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

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

Guo et al. (Bioscience Reports (2018) 38, BSR20180177) published a meta-analysis concerning the association between five single nucleotide polymorphisms (SNPs) in the high-affinity IgE receptor β chain (FcεRIβ) gene, namely E237G, -109 C/T, RsaI_in2, RsaI_ex7, and I181L, and risk of asthma and allergic rhinitis based on available 29 case–control studies. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of association of SNPs in FcεRIβ gene with allergic diseases risk. They found that FcεRIβ E237G (237G vs. 237E: OR = 1.28, 95% CI = 1.06–1.53) and −109 C/T (TT vs. CT+CC: OR = 1.58, 95% CI = 1.26–1.98) were risk factors for allergic diseases. Guo et al.’s findings are interesting, but we found that several issues should be clarified after carefully reading the paper. Here, we intended to comment on these data clarifications.

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.

Association of the MS4A2 gene promoter C-109T or the 7th exon E237G polymorphisms with asthma risk: a meta-analysis

BACKGROUND AND OBJECTIVE

A large number of studies have examined the association between the Membrane-spanning 4 domains, superfamily A, number 2 (MS4A2) gene C-109T (rs1441586) or E237G (rs569108) variants and asthma risk. However, the results are inconsistent and inconclusive. To derive a more precise estimation, a meta-analysis was performed.

METHODS

Meta-analyses were conducted with the data from case-control association studies (24 studies with 4496 asthmatics and 4571 controls for E237G variant and 9 studies including 2005 cases and 1868 control for C-109T polymorphisms, respectively). Random-effects model was used to calculate summary odds ratios (ORs).

RESULTS

For the MS4A2 gene E237G variant, no significant associations with asthma were found in overall population; we observed an elevated risk of atopic asthma among subjects with the 237G allele (OR=1.341, 95% CI: 1.039-1.732 for G versus E and OR=1.374, 95% CI: 1.032-1.828 for EG+GG versus EE) in the stratified meta-analysis. As for the MS4A2 gene C-109T polymorphism, no significant associations with asthma risk were observed in the total population; in subgroup analysis by ethnicity of subjects we found increased asthma risk among Asians carrying T allele (OR=1.140, 95% CI: 1.019-1.276 for T versus C and OR=1.359, 95% CI: 1.029-1.794 for TT versus CC).

CONCLUSIONS

Data indicated that the MS4A2 gene E237G variant may be a risk factor for developing atopic asthma and the promoter -109T allele is a potential risk factor of asthma in Asians.

The association between glutathione S-transferase P1, M1 polymorphisms and asthma in Taiwanese schoolchildren

STUDY OBJECTIVES

Genetic polymorphisms in the glutathione S-transferase P1 gene (GSTP1) and the glutathione S-transferase M1 gene (GSTM1) have been implicated as risk factors for asthma. However, their roles in asthma pathogenesis and the interaction between these two genes have not been extensively investigated. This study, therefore, examined the relationship among GSTP1 and GSTM1 genotypes and childhood asthma, and evaluated their gene-gene interactions.

SETTING

The population from three southern Taiwan communities of a 2001 national survey.

SUBJECTS AND METHODS

Two hundred sixty-six fourth-grade to ninth-grade schoolchildren were recruited for oral mucosa samplings based on questionnaire information. Polymerase chain reaction-based assays were performed to determine GSTP1 and GSTM1 genotypes among asthmatic subjects and nonasthmatic control subjects. Multiple logistic regression was used to adjust for potential confounding factors.

RESULTS

All of the participants were homozygous at the GSTP1 Ala-114 locus. After controlling for age, sex, and atopic eczema, compared with participants carrying any Val-105 allele, children who were homozygotic for GSTP1 Ile-105 had a significantly increased risk of physician-diagnosed asthma (adjusted odds ratio [adjOR], 1.94; 95% confidence interval [CI], 1.08 to 3.59). A positive risk for childhood asthma was also noted on the GSTM1 null genotype but did not reach statistical significance (adjOR, 1.37; 95% CI, 0.80 to 2.38). Among children with GSTM1 present genotypes, GSTP1-105 polymorphisms were associated with the increased risk of asthma. However, the reduced and statistically insignificant asthma risk was observed among those with GSTM1 null genotype.

CONCLUSIONS

We concluded that GSTP1-105 was a predictor for childhood asthma, whereas GSTM1 polymorphism might modify the risk. Our study also suggested a competitive effect for homozygous GSTP1 Ile-105 and GSTM1 null genotypes on childhood asthma.

Single nucleotide polymorphisms in four functionally related immune response genes in the horse: CD14,TLR4, Ce, andFce R1 alpha

The objective of this study was to identify single nucleotide polymorphisms (SNPs) within four functionally related immune response genes in the horse, and to develop genotyping techniques that could be useful for future genomic studies of horse infectious and allergic diseases. The genes analysed were: the lipopolysaccharide (LPS) receptor gene CD14, the toll-like receptor 4 gene TLR4, the gene Cepsilon encoding the IgE heavy chain molecule and the gene FcepsilonR1 alpha coding for the alpha subunit of the IgE receptor molecule. Horse-specific primers amplifying selected gene regions were designed and SNPs were searched by selective resequencing and/or by PCR-SSCP (polymerase chain reaction-sequence specific conformational polymorphism) or PCR-RFLP (PCR-restriction fragment length polymorphism). Gene expression was analysed by RT-PCR (reverse transcriptase-PCR) of all four genes examined. For CD14, the cDNA sequence was determined and a novel sequence of the 5'UTR region was identified. The protein-coding sequence was identical to that previously deposited in GenBank. 5'UTR, intronic and both synonymous and non-synonymous exonic SNPs were identified. Three SNPs were found in the CD14 gene, four in the TLR4 gene; two SNPs were identified in the Cepsilon gene, and one SNP was found in the FcepsilonR1 alpha gene. PCR-RFLP was developed for genotyping eight of the SNPs identified. The RT-PCR assay showed that all the SNPs reported here are parts of expressed genes. The results showed that important immunity-related genes in horses are polymorphic and that even non-synonymous SNPs with potential functional impact may occur. The methods developed for genotyping and haplotyping the SNPs identified represent, along with markers described previously, a potentially useful tool for genomic analysis of the function and role of these genes in immunity and in mechanisms of disease.

Gene-gene synergistic effect on atopic asthma: tumour necrosis factor-alpha-308 and lymphotoxin-alpha-NcoI in Taiwan's children

BACKGROUND

Asthma is now known to be an inflammatory response caused by the release of inflammatory mediators and cytokines. Tumour necrosis factor (TNF) is a potent cytokine in the inflammation response of the airway, and the polymorphisms of TNF genes have been associated with asthma.

OBJECTIVE

This study investigated two variants, TNF-alpha-308*2 and lymphotoxin (LT)-alpha-NcoI*1, which may predispose individuals to asthma and atopy pathogenesis.

METHODS

PCR-based assays were performed to determine LT-alpha-NcoI*1 and TNF-alpha-308*2 genotypes among our subjects, with 128 atopic asthmatics and 51 non-atopic asthmatics, 55 atopic controls, and 78 non-atopic controls in this genetic case-control study.

RESULTS

The TNF-alpha-308*2 polymorphism increased in subjects with atopic asthma vs. non-atopic controls after adjusting for age distribution (adjusted odds ratios, AOR=2.73, 95% confidence interval, CI=1.16-6.64), but was not associated with non-atopic asthma (AOR=2.40, 95% CI=0.81-7.09). LT-alpha-NcoI*1 did not show an independent association with either atopic asthma or any one phenotype of specific IgE. The synergistic effect between these two genes was conducted, and the interaction between TNF-alpha-308*2 and LT-alpha-NcoI*1 polymorphisms was seen for atopic asthma (OR=2.59, 95% CI=1.10-6.10) when compared with all controls.

CONCLUSION

We have concluded that TNF-alpha-308 may be a risk factor for atopic asthma, whereas the LT-alpha-NcoI polymorphism may modify risk to atopic asthma with TNF-alpha-308.

A Murine Locus on Chromosome 18 Controls NKT Cell Homeostasis and Th Cell Differentiation

Th cell differentiation is a critical event in the adaptive immune response. C57BL strains develop predominant Th1 responses while BALB/c develops a predominant Th2 response. To identify quantitative trait loci controlling this variation, we performed Th1/Th2 differentiation assays of F(1) x BALB/c progeny. A single strong quantitative trait locus was identified on chromosome 18, with weaker effects detectable on chromosomes 5, 12, and 14. By preparing a congenic BALB.B10.D2c18 strain, we were able to demonstrate that this single locus was sufficient to "repolarize" spleen cell cultures. This difference was not due to intrinsic differences in CD4(+) T cells. Rather, introgression of the chromosome 18 locus into BALB/c disrupted Va14Ja18 NKT cell homeostasis resulting in the almost complete absence of this T cell subset. Taken together, these data indicate that genes within chromosome 18 control strain-dependent development of Va14Ja18 NKT cells.

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.