IL-4 rs2243250 polymorphism associated with susceptibility to allergic rhinitis: a meta-analysis

Objective: The relationship between IL-4 rs2243250 polymorphism and the risk of allergic rhinitis is not clear at present. The present study aims to evaluate the exact association between IL-4 rs2243250 polymorphism and susceptibility to allergic rhinitis by a meta-analysis.Methods: The studies about IL-4 rs2243250 polymorphism associated with susceptibility to allergic rhinitis were searched using PubMed, Excerpta Medica Database (EMBASE), Web of Science, Cochrane Library, China National Knowledge Infrastructure (CNKI) and China Wanfang databases. The last search time was on March 1, 2021. Data analysis was performed using Stata 15.0 software.Results: Nine documents were enrolled, from which 1709 patients with allergic rhinitis were included. Among them, six genotype frequencies in the control group conformed to Hardy–Weinberg Equilibrium (HWE). The meta-analysis of all included studies showed significant heterogeneity of each gene model. After omitting the studies whose genotype frequency in the control group did not meet the requirements of HWE, no significant heterogeneity was found in each gene model. The meta-analysis results of the control group genotypes in line with the HWE showed statistically significant differences in the pooled odds ratio (OR) of allele model (T vs. C), recessive model (TT vs. TC+CC) and homozygous model (TT vs. CC), which were 1.19 (95%CI: 1.04–1.35), 1.28 (95%CI: 1.06–1.55) and 1.56 (95%CI: 1.13–2.17), respectively. No statistically significant difference was observed in dominant and heterozygous genetic models.Conclusion: IL-4 rs2243250 single nucleotide polymorphism associated with susceptibility to allergic rhinitis, allele T and genotype TT could increase the risk of allergic rhinitis.     

IFNG +874 T>A single nucleotide polymorphism is associated with leprosy among Brazilians

Leprosy is a chronic infectious disease caused by Mycobacterium leprae, a low virulence mycobacterium, and the outcome of disease is dependent on the host genetics for either susceptibility per se or severity. The IFNG gene codes for interferon-γ (IFN-γ), a cytokine that plays a key role in host defense against intracellular pathogens. Indeed, single nucleotide polymorphisms (SNPs) in IFNG have been evaluated in several genetic epidemiological studies, and the SNP +874T>A, the +874T allele, more specifically, has been associated with protection against infectious diseases, especially tuberculosis. Here, we evaluated the association of the IFNG locus with leprosy enrolling 2,125 Brazilian subjects. First, we conducted a case–control study with subjects recruited from the state of São Paulo, using the +874 T>A (rs2430561), +2109 A>G (rs1861494) and rs2069727 SNPs. Then, a second study including 1,370 individuals from Rio de Janeiro was conducted. Results of the case–control studies have shown a protective effect for +874T carriers (OR_adjusted = 0.75; p = 0.005 for both studies combined), which was corroborated when these studies were compared with literature data. No association was found between the SNP +874T>A and the quantitative Mitsuda response. Nevertheless, the spontaneous IFN-γ release by peripheral blood mononuclear cells was higher among +874T carriers. The results shown here along with a previously reported meta-analysis of tuberculosis studies indicate that the SNP +874T>A plays a role in resistance to mycobacterial diseases.     

The variant Arg110Gln of human IL-13 is associated with an immunologically hyper-reactive form of onchocerciasis (sowda)

Onchocerca volvulus infection usually results in a predominantly immunopermissive reaction called generalized onchocerciasis and characterized by high microfilarial burden and immunological tolerance to the worms. Rarely, however, infection leads to the sowda form of the disease displaying low microfilarial numbers, i.e. microfilarial control, and a T helper 2 (Th2)-type immune response including high immunoglobulin (Ig)E levels, and interleukin (IL)-13 being one of the key cytokines. The aim of this study was to investigate a possible association of a variant of the IL-13 gene, which confers an IgE-independent risk for asthma and atopy, with the immunologically hyper-reactive sowda form of onchocerciasis. Genotyping for the IL-13 variant Arg110Gln revealed a highly significant association of Arg110Gln with the sowda form (relative risk of 2.98, n = 19 patients), whereas the frequency of the variant was significantly lower in patients with generalized onchocerciasis (n = 92 individuals). Sowda patients had higher IgE levels than those with generalized onchocerciasis. Logistic regression analysis revealed that IgE and IL-13 are independent variables, each increasing the relative risk for sowda. Arg110Gln has been suggested to lead to enhanced IL-13 signaling and thus may be involved in shifting the immune reaction towards the hyper-reactivity characteristic for the sowda form, thereby promoting defense mechanisms.     

Association of XRCC1 Arg399Gln polymorphism with bladder cancer susceptibility: A meta-analysis

Genetic variations in DNA repair genes are thought to modify DNA repair capacity and may to be related to cancer susceptibility. However, epidemiological study results have been inconsistent. In this meta-analysis, we assessed 24 case–control studies of association between the X-ray repair cross complementing group 1 (XRCC1) Arg399Gln polymorphism and bladder cancer susceptibility in the general population and in Asian and non-Asian subgroups. A moderately significant association with bladder cancer risk was found for AG vs GG (OR = 1.110, 95% CI = 1.018–1.210). No significant associations with bladder cancer risk were found for AA vs GG (OR = 0.942, 95% CI = 0.823–1.077), the dominant model AA/AG vs GG (OR = 1.075, 95% CI = 0.990–1.167) and the recessive model AA vs AG/GG(OR = 0.890, 95% CI = 0.788–1.005). In subgroup analysis, a moderately significant association was also found for AG vs GG (OR = 1.091, 95% CI = 1.008–1.180) in non-Asian subgroup. The analysis suggests that the XRCC1 Arg399Gln polymorphism might be a moderate risk factor for bladder cancer, especially in non-Asian population.     

A single nucleotide polymorphism at the Vrn-D1 promoter region in common wheat is associated with vernalization response

Facultative wheat varieties adapt to a particular environment. But the molecular basis for the facultative growth habit is not clear relative to winter and spring growth habit. Two sets of wheat varieties were chosen for this study. Set 1 comprised ten spring accessions and Set 2 comprised ten facultative accessions. All accessions had been tested by the previously described allele-specific markers and shown having the same allelic composition of vrn-A1 vrn-B1 Vrn-D1 and vrn-B3. Here we examined whether differences in growth habit might be associated with as yet unidentified sequence variation at Vrn-D1 locus. A region including the intron 1 deletion, the entire reading frame from a cDNA template and a part of promoter region of the dominant Vrn-D1 gene in each of the accessions was sequenced, and a single nucleotide polymorphism was found between facultative accessions and spring accessions in the CArG-box at the promoter region. The novel allele in facultative accessions was designated as Vrn-D1b. The investigation of an F₂ population segregating for Vrn-D1b and Vrn-D1a (previously, Vrn-D1) in the greenhouse under long days without vernalization showed that the plants with Vrn-D1b homozygous allele headed 32?days later and had about three more leaves than the plants with Vrn-D1a homozygous allele. As Vrn-D1b has the same deletion in intron 1 as Vrn-D1a, and, in addition, a single nucleotide mutation at promoter region, and is associated with facultative growth habit, we suggest that the promoter mutation may modify the basal activity level of an allele of VRN1 that is already active (due to the loss of segments in intron 1). Our finding further supports that both the promoter and intron 1 regulatory affect vernalization response and work independently.     

变应性鼻炎患者外周血中IL-27和Treg细胞的相关性分析

目的探讨外周血IL-27和CD4^＋CD25^＋调节性T细胞（Treg）在变应性鼻炎（AR）发病机制中的作用。方法2012年3月至7月,收集AR患者32例（AR组）和20例健康志愿者（对照组）外周血,采用流式细胞术（FCM）检测外周血中Treg细胞比例;ELISA检测血清中IL-27、IL-10和TGF-β1的水平。结果AR组Treg细胞百分率[（1．75±0．56）％]明显低于对照组[（4．76±1．75）％],两组比较的差异有统计学意义（P〈0．01）。AR组IL-27、IL-10和TGF-β1的水平分别为（24．43±16．36）pg／ml、（14．29±6．16）pg／ml、（0．34±0．04）pg／ml,均低于对照组（44．09±13．12）pg／ml、（31．32±21．20）pg／ml、（O．49±0．06）pg／ml,两组之间的差异有统计学意义（P〈0．01）。AR患者外周血中IL-27和Treg细胞百分率、IL-10、TGF-β1存在正相关（r分别为0．825,0．646,0．517,P〈0．01）,Treg细胞百分率和IL-10、TGF-β1存在正相关（r=0.622,0．738,P〈0．01）,IL-10和TGF-β1无相关性（r=0．304,P〉0．05）结论AR患者外周血中IL-27水平降低,Treg细匏百分率降低及其主要分泌因子IL-10、TGF-β1水平降低,且IL-27与Treg细胞百分率、IL-10、TGF-β1水平呈正相关,提示在AR发病中IL-27对Treg细胞可能具有免疫调节作用。     

变应性鼻炎患者血清IL-17和IL-17R表达及其与IgE的相关性

目的:探讨变应性鼻炎患者血清中IL-17及其受体的表达,及其与血清中总IgE的关系.方法:采用酶联免疫法检测51例健康志愿者(对照组)和37例变应性鼻炎患者(实验组)血清中IL-17,IL-17R及IgE的含量.结果:与对照组相比,变应性鼻炎患者血清IL-17,IL-17R及IgE的含量均明显升高.IL-17与变应性鼻炎患者血清中IgE成正相关(r=0.9678,P＜0.05),而IL-17R与IgE无明显相关性.结论:IL-17和IL-17R均参与变应性鼻炎的发病过程,可作为诊断变应性鼻炎的新指标,且降低IL-17的含量有助于变应性鼻炎的临床治疗.     

Distribution of single nucleotide polymorphisms of IL-10 gene in patients with mucoviscidosis

Distribution of interleukin-10 promoter-1082 G-->A single nucleotide polimorphism (SNP) in the group of cystic fibrosis (CF) patients has been studied. As a whole 42 CF patients and 73 persons of the control group were genotyped for IL-10 promoter-1082 G-->A SNP. The frequences of IL-10-1082 G-allele and GG high expression genotype increased significantly in CF patients in comparison to the control group. In addition, study of IL-10-1082 SNP distribution in the separate CF groups showed statistically significant increasing of the G-allele and GG-genotype frequencies in the subgroup of homozygous delF508 cariers. The possible role of IL-10 promoter SNP as a phenotype modifiers at different CF genotypes is examined.     

Analysis of CTLA4 gene 49A/G polymorphism association with development of allergic rhinitis

CTLA4 gene 49A/G polymorphism was analyzed in 44 patients with allergic rhinitis and 70 nominally healthy donors of the Uzbek population. The unfavorable allele rate of this polymorphism in general studied groups and control groups did not differ significantly; it was 73.3 and 72.9% respectively. A comparative analysis of the distribution of CTLA4 gene 49A/G polymorphism in groups of patients with allergic rhinitis, depending on the clinical course and patient’s gender, with the control groups did not reveal statistically significant differences. However, in patients with year-round forms of allergic rhinitis, the rate of the functionally unfavorable allele 49A/G of CTLA4 gene was almost 1.29 times higher than the same rate in the group with the seasonal form and the slightly higher than the rate in the control group.     

MDR1 single nucleotide polymorphism C3435T in Turkish patients with non-small-cell lung cancer

We assessed whether single nucleotide polymorphisms (SNPs) in MDR1 gene C3435T predicted the outcome of platinum-based chemotherapies and survival in our non small cell lung cancer (NSCLC) patients. A total of 79 non-small cell lung cancer patients were enrolled to study. We determined the MDR1 C3435T single nucleotide gene polymorphisms. Median age was 60years: 91.7% male, 8.9% female. We found that CC, CT, TT genotype and T, C allele frequencies in lung cancer patients as 24.1%, 62%, 13.9% and 44.3%, 55.7%, respectively. Patients with CT genotype had a higher response rate (11.4%) than the other genotypes. However, this difference is not statistically significant (p=0.743). Cox regression analysis for overall survival showed that ECOG PS status 0 (HR PS 1 vs. 0, 5.68 p=0.002; HR of PS 2 vs. 0 is 21.579, p=0.001; HR of PS 3 vs. 0 is 35.35, p=0.001), stage ≤II (HR of stage III vs. I+II is 17.77; p=0.016, HR of stage IV vs. I+II is 26.97, p=0.006), and albumin level ≥3g/dl (HR of albumin <3g/dl vs. ≥3g/dl is 2.46, p=0.044) were the most important prognostic factors (also, time to progression was related to these factors). There was no significant association between the genotypes and clinicopathologic parameters; however, good performance status, early stage and ≥3g/dl albumin level were found to be the most important prognostic factors for overall survival and progression-free survival.     

Association of Interleukin-13 SNP rs20541 (Arg > Gln) to allergic rhinitis in an Asian population of ethnic Chinese in Singapore

In this study, we report our findings as we evaluated the association of IL-13 SNP rs20541 to AR as reported in the meta-analysis (Ying, X-J et al., April, Gene 2013) in an Asian population of 1322 ethnic Chinese recruited in Singapore well defined and characterized for allergic rhinitis. The SNP was significantly associated with AR at an odds ratio of 1.57 for the homozygous genotype comparisons indicating a strong risk for AR. This highlights the importance of this mutation in Asian populations for risk towards allergic phenotypes and also warrants further functional work to characterize the mechanism behind this genetic predisposition.     

A common single nucleotide polymorphism in endoplasmic reticulum aminopeptidase 2 induces a specificity switch that leads to altered antigen processing

Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) cooperate to trim antigenic peptide precursors for loading onto MHC class I molecules and help regulate the adaptive immune response. Common coding single nucleotide polymorphisms in ERAP1 and ERAP2 have been linked with predisposition to human diseases ranging from viral and bacterial infections to autoimmunity and cancer. It has been hypothesized that altered Ag processing by these enzymes is a causal link to disease etiology, but the molecular mechanisms are obscure. We report in this article that the common ERAP2 single nucleotide polymorphism rs2549782 that codes for amino acid variation N392K leads to alterations in both the activity and the specificity of the enzyme. Specifically, the 392N allele excises hydrophobic N-terminal residues from epitope precursors up to 165-fold faster compared with the 392K allele, although both alleles are very similar in excising positively charged N-terminal amino acids. These effects are primarily due to changes in the catalytic turnover rate (k(cat)) and not in the affinity for the substrate. X-ray crystallographic analysis of the ERAP2 392K allele suggests that the polymorphism interferes with the stabilization of the N terminus of the peptide both directly and indirectly through interactions with key residues participating in catalysis. This specificity switch allows the 392N allele of ERAP2 to supplement ERAP1 activity for the removal of hydrophobic N-terminal residues. Our results provide mechanistic insight to the association of this ERAP2 polymorphism with disease and support the idea that polymorphic variation in Ag processing enzymes constitutes a component of immune response variability in humans.     

Association of interleukin-13 SNP rs20541 with allergic rhinitis risk: A meta-analysis

Studies investigating the association between interleukin-13 (IL-13) single nucleotide polymorphism (SNP) rs20541 and allergic rhinitis (AR) risk have reported conflicting results. The aim of the present study was to conduct a meta-analysis assessing the possible association of IL-13 SNP rs20541 with AR risk. Eight studies were included in the present meta-analysis (2153 cases and 3931 controls). The combined results based on all studies showed that IL-13 SNP rs20541 was associated with increased AR risk (Gln versus Arg: odds ratio (OR) = 1.18, 95% confidence interval (CI) = 1.08–1.30; Gln/Gln versus Arg/Arg: OR = 1.52, 95% CI = 1.20–1.92; Arg/Gln + Gln/Gln versus Arg/Arg: OR = 1.19, 95% CI = 1.06–1.33; Gln/Gln versus Arg/Gln + Arg/Arg: OR = 1.42, 95% CI = 1.13–1.79). When stratifying for race, IL-13 SNP rs20541 exhibited increased AR risk in Asians (Gln versus Arg: OR = 1.20, 95% CI = 1.06–1.36; Gln/Gln versus Arg/Arg: OR = 1.57, 95% CI = 1.17–2.12; Arg/Gln + Gln/Gln versus Arg/Arg: OR = 1.22, 95% CI = 1.04–1.44; Gln/Gln versus Arg/Gln + Arg/Arg: OR = 1.45, 95% CI = 1.09–1.93), while no significant association was detected in Caucasians (Gln versus Arg: OR = 1.28, 95% CI = 0.93 ~ 1.78; Gln/Gln versus Arg/Arg: OR = 1.42, 95% CI = 0.96–2.11; Arg/Gln + Gln/Gln versus Arg/Arg: OR = 1.35, 95% CI = 0.89–2.05; Gln/Gln versus Arg/Gln + Arg/Arg: OR = 1.37, 95% CI = 0.93–2.02). This meta-analysis supported that IL-13 SNP rs20541 was associated with AR, particularly in Asians.     

A single nucleotide polymorphism in the matrix metalloproteinase-2 promoter is associated with colorectal cancer

Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix proteins, particularly basement membrane constituents. A single nucleotide polymorphism C-->T transition at -1306, which disrupts an Sp1-type promoter site (CCACC box), displayed a strikingly lower promoter activity with T allele. Our study investigated whether the MMP-2 -1306 C-->T polymorphism contributed to the development and progression of colorectal cancer in the Chinese population. One hundred twenty-six colorectal cancer patients and 126 age- and sex-matched controls were included in this study. PCR-based denaturing high performance liquid chromatography analysis and sequencing were used to determine the MMP-2 genotypes. MMP-2 expression of each genotype was analyzed in four colorectal cancer cell lines by semi-quantitative RT-PCR. The correlation between the genotypes and clinicopathological parameters among colorectal cancer cases was investigated. The results showed that the levels of MMP-2 mRNA expression in cell lines containing CC genotype were much higher compared with cell with CT genotype. The frequency of MMP-2 CC genotype was significantly higher in colorectal cancer patients when compared with controls (OR, 1.959; 95% CI, 1.055-3.637). Colorectal cancers with CC genotype were more common with serosa/adventitia layer involvement compared with CT+TT genotypes. Our data suggest that MMP-2 -1306 C-->T polymorphism may be associated with colorectal cancer development and invasion in the Chinese population.     

A dual-probe hybridization method for reducing variability in single nucleotide polymorphism analysis with oligonucleotide microarrays

DNA microarray technology has become powerful and popular in mutation/single nucleotide polymorphism (SNP) discovery and genotyping. However, this method is often associated with considerable signal noise of nonbiological origin that may compromise the data quality and interpretation. To achieve a high degree of reliability, accuracy, and sensitivity in data analysis, an effective normalization method to minimize the technical variability is highly desired. In the current study, a simple and robust normalization method is described. The method is based on introduction of a reference probe coimmobilized with SNP probes on the microarray for a dual-probe hybridization (DPH) reaction. The reference probe is used as an intraspot control for the customized microarrays. Using this method, the interassay coefficient of variation (CV) was reduced significantly by approximately 10%. After DPH normalization, the CVs and ranges of the ratios were reduced by two to five times. The relative magnitudes of variation of different sources were also analyzed by analysis of variance. Glass slides were shown to contribute the most to the variance, whereas sampling and residual errors had relatively modest contribution. The results showed that this DPH-based spot-dependent normalization method is an effective solution for reducing experimental variation associated with microarray genotyping data.     

Plasma resistin, associated with single nucleotide polymorphism -420, is correlated with C-reactive protein in Chinese Han patients with spontaneous basal ganglia hemorrhage

We examined a possible relationship -420C>G SNP of the resistin gene with plasma resistin and C-reactive protein concentrations in intracerebral hemorrhage. Three hundred and forty-four Chinese Han patients with intracerebral hemorrhage and 344 age- and gender-matched healthy controls were included in our study. Plasma resistin and C-reactive concentrations were measured and SNP -420C>G was genotyped. The genotype frequencies in controls and patients were not significantly different (P = 0.672). Plasma resistin and C-reactive protein levels were significantly different between the SNP -420C>G genotypes, even after adjustment for age, gender and body mass index. The common homozygote (C-C) had the lowest resistin and C-reactive protein plasma concentrations; the plasma resistin and C-reactive protein concentrations in the heterozygote (C-G) and the rare allele homozygote (G-G) did not differ significantly. Plasma resistin levels were significantly associated with plasma C-reactive protein level. We conclude that SNP -420C>G of the resistin gene could be involved in the inflammatory component of intracerebral hemorrhage through enhanced production of resistin.     

Validation of single nucleotide polymorphism quantification in pooled DNA samples with SNaPIT. A glycosylase-mediated methods for polymorphism detection method

Association studies using genome scans to identify quantitative trait loci for multifactorial disorders, with anything approaching reasonable power, have been compromised by the need for a very dense array of genetic markers and large numbers of affected individuals. These requirements impose enormous burdens on the genotyping capacity for most laboratories. DNA pooling has been proposed as a possible approach to reduce genotyping costs and effort. We report on the application of the SNaPIT™ technology to evaluate allele frequencies in pooled DNA samples and conclude that it offers a cost effective, efficient and accurate estimator and provides several advantages over competing technologies in this regard.