotes were 21 for HLA and 26 for chromosome 13 haplotypes using a model adjusted for overall inbreeding (P = 0.00031 for HLA and P = 0.019 for chromosome 13) and 18 for HLA and 22 chromosome 13 haplotypes using a model adjusted for both overall inbreeding and close inbreeding avoidance (P = 0. 0016 for HLA and P = 0.099 for chromosome 13). The model that takes into account both overall inbreeding and inbreeding avoidance provided a better fit to the observed genotype distributions for chromosome 13 haplotypes (P = 0.099), suggesting that nonrandom aspects of Hutterite mating structure, other than inbreeding and inbreeding avoidance, have small effects on genotype distributions in the population. The fact that significant deficiencies of HLA homozygotes persist after taking into account inbreeding avoidance further suggests that factors related to the HLA haplotype per se influence the genotype proportions at HLA loci in the Hutterites.

Genetics of allergy and bronchial hyperresponsiveness

Allergy and asthma are closely related complex diseases caused by a combination of both genetic and environmental influences. Two common genetic approaches, candidate gene studies and genome-wide screens, have been used to localize and evaluate potential genetic factors that confer susceptibility or modify the phenotype of these diseases. Four genome screens suggest multiple chromosomal locations likely to contain asthma and allergy genes and many potential candidate genes exist in these regions. These screens were performed in six different populations and identified many common susceptibility regions as well as novel regions for each population. Ideally, these genes may point towards key biological pathways that will eventually serve as targets for therapeutic agents.

Recent advances in the genetics of allergy and asthma

Asthma is a common condition that results from the interaction of an unknown number of genes with environmental factors. About 10% of children have asthma, usually as part of a syndrome of atopy, which is characterized by the presence of allergy, asthma, seasonal rhinitis and eczema, and tends to occur in familial clusters. The incidence of asthma is lower in adults (5%) and a significant proportion is seen without an atopic background. The prevalence of asthma has increased substantially over the past decades, particularly in the western world. Allergy and asthma are not inherited as single-gene disorders and do not show a simple pattern of inheritance. Environmental and genetic factors interact in a complex fashion to produce disease susceptibility and expression. Here, we describe the recent advances in the understanding of the inherited susceptibility to asthma and atopy and discuss their potential implications.