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

Influence of Polymorphisms in the Interleukin-18 Gene on Allergic Rhinitis: A Meta-Analysis

PURPOSE

Reported associations of interleukin-18 (IL-18) single-nucleotide polymorphisms (SNPs) with allergic rhinitis (AR) have been inconsistent, prompting a meta-analysis to obtain more precise estimates.

METHODS

We synthesized data from 8 articles and examined 3 IL-18 SNPs. Two SNPs (rs360721 and rs187238), in linkage disequilibrium, were combined and termed RS1. The rs1946518 SNP was analyzed separately (termed RS2). The recessive, dominant, and codominant (multiplicative) genetic models were used to estimate ORs and 95% CIs. Subgroup analysis was ethnicity-based. Sources of heterogeneity were investigated with outlier treatment. Sensitivity analysis was used to assess robustness of the associative effects. Multiple comparisons were Holm-Bonferroni corrected.

RESULTS

All significant (pa < 0.05) outcomes indicating increased risks were found in the dominant/codominant models in RS1 and RS2. Five aspects of differences marked the significant African (RS1) and overall (RS2) outcomes: (i) magnitude of effect (ORs): greater (3.01-5.15) versus less (1.20-1.47); (ii) precision of -effects (95% CIs): less (1.07-21.52) versus more (1.01-1.89); (iii) outlier treated: no versus yes; (iv) sensitivity outcomes: nonrobust versus robust (dominant model only); and (v) greater evidential strength for RS2 (pa = 0.002) compared to RS1 (pa = 0.02) rendered RS2 our core finding. These levels of statistical significance for RS1/RS2 enabled both to survive the Holm-Bonferroni correction.

CONCLUSIONS

The core outcome indicating a 1.5-fold increased risk could render the IL-18 polymorphisms useful in the clinical genetics of AR. Future studies that could focus on other IL-18 SNPs may find deeper associations with AR than what we found here.

Association of FcεRIβ polymorphisms with risk of asthma and allergic rhinitis: evidence based on 29 case-control studies

Purpose: Accumulating evidence has shown that allergic diseases are caused by a complex interaction of genetic and environmental factors, some single nucleotide polymorphisms (SNPs) existing in high-affinity IgE receptor β chain (FcεRIβ) are potential risk factors for allergic diseases. However, the results have been inconsistent and inconclusive due to the limited statistical power in individual study. Thus, we conducted a meta-analysis to systematically evaluate the association between FcεRIβ SNPs and allergic diseases risk.

Methods: Eligible studies were collected from PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure, and WanFang databases. Pooled odd ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were calculated to assess the strength of the relationships between five polymorphisms (E237G, -109 C/T, RsaI_in2, RsaI_ex7, and I181L) and the risk of allergic diseases by using five genetic models. In addition, the stability of our analysis was evaluated by publication bias, sensitivity, and heterogeneity analysis.

Results: Overall, a total of 29 case–control studies were included in this meta-analysis. We found that E237G (B vs. A: OR = 1.28, 95% CI = 1.06–1.53, P<0.001, I² = 63.1%) and -109 C/T (BB vs. AA + AB: OR = 1.58, 95%CI = 1.26–1.98, P<0.001, I² = 66.4%) were risk factors for allergic diseases.

Conclusion: Our meta-analysis suggests that polymorphisms in FcεRIβ may be associated with the development of allergic diseases.

An understanding of the genetic basis of asthma

Asthma is the most common chronic childhood disease in developed nations and its prevalence has increased in the world over the last 25 years. It is a complex disease with both genetic and environmental risk factors. Asthma is caused by multiple interacting genes, some having a protective effect and others contributing to the disease pathogenesis, with each gene having its own tendency to be influenced by the environment. This article reviews the current state of the genetics of asthma in six categories, viz. epidemiology, management, aetiology, family and twin studies, segregation and linkage studies, and candidate genes and single nucleotide polymorphisms (SNPs).

Pharmacogenomics of pediatric asthma

CONTEXT:

Asthma is a complex disease with multiple genetic and environmental factors contributing to it. A component of this complexity is a highly variable response to pharmacological therapy. Pharmacogenomics is the study of the role of genetic determinants in the variable response to therapy. A number of examples of possible pharmacogenomic approaches that may prove of value in the management of asthma are discussed below.

EVIDENCE ACQUISITION:

A search of PubMed, Google scholar, E-Medicine, BMJ and Mbase was done using the key words “pharmacogenomics of asthma”, “pharmacogenomics of β-agonist, glucocorticoids, leukotriene modifiers, theophylline, muscarinic antagonists in asthma”.

RESULTS:

Presently, there are limited examples of gene polymorphism that can influence response to asthma therapy. Polymorphisms that alter response to asthma therapy include Arg16Gly, Gln27Glu, Thr164Ile for β-agonist receptor, polymorphism of glucocorticoid receptor gene, CRHR1 variants and polymorphism of LTC4S, ALOX5. Polymorphic variants of muscarinic receptors, PDE4 and CYP450 gene variants.

CONCLUSION:

It was concluded that genetic variation can improve the response to asthma therapy. However, no gene polymorphism has been associated with consistent results in different populations. Therefore, asthma pharmacogenomic studies in different populations with a large number of subjects are required to make possible tailoring the asthma therapy according to the genetic characteristic of individual patient.

Association of IL-4 and ADAM33 gene polymorphisms with asthma in an Indian population

There are more than 100 candidate genes of asthma located on 23 human chromosomes. Interleukin-4 (IL-4), located on chromosome 5q31, and ADAM33, located on chromosome 20p13, and some single nucleotide polymorphisms (SNPs) of these genes have been shown to be associated with asthma and its manifestations in different populations. The most prominent SNPs of IL-4 and ADAM33 are 589C>T and 400A>G, respectively. There are also controversial reports on the association of these SNPs with asthma. In the present study, we analyzed these two SNPs in 100 patients with asthma and 50 controls through PCR amplification and restriction digestion to evaluate association of these two SNPs with asthma. The nonsignificant differences were observed for the IL-4 promoter polymorphism C589T and the ADAM33 T1 polymorphism between asthmatic patients and controls (P = 0.638 and 0.943, respectively). Our data revealed that there is no association of these SNPs with asthma indicating that other SNPs of these genes or other genes might be involved in the manifestation of asthma.

Association of interleukin-18 gene polymorphism with asthma in Chinese patients

Like other allergic diseases, asthma results from multiple conditions. Asthmatic beginning and severity are mediated by both environmental and genetic factors. In asthma studies, important work is realization of the genetic background and identification of genetic factors resulting in asthma development and phenomena. Here, we investigated whether interleukin (IL)-18 single nucleotide polymorphisms (SNPs) are involved in Chinese asthma patients. IL-18 (IL-18) SNP was detected by polymerase chain reaction (PCR)-based restriction analysis in 201 patients with asthma and 60 normal controls. Significant differences were found in the genotype distribution of IL-18 SNP between asthma patients and controls (P=0.000003). Allelic frequency of the IL-18 gene distinguished asthma patients from controls (P=0.000066). The results revealed a significant difference between asthma patients and normal controls in IL-18 SNP and a statistical correlation between IL-18 polymorphisms (105A/C) and asthma formation. We concluded that Chinese who carry the C/C homozygote of the IL-18-105A/C gene polymorphism in coding regions may have a higher risk of developing asthma.

Pharmacogenetics of antiparkinsonian drug treatment: a systematic review

Pharmacotherapy is the mainstay in the treatment of Parkinson's disease and the armamentarium of drugs available for the therapy of this disease is still expanding. Anti-Parkinson's disease drugs are effective in reducing the physical symptoms, such as hypokinesia, bradykinesia, rigidity and tremor. However, there is a large interindividual variability in response to anti-Parkinson's disease drugs with respect to both drug efficacy and toxicity. It is thought that genetic variability in genes encoding drug-metabolizing enzymes, drug receptors and proteins involved in pathway signaling is an important factor in determining interindividual variability in drug response. Pharmacogenetics aims at identifying genetic markers associated with drug response. Ideally, knowledge of these genetic markers will enable us to predict an individual's drug response in terms of both efficacy and toxicity. The role of pharmacogenetics in the treatment of Parkinson's disease is relatively unexplored. Therefore, we aim to present a systematic review of the published pharmacogenetic studies in Parkinson's disease and to describe polymorphic genes of interest for future research.

Recent development in pharmacogenomics: from candidate genes to genome-wide association studies

Genetic diversity, most notably through single nucleotide polymorphisms and copy-number variation, together with specific environmental exposures, contributes to both disease susceptibility and drug response variability. It has proved difficult to isolate disease genes that confer susceptibility to complex disorders, and as a consequence, even fewer genetic variants that influence clinical drug responsiveness have been uncovered. As such, the candidate gene approach has largely failed to deliver and, although the family-based linkage approach has certain theoretical advantages in dealing with common/complex disorders, progress has been slower than was hoped. More recently, genome-wide association studies have gained increasing popularity, as they enable scientists to robustly associate specific variants with the predisposition for complex disease, such as age-related macular degeneration, Type 2 diabetes, inflammatory bowel disease, obesity, autism and leukemia. This relatively new methodology has stirred new hope for the mapping of genes that regulate drug response related to these conditions. Collectively, these studies support the notion that modern high-throughput single nucleotide polymorphism genotyping technologies, when applied to large and comprehensively phenotyped patient cohorts, will readily reveal the most clinically relevant disease-modifying and drug response genes. This review addresses both recent advances in the genotyping field and highlights from genome-wide association studies, which have conclusively uncovered variants that underlie disease susceptibility and/or variability in drug response in common disorders.

Identifying novel genes contributing to asthma pathogenesis

PURPOSE OF REVIEW

To illustrate recent examples of novel asthma genes such as those encoding G-protein-coupled receptor for asthma susceptibility, filaggrin and tenascin-C, and to describe the process that is needed to translate these findings to the clinic.

RECENT FINDINGS

Many hundreds of studies have been published investigating the association of genetic polymorphisms in candidate genes with asthma. These genes were selected on the basis of the gene's product known involvement in the disease process. Moreover, it is the identification of novel genes through hypothesis-independent approaches such as genome-wide linkage studies that is likely to radically alter our understanding of asthma pathophysiology. The identification of a gene is, however, only the first step in a long process that may eventually lead from gene to treatment. This process includes replication, functional studies and, finally, intervention studies.

SUMMARY

While significant progress has been made in the identification of asthma susceptibility genes, it is clear that issues such as replication and functional characterization mean that considerably more research is required. This may enable us to realize benefits to patient treatment that studies of the genetic basis of asthma have the potential to deliver.

Association between ADAM33 polymorphisms and adult asthma in the Japanese population

BACKGROUND

ADAM33, a member of the ADAM (a disintegrin and metalloprotease) family, is a putative asthma susceptibility gene recently identified by positional cloning. It is important to know whether the association exists in ethnically diverse populations.

OBJECTIVE

To assess whether genetic functional variants of ADAM33 relate to the susceptibility or some phenotypes in adult patients with bronchial asthma in a Japanese population.

METHODS

We searched for single nucleotide polymorphisms (SNPs) in ADAM33 by PCR-directed sequencing and identified 48 SNPs. Fourteen SNPs were selected with regard to the LD pattern, and genotyped by Taq-Man and PCR-RFLP methods. We conducted an association study of ADAM33 with 504 adult asthmatic patients and 651 controls, and haplotype analyses of related variants were performed.

RESULTS

Significant associations with asthma were found for the SNPs T1 (Met764Thr), T2 (Pro774Ser), S2 and V-3 (with the lowest P-value for T1, P = 0.0015; OR 0.63). We analysed the haplotype using these four polymorphisms, and found a positive association with haplotype CCTG (P = 0.0024).

CONCLUSION

Our results replicate associations reported recently in other ethnic populations, and suggest that the ADAM33 gene is involved in the development of asthma through genetic polymorphisms.

Allergen-specific IgG1 provides parsimonious heritability estimates for atopy-associated immune responses to allergens

Although serum total immunoglobulin E (IgE) is generally elevated in atopic conditions, it is an unreliable trait for dissecting the genetic and environmental components contributing to atopic immune responses, because it can be significantly confounded by demographic factors (age, gender, and race) and clinical status (atopic vs nonatopic). Allergen-specific IgE is a discontinuous trait present only in those with sensitivity to allergens. However, all people will produce allergen-specific immunoglobulin G1 (IgG1), which is elevated among those atopically sensitized to specific allergens. We screened 91 Caucasian nuclear families (N = 367) with medical histories of atopic diseases and used variance components analysis to compare heritability estimates for total IgE and IgG1 produced against the common major allergen from house dust mite Dermatophagoides pteronyssinus (Der p 1). An estimate of total IgE heritability was about 48%, although this was significantly confounded by age, gender, and clinical atopic status. In contrast, Der p 1-IgG1 demonstrated a significant inherited component of about 62% that was not influenced by age, gender, or clinical status. For genetic studies of atopic humoral responses, allergen-specific IgG1 may be a more reliable quantitative trait than serum IgE. Moreover, atopy is an inherited deregulation of immune responses to noninfectious antigens, involving antibody isotypes other than IgE.

Functional polymorphism in the suppressor of cytokine signaling 1 gene associated with adult asthma

Suppressor of cytokine signaling (SOCS) 1 is an essential physiologic regulator of the IFN-gamma signaling that is crucial to lead appropriate immune responses, and impaired IFN-gamma production is considered a hallmark of atopic diseases. Recent study has shown that SOCS1 is also crucial in attenuating type 1 IFN signaling and in limiting the host response to viral infection. Clinical and experimental evidence suggest an important role for respiratory viral infections in the development of asthma. To assess genetic functional variants of SOCS1 related to susceptibility and clinical phenotypes in adult asthma in a Japanese population, we conducted association and haplotype analyses of 462 subjects with adult asthma and 639 control subjects. After screening for polymorphisms, we identified a total of 13 variants and characterized the linkage disequilibrium (LD) mapping of the gene. Three variants were selected for genotyping with regard to the LD pattern, and we found a significant association between an SOCS1 promoter polymorphism -1478CA > del and adult asthma (P = 0.0063). The three-locus haplotype of SOCS1 using these three polymorphisms also showed a positive association with a haplotype T-C-del (-5388T, -3969C, and -1478 del; P = 0.0097). Furthermore, reporter gene analysis revealed that related promoter variant -1478 del enhanced the transcriptional level of SOCS1 in human lung epithelial cells, and induced higher levels of protein expression of SOCS1 and lower phosphorylation of STAT1 stimulated with IFN-beta. These findings suggest that the SOCS1 gene might be involved in the development of adult asthma through functional genetic polymorphism.

Shaking the tree: mapping complex disease genes with linkage disequilibrium

Much effort and expense are being spent internationally to detect genetic polymorphisms contributing to susceptibility to complex human disease. Concomitantly, the technology for detecting and genotyping single nucleotide polymorphisms (SNPs) has undergone rapid development, yielding extensive catalogues of these polymorphisms across the genome. Population-based maps of the correlations amongst SNPs (linkage disequilibrium) are now being developed to accelerate the discovery of genes for complex human diseases. These genomic advances coincide with an increasing recognition of the importance of very large sample sizes for studying genetic effects. Together, these new genetic and epidemiological data hold renewed promise for the identification of susceptibility genes for complex traits. We review the state of knowledge about the structure of the human genome as related to SNPs and linkage disequilibrium, discuss the potential applications of this knowledge to mapping complex disease genes, and consider the issues facing whole genome association scanning using SNPs.

Genetic aspects of pulmonary responses to inhaled pollutants

Air pollution continues to be a major public health concern in industrialized cities throughout the world. Recent population and epidemiological studies that have associated ozone and particulate exposures with morbidity and mortality outcomes underscore the important detrimental effects of these pollutants on the lung. Inter-individual variation in human responses to air pollutants suggests that some subpopulations are at increased risk to the detrimental effects of pollutant exposure, and it has become clear that genetic background is an important susceptibility factor. Environmental exposures to inhaled pollutants and genetic factors associated with disease risk likely interact in a complex fashion that varies from one population to another. The relationships between the genetic background and disease risk and severity is often evaluated through traditional family-based linkage studies and positional cloning techniques. Case-control studies based on association of disease or disease subphenotypes with candidate genes may have certain advantages over family pedigree studies, and have become useful for understanding complex disease phenotypes. This is based in part on continued development of quantitative analysis and development of mapping technologies. Linkage analyses with genetically standardized animal models are useful to identify genetic determinants of host responses to environmental stimuli. For example, linkage analyses using inbred mice have identified chromosomal segments (quantitative trait loci, QTL) that contain genes that control susceptibility to the lung inflammatory and immune dysfunction responses to ozone, nitrogen dioxide, zinc oxide, and sulfate-associated particles. Candidate genes within the pollutant susceptibility QTLs have been tested for proof-of-concept using gene-targeting and overexpression models. Importantly, significant homology exists between the human and mouse genomes. Therefore, comparative mapping between the human and mouse genomes should yield candidate susceptibility genes that may be tested by association studies in humans. The combined human studies and mouse modeling will provide important insight to understanding genetic factors that contribute to differential susceptibility to pollutants in human populations.

A novel polymorphic GATA site in the human IL-12Rbeta2 promoter region affects transcriptional activity

Interleukin-12 (IL-12) is a potent inducer of interferon-gamma production by T cells and is a major factor for the development of T-helper 1 (Th1) cells. It exerts its biological effects through binding to the IL-12 receptor (IL-12R), a heterodimer composed of a 1 and a beta2 subunits. The signaling beta2 chain is expressed on Th1 cells and to a lesser extent on Th0 cells, but not on Th2 cells, rendering these latter cells unresponsive to IL-12. Polymorphisms in the coding region of the IL-12Rbeta2 gene were shown to be associated with atopic disease. Here, we analyzed the 5'-regulatory region of the human IL-12Rbeta2 gene by denaturing high-performance liquid chromatography (Transgenomic WAVE system, San Jose, CA). We found five novel single-nucleotide polymorphisms (SNPs) in the proximal 1.2 kb IL-12Rbeta2 promoter region, i.e. -237C/T, -465A/G, -1023A/G, -1033T/C, and -1035A/G. SNP -465A/G is of particular interest as it determines the integrity of a GATA consensus site. By functional comparison of both -465 alleles in transient transfection assays, we show that promoter activity is increased in case of the -465G allele, disrupting the intact GATA site. Comparison of the prevalence of -465A/G SNP alleles in small cohorts of allergic asthmatic and healthy control individuals provided no evidence for an altered distribution in the asthmatic population. In conclusion, we have identified a novel polymorphic GATA site that may affect transciptional activity of the human IL-12Rbeta2 gene under GATA3-mediated, Th2-polarizing conditions.

Therapeutic response to asthma medications: genotype predictors

Asthma is a major social and economic burden. Studies have shown that genetic polymorphisms can influence drug efficacy and/or toxicity. The understanding of the pharmacogenetics of asthma will allow therapeutic regimens to be tailored on an individual basis. It is hoped that linkage and association studies will define new therapeutic targets for asthma but until then, studies have focused on improving response to beta(2)-adrenoceptor agonist and leukotriene modifier therapy. Genetic polymorphism may account for interindividual differences in toxicity and efficacy of asthma medications. To date, single nucleotide polymorphism and limited haplotype analysis have provided inconclusive evidence as to how genotype predictors can be used to optimize current asthma therapies based on each patient's genetic profile.

Association between interleukin-18 gene polymorphism 105A/C and asthma

BACKGROUND

IL-18 has been shown to exert anti-allergic or allergy-promoting activities, but the existence of genetic polymorphisms in the coding regions of IL-18 gene has not been demonstrated.

OBJECTIVE

The aim of this study was to investigate whether polymorphism is present in the coding regions of the IL-18 gene and, if so, to further analyse the association between polymorphism and asthma in a case-control study.

METHODS

We screened the coding regions of the IL-18 gene for polymorphisms by using PCRsingle-stranded conformation polymorphism and direct sequencing of PCR products, followed by analysis of the association between polymorphism and asthma.

RESULTS

We identified one polymorphism (105A/C) in the coding regions. The frequency of the 105A allele was significantly higher in asthmatic patients than in controls (P<0.01; odds ratio (OR)=1.83 (1.37-2.26)). Significant linkage disequilibrium was observed between the 105A/C and -137G/C polymorphisms in the 5' flanking region of the IL-18 gene (D=0.58, P<0.0001). However, in asthmatic patients the 105A allele was not associated with either total serum IgE or IL-18 levels.

CONCLUSION

The 105A/C polymorphism of the IL-18 gene may be associated with the pathogenesis of asthma.

Respiratory syncytial virus bronchiolitis and the pathogenesis of childhood asthma

There is now convincing evidence that children who develop lower respiratory symptoms during infection with respiratory syncytial virus (RSV) in early life are at increased risk of developing asthma-like symptoms during the school years. What determines this association is not well-understood, but increased likelihood of allergic sensitization plays a minor role, if any, as a determinant of post-RSV wheeze. Current evidence suggests that both genetic and environmental factors determine the type of immune response to the acute RSV infection and that this response, in turn, may affect the development of the control mechanisms involved in the regulation of airway tone. Many different cytokines appear to play a role in this acute immune response, including interferon-gamma; interleukins 8, 10 and 12; and cytokines produced by T helper (Th) 1 and Th2 cells. Because asthma is a heterogeneous condition, future studies will need to determine the potentially different role of RSV infection as a risk factor for these different asthma phenotypes. It is likely, however, that strategies for the prevention of RSV infection may play a role in the prevention of the subsequent development of persistent wheezing and asthma-like symptoms in childhood.

Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease

Under selective pressure from infectious microorganisms, multicellular organisms have evolved immunological defense mechanisms, broadly categorized as innate or adaptive. Recent insights into the complex mechanisms of human innate immunity suggest that genetic variability in genes encoding its components may play a role in the development of asthma and related diseases. As part of a systematic assessment of genetic variability in innate immunity genes, we have thus far have examined 16 genes by resequencing 93 unrelated subjects from three ethnic samples (European American, African American and Hispanic American) and a sample of European American asthmatics. Approaches to discovering and understanding variation and the subsequent implementation of disease association studies are described and illustrated. Although highly conserved across a wide range of species, the innate immune genes we have sequenced demonstrate substantial interindividual variability predominantly in the form of single nucleotide polymorphisms (SNPs). Genetic variation in these genes may play a role in determining susceptibility to a range of common, chronic human diseases which have an inflammatory component. Differences in population history have produced distinctive patterns of SNP allele frequencies, linkage disequilibrium and haplotypes when ethnic groups are compared. These and other factors must be taken into account in the design and analysis of disease association studies.