Genetic linkage of T-cell receptor alpha/delta complex to specific IgE responses

[Allergic reactions to bioimplants]

BACKGROUND

Bioimplants are used in a variety of ways in otorhinolaryngology, most commonly in facial reconstructive surgery, cochlear implants (CI), bone-anchored hearing aids, and partial/total ossicular replacement prostheses (PORP/TORP), but also for tympanic drainage, laryngeal cannula, voice prostheses after laryngectomy, etc., and in otorhinolaryngology-related procedures as dental implants in dentistry.

METHODS

A literature search was performed to analyze the immunology of allergic reactions to bioimplants and to determine the available evidence by searching Medline, PubMed, and national and international study and guideline registries and the Cochrane Library. Human studies published in the period up to and including 12/2021 were considered.

RESULTS

Based on the international literature and previous experience, a review of allergies to bioimplants in otolaryngology is presented.

CONCLUSION

Otorhinolaryngologists should always consider the possibility of allergic reactions when inserting allogeneic materials, particularly, but not only, when using bioimplants.

Association analysis of single nucleotide polymorphisms at five loci: comparison between atopic dermatitis and asthma in the Chinese Han population

Atopic diseases, such as atopic dermatitis (AD) and asthma, are closely related to clinical phenotypes with hypersensitivity, and often share some similar genetic and pathogenic bases. Our recent GWAS identified three susceptibility gene/loci FLG (rs11204971 and rs3126085), 5q22.1 (rs10067777, rs7701890, rs13360927 and rs13361382) and 20q13.33 (rs6010620) to AD. The effect of these AD associated polymorphisms in asthma is so far unknown. To investigate whether AD relevant genetic variants is identical to asthma and reveal the differences in genetic factors between AD and asthma in Chinese Han population, seven AD associated single nucleotide polymorphisms (SNPs) as well as 3 other SNPs (rs7936562 and rs7124842 at 11q13.5 and rs4982958 at 14q11.2) from our previous AD GWAS were genotyped in 463 asthma patients and 985 controls using Sequenom MassArray system. We found rs4982958 at 14q11.2 was significantly associated with asthma (P = 3.04×10⁻⁴, OR = 0.73). We also detected one significant risk haplotype GGGA from the 4 SNPs (rs10067777, rs7701890, rs13360927 and rs13361382) at 5q22.1 in AD cases (P_correction = 3.60×10⁻¹⁰, OR = 1.26), and the haplotype was suggestive of risk in asthma cases in this study (P = 0.014, P_correction = 0.084, OR = 1.38). These SNPs (rs11204971, rs3126085, rs7936562, rs712484 and rs6010620) at AD susceptibility genes/loci FLG, 11q13.5 and 20q13.33 were not associated with asthma in this study. Our results further comfirmed that 14q11.2 was an important candidate locus for asthma and demonstrated that 5q22.1 might be shared by AD and asthma in Chinese Han population.

Allelic polymorphism in the T cell receptor and its impact on immune responses

In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01(+) public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2beta loop (Gln55-->His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55-->Ala55) in complex with HLA-B*3501(HPVGEADYFEY) revealed that the Gln55-->His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.

Unraveling the genetic basis of asthma and allergic diseases

Asthma and allergic diseases are believed to be complex genetic diseases which may result from the interaction of multiple genetic factors and environmental stimuli. In past decades, great efforts have been exerted in unraveling their genetic basis. The strategies in discovering genes and genetic variants, confirming their importance in pathogenesis of asthma and allergic diseases, as well as their strengths and limitations are summarized comprehensively and concisely. The current consensus about the genetic basis of asthma and allergic diseases is briefly described as well.

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.

The genetic and environmental basis of atopic diseases

The prevalence of atopic diseases has increased abruptly in recent years in most Westernized societies, making the question why this happened the topic of a heated debate. The best paradigm available to date to explain this steep rise, the 'hygiene hypothesis', supports that it is the excess 'cleanliness' of our environments that has led to the decline in the number of infectious stimuli that are necessary for the proper development of our immune system. Recent findings support that it is the combined effect that not only pathogenic, but also non-pathogenic microorganisms, and even their structural components,can exert on the immune system that deters from the development of atopic responses. Adding to these results are intriguing new findings on the effect different gene polymorphisms can have on an individual's predisposition to allergic diseases. The most important linkages produced, to date, include those among the genes for IL-4, IL-13, HLA-DRB, TNF, LTA,FCER1B, IL-4RA, ADAM33, TCR alpha/delta, PHF11, GPRA, TIM, p40, CD14, DPP10, T-bet, GATA-3, and FOXP3 and allergic disorders. The two parallel research efforts, epidemiologic and genetic, are only recently starting to converge,producing fascinating results on the effect particular gene-environment interactions might have in the development of atopy.The most important lesson learned through this tremendous research effort is that not only a small number but thousands and millions of separate risk factors act in concordance in the production of the allergic phenotype.

Blocking IL-25 prevents airway hyperresponsiveness in allergic asthma

BACKGROUND

IL-25 (IL-17E), a member of the IL-17 family of immunoregulatory cytokines, has been implicated in the regulation of type 2 immunity. Its roles in antigen-driven airway inflammation and airway hyperresponsiveness (AHR) remain to be fully established.

OBJECTIVE

We sought to determine whether a neutralizing antibody against IL-25 represents a novel therapeutic for airway inflammation and hyperresponsiveness.

METHODS

We generated a neutralizing mAb against IL-25 and used this to inhibit IL-25 in a mouse model of allergic airway disease.

RESULTS

Blocking IL-25 in an experimental model of allergic asthma prevented AHR, a critical feature of clinical asthma. Administration of anti-IL-25 mAb during the sensitization phase resulted in significantly reduced levels of IL-5 and IL-13 production, eosinophil infiltration, goblet cell hyperplasia, and serum IgE secretion, and prevented AHR. Even more striking was the ability of anti-IL-25 mAb, administered only during the challenge phase of the response, specifically to prevent AHR even during an ongoing type 2 inflammatory response in the lungs.

CONCLUSION

IL-25 is critical for development of AHR.

CLINICAL IMPLICATIONS

We define a novel pathway for the induction of AHR and suggest that IL-25 represents an important therapeutic target for the treatment of asthma. Significantly, our antibody also blocks the binding of human IL-25 to its receptor.

Expression of Vascular Adhesion Protein-1 in Atopic Eczema

BACKGROUND

Vascular adhesion protein-1 (VAP-1) is an adhesion molecule with an enzymatic activity which partakes in the migration process of lymphocytes. The aim of this study was to investigate VAP-1 expression in atopic eczema (AE) in comparison with healthy controls and psoriatic individuals.

MATERIAL AND METHODS

Forty adult patients suffering from AE aged between 18 and 56 years were included in the study. The control group consisted of 35 healthy volunteers aged between 19 and 49 years and of 71 psoriatic patients aged between 23 and 89 years. The serum concentration of soluble VAP-1 (sVAP-1) was evaluated by ELISA and VAP-1 expression in the skin by immunohistochemistry.

RESULTS

Serum level of sVAP-1 in AE patients before treatment was significantly higher compared with healthy volunteers. Similarly, a higher mean number of VAP-1-positive vessels was found in both lesional and nonlesional atopic skin compared with healthy skin. Treatment of AE resulted in a significant reduction in the serum level of sVAP-1. On the other hand, both the serum level of sVAP-1 and the number of dermal vessels with expression of VAP-1 were significantly lower in AE patients compared with psoriatic individuals.

CONCLUSION

This study indicates the important role of VAP-1 in the pathogenesis of chronic inflammatory cutaneous disorders, including AE.

Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus

T cell receptors (TR), through their interaction with the major histocompatibility complex, play a central role in immune responsiveness and potentially immune-related disorders. We resequenced all 57 variable (V) genes in the human T cell receptor alpha and delta (TRA/TRD) locus in 40 individuals of Northern European, Mexican, African-American and Chinese descent. Two hundred and eighty-four single nucleotide polymorphisms (SNPs) were identified. The distribution of SNPs between V genes was heterogeneous, with an average of five SNPs per gene and a range of zero to 15. We describe the patterns of linkage disequilibrium for these newly discovered SNPs and compare these patterns with other emerging large-scale datasets (e.g. Perlegen and HapMap projects) to place our findings into a framework for future analysis of genotype-phenotype associations across this locus. Furthermore, we explore signatures of natural selection across V genes. We find evidence of strong directional selection at this locus as evidenced by unusually high values of Fst.

PDCD1: a tissue-specific susceptibility locus for inherited inflammatory disorders

Variation in genes encoding costimulatory molecules expressed on lymphocytes has been expected to contribute to the genetic component of inflammatory disease, but only the gene encoding the inhibitory protein, CTLA-4, seems consistently to confer disease susceptibility. Studies in murine models implicate the inhibitory product of the pd1 gene, programmed death-1, in the maintenance of peripheral tolerance to self-antigens. We identify 22 single-nucleotide polymorphisms (SNPs) in the equivalent human gene, PDCD1, a number of which show significant associations with the specific immunoglobulin E response to grass allergens in atopic individuals. Stepwise analyses indicate that four of the disease-associated SNPs have independent effects. The two most common haplotypes show positive and negative associations but rarer haplotypes are also likely to be of influence. In a case-control study, multiple regression analysis of genotypic data implies that PDCD1 also confers susceptibility to rheumatoid arthritis. Along with work linking PDCD1 with susceptibility to another autoimmune condition, systemic lupus erythematosus, our data identify PDCD1 as a second immunomodulatory gene with pleiotropic effects in human disease. Genes encoding negative regulators may generally confer a significant fraction of the genetic risk associated with inherited inflammatory disorders.

CD1d-Independent Developmental Acquisition of Prompt IL-4 Gene Inducibility in Thymus CD161(NK1)−CD44lowCD4+CD8− T Cells Is Associated with Complementarity Determining Region 3-Diverse and Biased Vβ2/Vβ7/Vβ8/Vα3.2 T Cell Receptor Usage

Among Ag-inexperienced naive T cells, the CD1d-restricted NKT cell that uses invariant TCR-alpha-chain is the most widely studied cell capable of prompt IL-4 inducibility. We show in this study that thymus CD161-CD44lowCD4+CD8- T cells promptly produce IL-4 upon TCR stimulation, a response that displays biased Vbeta(2/7/8) and Valpha3.2 TCR usage. The association of Vbeta family bias and IL-4 inducibility in thymus CD161-CD44lowCD4+CD8- T cells is found for B6, B10, BALB/c, CBA, B10.A(4R), and ICR mouse strains. Despite reduced IL-4 inducibility, there is a similarly biased Vbeta(2/7/8) TCR usage by IL-4 inducibility+ spleen CD161-CD44lowCD4+CD8- T cells. Removal of alpha-galacotosylceramide/CD1d-binding cells from CD161-CD44lowCD4+CD8- thymocytes does not significantly affect their IL-4 inducibility. The development of thymus CD161-CD44lowCD4+CD8- T cells endowed with IL-4 inducibility and their associated use of Vbeta(2/7/8) are beta2-microglobulin-, CD1d-, and p59fyn-independent. Thymus CD161-CD44lowCD4+CD8- T cells produce low and no IFN-gamma inducibility in response to TCR stimulation and to IL-12 + IL-18, respectively, and they express diverse complementarity determining region 3 sequences for both TCR-alpha- and -beta-chains. Taken together, these results demonstrate the existence of a NKT cell distinct, TCR-repertoire diverse naive CD4+ T cell subset capable of prompt IL-4 inducibility. This subset has the potential to participate in immune response to a relatively large number of Ags. The more prevalent nature of this unique T cell subset in the thymus than the periphery implies roles it might play in intrathymic T cell development and may provide a framework upon which mechanisms of developmentally regulated IL-4 gene inducibility can be studied.

Intervention during pregnancy and allergic disease in the offspring

The etiology of allergy is multifactorial, with many variables contributing to the final expression of atopic disease. Three breeding grounds are needed to develop allergic disease: the appropriate genetic background, contact with the allergen(s) and environmental factors. Timing and dosing of allergen(s) are of major importance. Contact with (dietary) allergens and various agents such as tobacco smoke and infections occur not only during post-natal life, but also perinatally and even pre-natally. A critical review of published evidence regarding the impact of maternal exposure to antigens during pregnancy on later development of allergy in the offspring can only conclude that more research is urgently needed. Contact with multiple dietary allergens should be in general of benefit to the fetus to develop tolerance. Current knowledge suggests that pregnant women should have a normal diversified diet, avoiding toxic agents such as tobacco and alcohol. The role of maternal intake of poly-unsaturated fatty acids on the development of atopy in the infants needs to be further evaluated. If parental history would be insufficient to determine the fetal risk, preventive measurements would be advisable for all fetuses.

Association study of mast cell chymase polymorphisms with atopy

BACKGROUND

Atopic disorders are the result of complex interactions between genetic and environmental factors. Associations analyses between the promoter polymorphism rs1800875 in the mast cell chymase gene (CMA1) and atopy-related phenotypes have yielded inconsistent results.

METHODS

We sequenced the CMA1 locus in 24 unrelated healthy individuals with serum IgE levels <50% percentile and 24 individuals with atopic eczema and serum IgE levels >90% percentile. Seven CMA1 single nucleotide polymorphisms (SNPs) were evaluated for evidence of associations with atopic phenotypes within a large population of German adults (n = 1875). Subjects were phenotyped by standardized questionnaires and interviews, skin prick testing and serum IgE measurements. Genotyping was performed using MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry).

RESULTS

Promoter polymorphism rs1800875 was significantly associated with atopic eczema. No associations between any other single SNP and atopic phenotypes could be detected. Haplotype reconstruction revealed four of 128 possible haplotypes reaching estimated frequencies of 3% or more. Two of these haplotypes showed a borderline-significant association with atopic eczema, which did not remain significant after correction for multiple testing.

CONCLUSIONS

Results confirm previous observations of a significant association between the CMA1 promoter polymorphism rs1800875 and atopic eczema, but not with serum IgE levels, and support the hypothesis that CMA1 serves as candidate gene for atopic eczema.

Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma

CD4 + lymphocytes play a key role in asthma pathogenesis, but much remains unknown about the genetic mechanisms that affect disease severity. In this study we sought to investigate global patterns of gene expression in CD4 + lymphocytes isolated from subjects with severe asthma through the use of microarray technology. CD4 + lymphocytes were separated from peripheral blood, total RNA was purified, and biotinylated complementary RNA was prepared and hybridized to Affymetrix HU133 chips (Affymetrix, Santa Clara, Calif). Using the robust multi-chip average procedure, we compared the messenger RNA expression profiles of more than 33,000 genes of CD4 + lymphocytes in subjects with severe ( n = 5) and mild ( n = 5) asthma. Forty genes had 2-fold mean expression differences or greater. Thirty-seven genes were up-regulated, including transforming growth factor-beta and those involved in T-cell activation, proliferation, and cytoskeletal changes. Three genes were down-regulated, including the T-cell-receptor delta locus. This study demonstrates a method by which CD4 + lymphocytes can be extracted from blood for the purpose of microarray analysis. Furthermore, we show that T-lymphocytes from the peripheral blood of subjects with severe and mild asthma differ in their gene-expression profiles, supporting the view that asthma is a systemic disease. These differentially expressed genes identify potential molecular targets for preventive and therapeutic options for severe asthma.

Linkage/association study of a locus modulating total serum IgE on chromosome 14q13-24 in families with asthma

BACKGROUND

A study was undertaken to validate a locus modulating total serum IgE levels on 14q13-24.

METHODS

A linkage and association study was performed between total serum IgE and a panel of seven microsatellites which map to the 14q13-24 region in 69 families with asthma recruited from Leeds, UK.

RESULTS

Non-parametric, multipoint, sib pair analysis showed no evidence of genetic linkage between the quantitative trait "log IgE" and any of the tested markers. However, a significant association was observed between locus D14S63 (14q23) and total serum IgE (p = 0.017). Allelic analysis showed an association between low total IgE and allele 157 of D14S63 (p = 0.01, OR = 0.63, 95% CI 0.44 to 0.90). Modelling of allele 157 genotypes as a continuous covariate indicated evidence of a significant inverse linear trend across the three genotypes where 157 homozygotes had the lowest mean log IgE (p = 0.045). Association of D14S63 with log IgE was confirmed in the analysis of a combined dataset of 53 families from Southampton, UK and the 69 families from Leeds (total 122 families). An association was observed at the locus level (p = 0.022) and the allelic level where allele 165 showed an association with high total IgE (p = 0.001, OR = 3.79, 95% CI 1.54 to 9.7) and allele 157 showed an association with low total IgE (p = 0.041, OR = 0.77, 95% CI 0.6 to 0.99). The transmission disequilibrium test was positive for allele 165 (p<0.05) and negative for allele 157 (p>0.05).

CONCLUSIONS

Despite the lack of linkage, the findings of this study support the previous observation of a gene(s) at 14q23 that modulates total serum IgE.

Gene polymorphisms within the immune system that may underlie drug allergy

Drug allergy encompasses a broad spectrum of different diseases. It occurs in some individuals, whereas it does not occur in many others. This suggests, among others, the involvement of hereditary factors, and thus of gene polymorphisms. Since drug metabolising enzymes as well as the immune system itself may be responsible for drug allergy, gene polymorphisms are relevant in both systems. While already some information exists on gene polymorphisms of drug metabolising enzymes that result in drug allergy, little information is available on gene polymorphisms within the immune system that result in such allergy. This review sets out to provide an avenue for future research aimed at discovering such polymorphisms. To this end, immune mechanisms that underlie drug allergy will be discussed. A pivotal mechanism underlying several types of drug allergy, immediate-type (type I) hypersensitivity, is also a hallmark of asthma, and therefore drug allergy and asthma share a range of candidate genes. Research on asthma has come relatively far in establishing associations of disease with polymorphisms in these genes. Therefore, these polymorphisms and their associations with asthma will be discussed. These studies on asthma provide us with lessons on how to conduct such studies on drug allergy.

Novel association suggests multiple independent QTLs within chromosome 5q21-33 region control variation in total humans IgE levels

Asthma is a common, heterogeneous, complex disease accompanied by raised total and specific immunoglobulin-E (IgE) antibody levels. Despite numerous previous reports of linkage and association of asthma, atopy and serum IgE levels to genes within the 5q21-33 region, definitive, replicable results are still not available. We used the classical twin design to (i) estimate the relative contributions of genes and environment to variation in total IgE levels, (ii) assess genetic linkage, and (iii) examine allelic association of 11 microsatellite markers spanning the 5q21-33 region to total IgE. Variation in total IgE level was shown to be highly heritable (65%). Although evidence for linkage of the 11 microsatellites to IgE was not observed, the omnibus test of association, not confounded by population substructure, showed positive association of D5S393 and D5S673 to IgE. Genes in the vicinity of D5S673 include hepatitis A virus receptor (HAVCR-1) and IL-12B. Recently, the mouse orthologue of HAVCR-1, the T-cell membrane family of proteins, have been shown to be in strong association with expression of airway hyperactivity in a mouse model of human asthma and atopy. IL-12B subserves many proinflammatory functions and also induces B cells proliferation.

Genetic analyses in asthma: current concepts and future directions

Asthma is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. Numerous loci and candidate genes have been reported to show linkage and association of asthma and the asthma-associated phenotypes, atopy, elevated immunoglobulin E (IgE) levels, and bronchial hyper-responsiveness to alleles of microsatellite markers and single nucleotide polymorphisms (SNPs) within specific cytokine/chemokine, and IgE regulating genes. While many studies reporting these observations are compelling, only one asthma gene conferring high risk has been mapped. In this review, we present studies that support linkage and/or associations to the various genetic loci and genes in asthma. The first genome-wide scan for linkage to quantitative traits underlying asthma identified linkage on chromosome 4q, 6, 7, 11q, 13q and 16. A genome scan in American families from three racial groups revealed linkage to chromosome 2q, 5q, 6p, 12q, 13q and 14q. A two-stage scan in Hutterite families from the US found linkage on chromosome 5q, 12q, 19q and 21q. A screen in German families identified linkage to asthma on chromosome 2q, 6p, 9 and 12q and a two-stage genome scan in French families found replicated linkage on chromosomes 1p, 12q and 17q. A study of asthma in Finland showed linkage to high IgE on 7q14. Apart from a European linkage study of 199 families with atopic dermatitis, which demonstrated significant linkage to chromosome 3q21, three other studies have reported linkage results of genome-wide significance, including a linkage study in 175 Icelandic asthma families (14q24), a study in 533 Chinese families with bronchial hyper-responsiveness (chromosome 2) and a study in 47 Japanese families with mite-sensitive atopic asthma (5q31), suggesting that these regions may harbor genes contributing to the development of asthma and allergies. While significant progress has been made in the field of asthma genetics in the past decade, the clinical implications of the genes and genetic variations within the numerous candidate asthma genes that have been found to associate with the expression of the asthmatic phenotype, remain undetermined.

5. Genetics of hypersensitivity

Genetics provides the basis for the host response to a variety of environmental factors that can play a role in the generation of complex genetic diseases, such as asthma and atopy. An understanding of the genetic bases for these conditions is therefore essential to understand their pathophysiology. Studies of the genetics of asthma and atopy have suffered from several daunting challenges. These include the recognition that these are conditions caused by numerous genes, with each gene assuming variable roles in different individuals. In addition, each gene presumably contributes only a small percentage to a given individual's genetic risk of asthma. This has led to the current situation, in which studies often demonstrate a lack of replication that can be explained by their being insufficiently powered. Furthermore, the pathophysiologies of asthma and atopy are incompletely understood, and the lack of clearly defined phenotypes also contributes to the inadequacies of the current literature. Nonetheless, regions of the human genome have been reproducibly associated with asthma and atopy. These regions have undergone intense study, and many genetic variants within them have been implicated as asthma and allergy genes. In addition, through candidate gene approaches, several genetic polymorphisms have been convincingly linked to increased risks for the development of asthma and atopy. Many of these genes are associated with alterations in responsiveness to therapeutic agents used in the treatment of these conditions. These genetic studies have an exciting potential for individually tailoring the therapeutic regimen to a given subject's genotype. It is to be hoped that they will also define new targets for the next generation of asthma and allergy therapeutic agents.

Genetics and genomics of asthma and allergic diseases

Asthma and eczema (atopic dermatitis) are characterized by a number of unexplained phenomena: the familial aggregation of disease, the initiation of disease by apparently trivial exposure to allergens, the preferential transmission of disease from affected mothers and the large increase in prevalence of disease in Westernized societies in the last century. A number of genes and chromosomal regions have been identified that consistently show linkage to asthma and its related phenotypes. Known loci modify the strength of the atopic response, nonspecific inflammation, the ability to respond to particular allergens and nonspecific airway reactivity. Eczema has been shown to be due to a different set of genetic loci that are shared with other skin diseases such as psoriasis and leprosy. Genetic and genomic studies both provide evidence that epithelial surfaces are active in the induction of allergic disease.

Sequence variation in the human T-cell receptor loci

Identifying common sequence variations known as single nucleotide polymorphisms (SNPs) in human populations is one of the current objectives of the human genome project. Nearly 3 million SNPs have been identified. Analysis of the relative allele frequency of these markers in human populations and the genetic associations between these markers, known as linkage disequilibrium, is now underway to generate a high-density genetic map. Because of the central role T cells play in immune reactivity, the T-cell receptor (TCR) loci have long been considered important candidates for common disease susceptibility within the immune system (e.g., asthma, atopy and autoimmunity). Over the past two decades, hundreds of SNPs in the TCR loci have been identified. Most studies have focused on defining SNPs in the variable gene segments which are involved in antigenic recognition. On average, the coding sequence of each TCR variable gene segment contains two SNPs, with many more found in the 5', 3' and intronic sequences of these segments. Therefore, a potentially large repertoire of functional variants exists in these loci. Association between SNPs (linkage disequilibrium) extends approximately 30 kb in the TCR loci, although a few larger regions of disequilibrium have been identified. Therefore, the SNPs found in one variable gene segment may or may not be associated with SNPs in other surrounding variable gene segments. This suggests that meaningful association studies in the TCR loci will require the analysis and typing of large marker sets to fully evaluate the role of TCR loci in common disease susceptibility in human populations.

Asthma

Asthma is one of the commonest chronic diseases of affluent societies. The striking increase in prevalence of asthma over recent decades and the rarity of this disease in less affluent populations confirms the importance of environmental factors in the cause of asthma--although which environmental factors are responsible is still not clear. Family studies show that genetic factors are also important in determining individual susceptibility to asthma, with results of genetic studies suggesting that there are many genes with moderate effects rather than a few major genes. Asthmatic airways show inflammation and remodelling, with CD4+ helper cells, mast cells, and eosinophils characterising the inflammatory response. Inhaled corticosteroids remain the cornerstone of treatment with the addition of long-acting beta agonists as the next step if symptoms continue. Leukotriene antagonists, the only new drugs to reach the market in the past decade, have modest effects. However, a better understanding of the mechanisms underlying asthma and the genetic and environmental factors that predispose individuals to asthma should lead to better preventative strategies and new therapeutic approaches.

Association analysis of polymorphisms in the interleukin-4 receptor (alpha) gene with atopic asthma in patients from western Mexico

We undertook an association analysis between the ile50val, glu375ala, cys406arg, and ser761pro polymorphisms of the IL-4Ralpha gene and atopic asthma, total IgE levels and IL-4 serum levels in a population from western Mexico. We found that the ser761pro polymorphism was monomorphic for ser761, while there was no association between any of the other polymorphisms and the three phenotypes analysed.

Asthma and atopy - a total genome scan for susceptibility genes

BACKGROUND

Allergic asthma is an increasingly common disease of complex inheritance. Several studies have suggested candidate regions, but genetic heterogeneity, ethnic differences and varying study designs may in part explain the lack of identified and confirmed susceptibility genes. Investigation of different populations will further clarify the topic. We therefore evaluated allergic asthma and increased total and specific IgE in 39, 45 and 57 sib-pairs from 100 Danish allergy families.

METHODS

Affected sib-pairs meeting a narrow phenotype definition were selected for the three phenotypes atopy, allergic asthma and increased total IgE. We performed a total genome scan using 446 microsatellite markers and obtained nonparametric linkage results from the MAPMAKER/SIBS computer program.

RESULTS

Our study revealed four candidate regions (MLS > 2) on chromosome 1p36, 3q21-q22, 5q31 and 6p24-p22, and 15 candidate regions (1 < MLS < 2) that may contain susceptibility genes for asthma and atopy. We did not find linkage to the candidate genes TNF-beta, FcER1beta and Il4R-alpha, except for weak support for linkage of the asthma phenotype to TNF-beta (MLS = 1.18).

CONCLUSIONS

We found evidence for two new asthma and atopy loci, 1p36 and 3q21-q22, and supported linkage in the Danish population to seven previously reported candidate regions.

Candidate genes for atopic asthma: current results from genome screens

Atopic asthma is one of the most common childhood diseases in developed countries. Asthma is characterized by reversible airway obstruction, bronchial hyper-responsiveness, and airway inflammation. Atopy in childhood is considered the strongest predisposing factor for asthma. The etiology of asthma is complex and is thought to involve the interaction of multiple genes and a variety of environmental factors such as allergens and viral and bacterial infections. To identify genes conferring susceptibility for asthma and atopy, many genome-wide screens for asthma and its associated traits have now been carried out, and genetic linkage has been consistently identified in several regions. Several independent genome-wide screens found regions of linkage with asthma on chromosomes 5, 6, 11, 12, 13, 16 and 19, identifying candidate susceptibility genes including FCER1B, the IL-4 gene cluster, TNFalpha, HLA loci and others. However, the evidence for linkage is still only suggestive for most regions. In an effort to clarify the mechanism underlying the development of asthma, further studies utilizing new technologies and data from the Human Genome Project are ongoing. It is hoped that this accumulation of data will lead to improved genetic testing and assist in the development of new drugs.

Polymorphism in the STAT6 gene encodes risk for nut allergy

Nut allergy is an important and potentially life threatening food allergy with a prevalence of one in 150 children in the UK population. STAT6 (signal transducer and activator of transcription) is an important molecule in the induction and regulation of an allergic response, which maps to chromosome 12q in a region previously linked with total serum IgE concentration and atopy in different populations. We have examined the frequency of a single nucleotide polymorphism (SNP) in the 3'UTR region of STAT6 gene in 71 UK Caucasoid patients diagnosed with nut allergy and 45 atopic patients without nut allergy using PCR-RFLP and compared these with 184 UK healthy controls. The STAT6 G allele frequency was significantly increased in nut allergy patients compared with blood donor controls (P < 0.0001, OR = 2.9, 95% CI: 1.7-4.9), which was under a recessive model (GG vs GA+AA, P = 0.0001, OR = 3.2, 95% CI: 1.7-5.8) but not in atopic patients without nut allergy. The G allele was most frequent in the severe cases and GG homozygosity was associated with the increased risk of severe reaction (OR = 3.9, 95% CI: 1.9-8.3). We conclude that STAT6 3'UTR polymorphism is associated with susceptibility and severity in nut allergic patients in our population.

The pathophysiology of asthma

Asthma is a chronic disorder of the airways that is characterized by reversible airflow obstruction and airway inflammation, persistent airway hyperreactivity, and airway remodeling. The etiology of asthma is complex and multifactorial. Recent advances have demonstrated the importance of genetics in the development of asthma, particularly atopic asthma. Environmental stimuli, particularly early childhood infections, have also been associated with the development of asthma. Most current data seem to suggest that these factors drive the development of a Th-2 lymphocyte-predominant immune response, which has been associated with atopy and IgE-mediated inflammation. The concept of reversible airflow obstruction has also recently been challenged. It is now clear that chronic airway changes occur, which may contribute to progressive airflow obstruction. We discuss the important influence of genetic and environmental factors on the emergence of the asthmatic phenotype. The significance of Th-1 and Th-2 lymphocyte-mediated immunity are discussed, and the inflammatory processes leading to chronic airway inflammation are detailed.

Asthma genetics

Asthma is the most common chronic childhood disease in developed nations and 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. Identifying the genes underlying asthma offers a means of better understanding its pathogenesis, with the promise of improving preventive strategies, diagnostic tools, and therapies. A number of chromosomal regions containing genes influencing asthma and atopy have been identified consistently by different groups, and a role for several candidate genes has been established.

Vbeta18.1(+) and V(alpha)2.3(+) T-cell subsets are associated with house dust mite allergy in human subjects

BACKGROUND

The recognition of allergenic peptides by T cells through their T-cell receptor (TCR) represents a crucial step in the initiation of an allergen-specific immune response. In parallel to the superantigen-driven restricted expansion of Vbeta subsets in autoimmune and infectious diseases, reports in animals and human subjects have shown a similar capacity of classical antigens.

OBJECTIVE

The study was performed to analyze the V(alpha)/Vbeta expression in house dust mite (HDM) allergy.

METHODS

The TCR repertoire of 15 subjects with HDM allergy, 22 atopic subjects without HDM allergy, and 19 nonatopic individuals, members of 2 extended and 4 nuclear families, was determined. By using flow cytometry, the expression of 22 Vbeta and 3 V(alpha) elements was analyzed in vivo and after in vitro allergen stimulation.

RESULTS

In comparison with nonatopic and atopic individuals without HDM allergy, freshly isolated PBMCs of individuals with HDM allergy showed a significantly higher frequency of Vbeta18(+) and V(alpha)2.3(+) T cells. Although members of all 3 groups had a similar lymphocyte proliferation response after in vitro stimulation with Der p 1 or Der p 1 peptide(101-131), a significant expansion of Vbeta18(+) and V(alpha)2.3(+) T cells in vitro occurred only in individuals with HDM allergy. Moreover, the degree of expansion correlated with the levels of allergen-specific IgE antibodies. No expansion of Vbeta18(+) and V(alpha)2.3(+) was observed after mitogen stimulation with PHA, indicating allergen specificity of the response.

CONCLUSION

Our results strongly suggest restricted TCR V(alpha)/Vbeta gene use in HDM allergy and might be a step toward TCR-based immunotherapy.

Lack of association between atopic eczema and the genetic variants of interleukin-4 and the interleukin-4 receptor alpha chain gene: heterogeneity of genetic backgrounds on immunoglobulin E production in atopic eczema patients

BACKGROUND

The genetic background of atopic eczema might be heterogeneous and there is a possibility that immunoglobulin (Ig)E responsiveness in patients with atopic eczema is controlled separately from the development of atopic eczema. Although both interleukin (IL)-4 and the IL-4 receptor alpha chain have an important role for IgE production and are therefore possible candidate genes for atopy, it has not been clarified whether these genes play any roles in atopic eczema patients who have normal IgE productivity.

OBJECTIVE

We aimed to assess whether the polymorphisms of the IL-4 gene and the IL-4 receptor alpha chain gene play any roles in atopic eczema patients, particularly in patients who have normal IgE productivity.

METHOD

We determined the genotype with regard to polymorphisms in the genes for IL-4 and the IL-4 receptor alpha chain (- 589C/T of IL-4; Ile50Val, Ala375Glu and Arg551Gln of IL-4 receptor alpha chain) in patients with atopic eczema using the fluorogenic 5' nuclease assay.

RESULTS

IL-4 and the IL-4 receptor alpha chain genotypes were not significantly associated with either total patients with atopic eczema or atopic eczema patients who had normal IgE productivity. The distribution of genotypes of IL-4-589C/T differed by the serum IgE levels in patients with atopic eczema.

CONCLUSION

These results suggest that the polymorphisms in the IL-4 gene and the IL-4 receptor alpha chain gene play no role in the development of atopic eczema in patients who have normal IgE productivity.

T cell receptor Vbeta expression in patients with allergic asthma before and after repeated low-dose allergen inhalation

The objective of this study was to identify disease-associated T cell subsets by characterizing the lung and blood T cell receptor (TCR) repertoires in allergic asthmatics before and after repeated low-dose allergen challenge. Peripheral blood lymphocyte (PBL) and bronchoalveolar lavage (BAL) samples were obtained from eight patients with allergic asthma before and after a period of repeated low-dose allergen inhalations. RT-PCR followed by Southern blot allowed the quantification of relative Vbeta gene segment usage. Thirteen healthy individuals served as controls at PBL level. PBL as well as BAL T cells of asthmatics displayed a higher usage of Vbeta3, Vbeta5.2, and Vbeta6.1-3 and a lower usage of Vbeta16, Vbeta18, and Vbeta19 compared to PBL of healthy controls. Interestingly, TCR Vbeta7 and Vbeta9 usage was significantly higher in BAL than in PBL in asthmatics before as well as after challenge. TCR repertoire alterations after allergen challenge differed between individuals, with relatively mild changes.

Pathophysiological mechanisms of asthma. Application of cell and molecular biology techniques

Asthma is a common increasing and relapsing disease that is associated with genetic and environmental factors such as respiratory viruses and allergens. It causes significant morbidity and mortality. The changes occurring in the airways consist of a chronic eosinophilic and lymphocytic inflammation, together with epithelial and structural remodeling and proliferation, and altered matrix proteins, which underlie airway wall narrowing and bronchial hyperresponsiveness (BHR). Several inflammatory mediators released from inflammatory cells such as histamine and cysteinyl-leukotrienes induce bronchoconstriction, mucus production, plasma exudation, and BHR. Increased expression of T-helper 2 (Th2)-derived cytokines such as interleukin-4 and 5 (IL-4, 5) have been observed in the airway mucosa, and these may cause IgE production and terminal differentiation of eosinophils. Chemoattractant cytokines (chemokines) such as eotaxin may be responsible for the chemoattraction of eosinophils to the airways. The initiating events are unclear but may be genetically determined and may be linked to the development of a Th2-skewed allergen-specific immunological memory. The use of molecular biology techniques on tissues obtained from asthmatics is increasing our understanding of the pathophysiology of asthma. With the application of functional genomics and the ability to transfer or delete genes, important pathways underlying the cause if asthma will be unraveled. The important outcome of this is that new preventive and curative treatments may ensue.

Current concepts on the genetics of asthma

Asthma is a complex genetic disorder with variable phenotype, largely attributed to the interactions of the environment and multiple genes, each potentially having small effects. Numerous asthma and atopy loci have been reported in studies demonstrating associations and/or linkage of the asthma-associated phenotypes, atopy, elevated IgE levels, and bronchial hyperresponsiveness to alleles of microsatellite markers and single nucleotide polymorphisms within specific cytokine/chemokine and IgE regulating genes. Although the studies reporting these observations are compelling, most of them lack statistical power. This review compiles the evidence that supports linkage and associations to the various genetic loci and candidate genes. Whereas significant progress has been made in the field of asthma genetics in the past decade, the roles of the genes and genetic variations within the numerous candidate asthma genes that have been found to associate with the expression of the asthmatic phenotype remain to be determined.

Chromosome 14 linkage analysis and mutation study of 2 serpin genes in allergic asthmatic families

BACKGROUND

Genome and chromosome screens reported DNA markers on chromosome 14 linked to allergic asthma or intermediate phenotypes in several populations.

OBJECTIVE

We sought to perform a linkage study on chromosome 14 and a further association study on candidate genes mapped in the region found to be linked to allergic asthma or intermediate phenotypes.

METHODS

The study consisted of a sample of 189 families (847 genotyped individuals) from a restricted geographic area in northeastern Italy. The subjects were characterized for the following phenotypes: allergic asthma, total serum IgE levels, skin prick test responses, and bronchial hyperresponsiveness (BHR) to methacholine. Genotyping was done with 14 DNA markers and 4 polymorphisms in the genes encoding alpha(1)-anti-trypsin and alpha(1)-antichymotrypsin (ACT).

RESULTS

Multipoint analysis indicated a potential linkage of BHR with marker D14S617 (nonparametric linkage z score = 2.32, P =.01). Transmission disequilibrium of Thr -15Ala in the gene encoding ACT was observed with all the phenotypes investigated: allergic asthma, BHR, total IgE levels, or skin prick test responses (P =.041,.02,.0053, or.026, respectively).

CONCLUSION

Chromosome 14 screening and transmission disequilibrium testing on the gene encoding ACT suggest that it or a closely located gene may be involved in susceptibility to allergic asthma in the Italian population.

Association study of proposed candidate genes/regions in a population of Spanish asthmatics

A number of genes/regions have recently been reported to be linked to asthma or its related phenotypes (i.e. atopy and bronchial hyperresponsiveness), by genetic linkage and allele-sharing methods. We have performed a case-control study comparing the allelic distribution of nine microsatellite markers and two genetic variants in a group of patients attended at emergency room departments because of an acute attack of asthma with respect to an external healthy population of controls. A total of 146 asthmatic subjects and 50 population controls from Barcelona, Spain, were genotyped for nine microsatellite markers from some asthma/atopy candidate genes/regions: the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) located on chromosome 11; the 5q31-32 candidate region; the T-cell receptor genes, TCR-alpha on chromosome 14 and TCR-beta on chromosome 7. Two genetic variants of the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) gene were also analyzed. None of the asthmatic or control individuals carried the Ile181Leu variant. There were no significant differences between asthmatic and control subjects neither for the polymorphic markers nor for the other variant of the beta-subunit of the high-affinity IgE receptor (Fc epsilonRI-beta) gene. No association could be observed in this sample of Spanish asthmatics with the genes/regions studied.

Extent and distribution of linkage disequilibrium in three genomic regions

The positional cloning of genes underlying common complex diseases relies on the identification of linkage disequilibrium (LD) between genetic markers and disease. We have examined 127 polymorphisms in three genomic regions in a sample of 575 chromosomes from unrelated individuals of British ancestry. To establish phase, 800 individuals were genotyped in 160 families. The fine structure of LD was found to be highly irregular. Forty-five percent of the variation in disequilibrium measures could be explained by physical distance. Additional factors, such as allele frequency, type of polymorphism, and genomic location, explained <5% of the variation. Nevertheless, disequilibrium was occasionally detectable at 500 kb and was present for over one-half of marker pairs separated by <50 kb. Although these findings are encouraging for the prospects of a genomewide LD map, they suggest caution in interpreting localization due to allelic association.

Using single nucleotide polymorphisms as a means to understanding the pathophysiology of asthma

Asthma is the most common chronic childhood disease in the developed nations, and is a complex disease that has high social and economic costs. Studies of the genetic etiology of asthma offer a way of improving our understanding of its pathogenesis, with the goal of improving preventive strategies, diagnostic tools, and therapies. Considerable effort and expense have been expended in attempts to detect specific polymorphisms in genetic loci contributing to asthma susceptibility. Concomitantly, the technology for detecting single nucleotide polymorphisms (SNPs) has undergone rapid development, extensive catalogues of SNPs across the genome have been constructed, and SNPs have been increasingly used as a method of investigating the genetic etiology of complex human diseases. This paper reviews both current and potential future contributions of SNPs to our understanding of asthma pathophysiology.

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.

Mutation screening of interferon regulatory factor 1 gene (IRF-1) as a candidate gene for atopy/asthma

BACKGROUND

IL-4 gene cluster on chromosome 5 contains several candidate genes for atopy and asthma. Several independent studies have shown evidence for linkage between the markers flanking IL-4 gene cluster and asthma and/or asthma-related traits. Interferon regulatory factor 1 (IRF-1) is located approximately 300 kb telomeric to IL-4 and recent study reveals that IRF-1 deficiency results in an elevated production of Th2-related cytokines and a compensatory decrease in the expression of native cell- and Th1-related cytokines.

OBJECTIVE

To determine if there are any mutations associated with the development of atopy and asthma present in the coding exons and 5' flanking region of the IRF-1 gene.

METHODS AND RESULTS

We have screened the promoter and coding regions of the IRF-1 gene in atopic asthmatics and controls by SSCP method. We found three novel nuclear variants (the -300G/T and 4396 A/G polymorphisms and the 6355G > A rare variant) in the IRF-1 gene. No variants causing amino acid alterations of IRF-1 were detected. The -300G/T polymorphism was in nearly complete linkage disequilibrium with the 4396 A/G polymorphism. An association between the 4396 A > G polymorphism and atopy/asthma was examined by transmission disequilibrium test in 81 asthmatic families. Either of 4396 A or 4396G alleles was not significantly preferentially transmitted to atopy- or asthma-affected children.

CONCLUSION

The IRF-1 gene is less likely to play a substantial role in the development of atopy and asthma in the Japanese population.