Testing for gene-gene interaction controlling total IgE in families from Barbados: evidence of sensitivity regarding linkage heterogeneity among families

Novel cooperation between CX3CL1 and CCL26 inducing NK cell chemotaxis via CX3CR1: a possible mechanism for NK cell infiltration of the allergic nasal tissue

BACKGROUND

Recent data indicated that natural killer (NK) cells and chemokines could play a pivotal role in nasal inflammation. CX3CR1, the only receptor for fractalkine/CX3CL1, is abundantly expressed by NK cells, and was recently shown to also be a receptor for eotaxin-3/CCL26. However, no reports explored the NK cells-CX3CL1-CCL26 axis via CX3CR1 in allergy.

OBJECTIVE

Our goals were first to determine specifically NK cell recruitment pattern in nasal tissue of allergic chronic rhinosinusitis (ACRS) and non-allergic chronic rhinosinusitis (NACRS) patients in comparison with healthy controls, and secondly, to investigate the function of CX3CR1 in NK cell migration.

METHODS

Immunohistochemistry, microchemotaxis chambers, flow cytometry and confocal microscopy were used in this study.

RESULTS

Herein, we showed that NK cells infiltrated the epithelial layers of nasal tissue only in ACRS patients and not in NACRS patients or controls. NK cells were also more numerous in the stroma of the nasal tissue from ACRS patients compared with NACRS patients or controls. This migration could be mediated by both CX3CL1 and CCL26, as these two chemokines induced NK cell migration. Moreover, both molecules also stimulated cytoskeleton changes and F-actin reorganisation in NK cells. Chemotaxis and cytoskeleton changes were sensitive to genistein, a tyrosine kinase inhibitor. By flow cytometry, we demonstrated that a single antigen nasal provocation challenge increased the expression of CX3CR1 on NK cells in allergic rhinitis (AR) patients. The function of this receptor was associated with a significant augmentation of NK cell chemotaxis against the optimal doses of CX3CL1 and CCL26.

CONCLUSIONS AND CLINICAL RELEVANCE

Our results highlight a novel role for CX3CR1 in NK cell migration that may contribute to the NK cell trafficking to the allergic upper airway. This could be mediated largely by CX3CL1 and CCL26 stimulation of the tyrosine kinase pathway.

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

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

The genetics of atopic dermatitis

BACKGROUND

Atopic dermatitis (AD) is a complex genetic disorder influenced by environmental factors. The mode of inheritance and genes involved are not clear.

RESULTS

This report here is focusing on the current progress in searching the disease-susceptibility genes of AD via both the linkage studies and candidate gene approaches. Genome-wide linkage studies have identified multiple susceptibility loci on 3q and 17q. Candidate region linkage studies identify other susceptibility loci on 5q23-33, 11q13, and 13q12-14. At least 28 candidate genes have to date been verified in association studies, but only association with genes of interleukin (IL)-4, IL-13, IL-4RA, mast cell chymase, and serine protease inhibitor, kazal-type 5 have been replicated in more than two different studies. More halpotype tests and family-based association studies may help to shed more light for the candidate gene approach.

CONCLUSION

Determining the candidate susceptibility genes for AD is not only helping understanding the pathophysiology but also affecting the response to therapy, which is important in pharmacogenetics. The effect of environmental trigger may also have to be considered to elucidate the real face of the disease.

Analysis of the inducible nitric oxide synthase gene polymorphisms in Czech patients with atopic diseases

BACKGROUND

Nitric oxide (NO) is an important mediator of physiologic processes in the airways; it plays a significant role in the regulation of the T helper type 1/type 2 balance and contributes to the development of atopic diseases.

OBJECTIVE

We analysed several polymorphisms mainly in the promoter region of the inducible NO synthase (NOS2, iNOS) gene and investigated their associations with asthma and/or atopic phenotypes.

METHODS

We performed a case-control study in 994 subjects (661 patients with atopic disorders, with subgroups of 304 patients with allergic asthma, and 333 healthy individuals), matched for sex, living in the same geographical area. Screening for polymorphisms was performed by combination of PCR and direct sequencing analysis.

RESULTS

We analysed 14 nucleotide sequence variants, seven most common of which were typed in quite large groups of our asthmatic, atopic and control populations. None of these seven frequent polymorphisms was associated with the phenotype bronchial asthma or other atopic diseases. Nevertheless, three from six common promoter polymorphisms showed a significant relation to feather's positivity (P value from 0.01 to 0.03) and the NOS2 608Leu variant was significantly associated with asthma severity [p(corr) = 0.0005; odds ratio (OR) = 5.00, 95% confidence interval (CI): 1.88-13.33]. In haplotype analysis, the most common -2447C/-1659C/-1026G/-0.7del/-277A/Ser608 haplotype was associated with a lower risk of asthma when compared with the common haplotypes with frequency more than 5% (P = 0.01, p(corr) < 0.05; OR = 0.65, 95% CI: 0.56-0.77).

CONCLUSION

Our findings suggest that inducible NOS can play a role in atopic disorders, and several polymorphisms in its gene may be important for asthma protection or susceptibility.

Detection of gene x gene interactions in genome-wide association studies of human population data

Empirical evidence supporting the commonality of gene x gene interactions, coupled with frequent failure to replicate results from previous association studies, has prompted statisticians to develop methods to handle this important subject. Nonparametric methods have generated intense interest because of their capacity to handle high-dimensional data. Genome-wide association analysis of large-scale SNP data is challenging mathematically and computationally. In this paper, we describe major issues and questions arising from this challenge, along with methodological implications. Data reduction and pattern recognition methods seem to be the new frontiers in efforts to detect gene x gene interactions comprehensively. Currently, there is no single method that is recognized as the 'best' for detecting, characterizing, and interpreting gene x gene interactions. Instead, a combination of approaches with the aim of balancing their specific strengths may be the optimal approach to investigate gene x gene interactions in human data.

Eotaxin polymorphisms and serum total IgE levels in children with asthma

BACKGROUND

Eotaxin (chemokine, CC motif, ligand; CCL11) is a potent eosinophil chemoattractant strongly implicated in the pathobiology of asthma. Genetic variation at the CCL11 locus has been correlated with serum total IgE, blood eosinophil counts, and circulating eotaxin protein levels in several case-control asthma studies. Family-based association studies of CCL11 genetic variants have not been reported to date.

OBJECTIVE

To evaluate 9 common CCL11 single nucleotide polymorphisms (SNPs) in nuclear families ascertained through patients with asthma participating in the Childhood Asthma Management Program study.

METHODS

Single nucleotide polymorphism genotyping was performed by using minisequencing and probe hybridization platforms. Family-based association analysis for asthma and 4 asthma-related intermediate quantitative phenotypes was performed by using FBAT.

RESULTS

One SNP, -384A>G, was associated with asthma among African American families (P = .01). CCL11 SNPs and haplotypes were not associated with asthma among white or Hispanic families. Two low-frequency alleles in strong pairwise linkage disequilibrium, -426C and IVS2+199A, were associated with lower serum total IgE levels (P = .0006 and P = .009, respectively) in white families, whereas 2 more common variants, -576C and g.4438C, were associated with higher IgE levels in African American families (P = .01-.04). Haplotype analysis in the white cohort provided additional evidence of association with serum total IgE, implicating 2 haplotypes. No single SNP or haplotype associations were observed with blood eosinophil levels, FEV(1), or airway responsiveness.

CONCLUSION

These findings provide further evidence that genetic variation at the CCL11 locus is an important determinant of serum total IgE levels among patients with asthma.

Human leucocyte antigen polymorphisms in nut-allergic patients in South Wales

BACKGROUND

Peanuts and tree nuts are among the most common foods provoking severe allergic reactions including fatal anaphylaxis. However, little is known of the underlying genetic and immunological mechanisms involved.

OBJECTIVE

Based on findings in other allergic diseases, we have investigated whether specific human leucocyte antigens (HLA) are associated with nut allergy.

METHOD

Eighty-four patients presenting at the allergy clinic with symptoms of nut allergy were typed for the HLA Class I (HLA-A and B) and Class II (HLA-DRB1 and DQB1) loci by PCR using sequence-specific primers. Carriage frequencies were compared with 82 atopic non-nut-allergic subjects and 1798 random blood donors.

RESULTS

The frequency of HLA-B(*)07 (28.57%) and DRB1(*)11 (15.48%) was increased in the nut-allergic patients compared to the atopic controls (12.20% and 3.66%, respectively) but not when compared to the blood donors (28.86% and 10.12%). DRB1(*)13 and DQB1(*)06 were both increased in frequency in the nut allergy patients over both the atopic and blood donor controls. However, none of these increased frequencies were significant when corrected for the number of comparisons undertaken.

CONCLUSION

At HLA '2-digit resolution' and with undifferentiated patients with nut allergy, there are no major disturbances in the frequency of HLA-A, B, DRB1 or DQB1 types. However, the difference in frequency of HLA-DRB1(*)11 between the nut allergy patients and the atopic controls merits further investigation as this may represent an important phenotypic relationship.

Mapping of gene loci for nephronophthisis type 4 and Senior-Løken syndrome, to chromosome 1p36

For nephronophthisis (NPHP), the primary genetic cause of chronic renal failure in young adults, three loci have been mapped. To identify a new locus for NPHP, we here report on total-genome linkage analysis in seven families with NPHP, in whom we had excluded linkage to all three known NPHP loci. LOD scores >1 were obtained at nine loci, which were then fine mapped at 1-cM intervals. Extensive total-genome haplotype analysis revealed homozygosity in one family, in the region of the PCLN1 gene. Subsequent mutational analysis in this gene revealed PCLN1 mutations, thereby allowing exclusion of this family as a phenocopy. Multipoint linkage analysis for the remaining six families with NPHP together yielded a maximum LOD score (Z(max)) of 8.9 (at D1S253). We thus identified a new locus, NPHP4, for nephronophthisis. Markers D1S2660 and D1S2642 are flanking NPHP4 at a 2.9-cM critical interval. In one family with NPHP4, extensive genealogical studies were conducted, revealing consanguinity during the 17th century. On the basis of haplotype sharing by descent, we obtained a multipoint Z(max) of 5.8 for D1S253 in this kindred alone. In addition, we were able to localize to the NPHP4 locus a new locus for Senior-Løken syndrome, an NPHP variant associated with retinitis pigmentosa.

Interactions between genes and environmental factors in asthma and atopy: new developments

Asthma and associated phenotypes are complex traits most probably caused by an interaction of multiple disease susceptibility genes and environmental factors. Major achievements have occurred in identifying chromosomal regions and polymorphisms in candidate genes linked to or associated with asthma, atopic dermatitis, IgE levels and response to asthma therapy. The aims of this review are to explain the methodology of genetic studies of multifactorial diseases, to summarize chromosomal regions and polymorphisms in candidate genes linked to or associated with asthma and associated traits, to list genetic alterations that may alter response to asthma therapy, and to outline genetic factors that may render individuals more susceptible to asthma and atopy due to environmental changes.