Association of polymorphisms in the IL‐10 promoter region with Crohn's disease

BackgroundIL‐10 is thought to play an important role in preventing inflammatory bowel disease (IBD), although its efficacy is limited in IBD inflammation treatment. The purpose of this study is to investigate the association between SNP polymorphism in the promoter region of the IL‐10 gene and Crohn''s disease (CD).MethodsIn 86 children with CD disease and 142 healthy controls, polymorphisms of three SNPs (rs3790622, rs1800872, and rs1800896) in the IL‐10 promoter region were successfully identified. The risk alleles, genotypes, and haplotypes were also analyzed in the CD patient group and the control group. 2 × 2 chi‐square test was used to identify whether there is a statistically significant association between CD risk and SNP polymorphisms.ResultsAccording to the chi‐square test results, only the polymorphism of rs1800872 was associated with pediatric CD. T allele in rs1800872 showed a high risk for pediatric CD (Pearson χ ² p = 0.030). TT genotype of rs1800872 was associated with a higher risk of CD in the pediatric population (OR 1.986, 95% CI 1.146–3.442, p = 0.020, TT vs. TG + GG). Finally, a risk haplotype GTT (rs3790622‐rs1800872‐rs1800896) in IL‐10 was found (OR 1.570, 95% CI 1.054–2.341, p = 0.028).ConclusionsOur data suggested that T allele, TT genotype, and haplotype GTT in rs1800872 were associated with the susceptibility to pediatric CD in China.     

Correlation between single nucleotide polymorphisms in CXCR4 microRNA binding site and the susceptibility to knee osteoarthritis in Han Chinese population

BackgroundThis study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) at the microRNA target sequence in CXCR4 and the susceptibility to knee osteoarthritis (KOA).MethodsA total of 305 patients with KOA and 305 healthy controls were recruited into this study. The genotypes of CXCR4 rs1804029 and rs17848060 loci were analyzed.ResultsThe susceptibility to KOA of CXCR4 rs1804029 G allele carriers was 1.33 times (95% CI: 1.09‐1.54, P = .006) that of T allele carriers. The KOA susceptibility in individuals carrying T allele at CXCR4 rs17848060 locus was 1.38 times that of individuals carrying A allele (95% CI: 1.17‐1.57, P < .001). The G allele at CXCR4 rs1804029 locus was the target of hsa‐miR‐146a‐3p, while the A allele at CXCR4 rs17848060 locus could be targeted by hsa‐miR‐20a‐3p. The plasma level of hsa‐miR‐146a‐3p was lower in rs1804029 G allele carriers than T allele carriers (P < .001), whereas plasma level of hsa‐miR‐20a‐3p was higher in rs17848060 T allele carriers than A allele carriers (P < .001).ConclusionThe SNPs at rs1804029 and rs17848060 loci in CXCR4 were significantly associated with the susceptibility to KOA in Han Chinese population.     

Association between interleukin gene polymorphisms and susceptibility to gastric cancer in the Qinghai population

ObjectiveTo investigate the associations between interleukin (IL) gene polymorphisms and susceptibility to gastric cancer in the Qinghai population, China.MethodsPatients with gastric cancer and cancer-free controls were enrolled into the study from Qinghai Provincial People’s Hospital between September 2016 and September 2018. Single nucleotide polymorphisms (SNPs) were genotyped with the Sequenom MassARRAY® SNP genotype system. The Hardy–Weinberg equilibrium in allele and genotype frequencies, and general characteristics between patients with gastric cancer and cancer-free controls, were evaluated using χ²-test. Potential associations between interleukin gene variants and the risk of gastric cancer were analysed by logistic regression.ResultsAmong eight candidate SNPs, the allele and genotype frequency distribution of IL-1B rs1143634 polymorphism was significantly different between patients with gastric cancer (n = 190) and cancer-free controls (n = 186). The IL-1B rs1143634 GA genotype and IL-1B rs1143634 GA + AA genotype were associated with a reduced risk of gastric cancer, however, the remaining SNPs were not statistically associated with gastric cancer risk in the Qinghai population.ConclusionThe IL-1B rs1143634 polymorphism might be associated with a decreased risk of gastric cancer, and may be a protective factor against gastric cancer.     

Meta-analysis reveals significant association between FOXP3 polymorphisms and susceptibility to Graves’ disease

ObjectiveThis meta-analysis aimed to determine the associations between the rs3761547, rs3761548, and rs3761549 single-nucleotide polymorphisms (SNPs) of the forkhead box P3 (FOXP3) gene and susceptibility to Graves’ disease (GD).MethodsCase–control studies with information on the associations between the rs3761547, rs3761548, and rs3761549 FOXP3 SNPs and GD published before 01 May 2020 were identified in the PubMed, Embase, Web of Science, and China National Knowledge Infrastructure databases. Data from the studies were analyzed using RevMan version 5.3.ResultsSeven independent case–control studies including 4051 GD patients and 4569 controls were included in the meta-analysis. The overall pooled analysis indicated that FOXP3/rs3761548 and FOXP3/rs3761549 polymorphisms were significantly associated with GD susceptibility (rs3761548: A vs. C, odds ratio [OR] = 1.32, 95% confidence interval [CI] 1.05–1.67; rs3761549: TT vs. CC, OR = 1.98, 95%CI 1.49–2.65; (TT + TC) vs. CC, OR = 1.44, 95%CI 1.11–1.88). In contrast, the FOXP3/rs3761547 polymorphism was not associated with GD susceptibility. Subgroup analysis according to ethnicity showed that rs3761548 was associated with GD in Asians but not in Caucasians, whereas rs3761549 was associated in both Asians and Caucasians.ConclusionThis meta-analysis demonstrated that FOXP3/rs3761548 and FOXP3/rs3761549 SNPs were significantly associated with susceptibility to GD, at least in Asian populations.     

Relationships of interleukin-17 polymorphisms with recurrent aphthous ulcer risk in a Han Chinese population

ObjectiveInterleukin (IL)-17 is a multifunctional cytokine with important roles in inflammatory and autoimmune diseases. This case–control study explored the relationships of IL-17A rs2275913 and IL-17F rs763780 single-nucleotide polymorphisms (SNPs) with recurrent aphthous ulcer (RAU) morbidity and severity.MethodsIL-17A rs2275913 and IL-17F rs763780 SNPs were measured in 125 patients with RAU and 116 healthy control participants. The genotype distributions, disease risks, and relationships with RAU severity were analyzed.ResultsRAU risk was associated with rs2275913 after adjustment for age, body mass index, sex, smoking status, and drinking status (AA vs. GG: odds ratio [OR], 2.759; 95% confidence interval [CI], 1.381–5.512; A allele vs. G allele: OR, 1.783; 95% CI, 1.242–2.560). TC and CC genotypes in rs763780, and the corresponding C allele, demonstrated greater prevalence among patients with RAU, compared with the TT genotype (TC vs. TT, OR: 1.895; 95% CI: 1.088–3.301; CC vs. TT, OR: 4.080, 95% CI: 1.079–15.425; C allele vs. T allele, OR: 1.969, 95% CI: 1.257–3.083). Serum IL-17 concentrations were also higher in patients with RAU than in control participants. These concentrations were associated with IL-17 polymorphisms.ConclusionsIL-17 polymorphisms might be associated with greater risk of RAU pathogenesis.     

Genetic variant in microRNA-146a gene is associated with risk of rheumatoid arthritis

ObjectiveTo investigated the association between single nucleotide polymorphisms (SNPs) in microRNA-146a (miR-146a) gene and susceptibility of rheumatoid arthritis (RA).MethodsWe systemically extracted the genetic data of miR-146a from previous genome-wide association studies (GWASs) of RA. Subsequently, we performed a replication study in an independent Chinese cohort for selected variant. A meta-analysis combined the previous GWASs with the replication study was also conducted. The epigenetic annotation and cytokine assay were used for exploring potential variant function.ResultsThe extracted genetic association data from three previous GWASs showed that the allele T of functional SNP rs2431697 increased RA susceptibility. The significant association for the SNP was also found in the Chinese replication cohort (OR = 1.24, 95% CI = 1.06–1.46, p = 8.69E-03). The estimated effect size for this SNP was larger in Asian population than that in European population (Asian meta-analysis: OR = 1.15, 95% CI = 1.09–1.22, p = 4.37E-07; Tran-ethnic meta-analysis: OR = 1.07, 95% CI = 1.04–1.10, p = 1.79E-06). The cytokine assay also showed that the risk allele T of the SNP rs2431697 is inversely associated with plasma TNF-α levels in health controls (p = .016).ConclusionsIn summary, this study supports that genetic variant in miR-146a gene is associated with RA risk.

KEY MESSAGES

1. The association between SNPs in miR-146a gene and susceptibility of RA was unclear.
2. We investigated the genetic association using GWASs data and a replication study.
3. The SNP rs2431697 in miR-146a gene is associated with RA risk.

     

Genetic variants associated with metabolic dysfunction‐associated fatty liver disease in western China

IntroductionWe aimed to confirm the association between some single nucleotide polymorphisms (SNPs) and metabolic dysfunction‐associated fatty liver disease (MAFLD) in western China.MethodsA total of 286 cases and 250 healthy controls were enrolled in our study. All samples were genotyped for patatin‐like phospholipase domain containing 3 (PNPLA3) rs738409, transmembrane 6 superfamily member 2 (TM6SF2) rs58542926, membrane‐bound O‐acyltransferase domain containing 7 (MBOAT7) rs641738, glucokinase regulator (GCKR) rs1260326 and rs780094, and GATA zinc finger domain containing 2A (GATAD2A) rs4808199. Using logistic regression analysis, we evaluated the association between MAFLD and each SNP under different models. Multiple linear regression was used to find the association between SNPs and laboratory characteristics. Multifactor dimensionality reduction was applied to test SNP–SNP interactions.ResultsThe recessive model and additive model of PNPLA3 rs738409 variant were related to MAFLD (odds ratio [OR] = 1.791 and 1.377, respectively, p = 0.038 and 0.027, respectively). However, after Benjamini‐Hochberg adjustment for multiple tests, all associations were no longer statistically significant. PNPLA3 rs738409 correlated with AST levels. GCKR rs780094 and rs1260326 negatively correlated with serum glucose but positively correlated with triglycerides in MAFLD. Based on MDR analysis, the best single‐locus and multilocus models for MAFLD risk were rs738409 and six‐locus models, respectively.ConclusionsIn the Han population in western China, no association was found between these SNPs and the risk of MAFLD. PNPLA3 rs738409 was associated with aspartate aminotransferase levels in MAFLD patients. GCKR variants were associated with increased triglyceride levels and reduced serum fasting glucose in patients with MAFLD.     

Dysregulation of vitamin D synthesis pathway genes in colorectal cancer: A case‐control study

BackgroundThe cytochromes P450 are a superfamily of enzymes that control the synthesis of the biologically active form of vitamin D, 1,25‐dihydroxyvitamin D3. These enzymes contribute to the formation of 1,25‐dihydroxyvitamin D3, which starts with a 25‐hydroxylation by CYP2R1 and CYP27A1 and a subsequent 1α‐hydroxylation via CYP27B1.MethodsBy using quantitative real‐time polymerase chain reaction (qRT‐PCR), we analyzed the expression ratio of CYP2R1, CYP27A1 and CYP27B1 genes within the vitamin D metabolic pathway in a total of 75 colorectal cancer (CRC) tissues compared to the adjacent tissues. Furthermore, we evaluated the association of CYP27B1 rs4646536 and CYP2R1 rs12794714 and rs10766196 polymorphisms with CRC risk in a total of 490 subjects, including 245 CRC patients and 245 non‐cancer controls. The genotyping was performed using tetra‐primer amplification refractory mutation system polymerase chain reaction (TP‐ARMS–PCR) method.ResultsThe results indicated 2.3 and 2.7 upregulation of CYP2R1 and CYP27B1 genes in colorectal cancer tissues compared to the adjacent tissues, respectively. Rs12794714 AG genotype increased the risk of CRC (P = .03). Furthermore, a significant association was observed under the dominant inheritance model (P = .039).Conclusion CYP2R1 and CYP27B1 genes were over‐expressed in CRC samples compared to the adjacent control tissues. Furthermore, CYP2R1 rs12794714 variant was associated with the risk of CRC in the studied samples. CYP2R1 rs10766196 and CYP27B1 rs4646536 are not responsible for CYP2R1 and CYP27B1 genes expression alteration, respectively, but CYP2R1 rs12794714 polymorphism may be the reason of CYP2R1 upregulation and increased the risk of CRC.     

APOE gene ɛ4 allele (388C‐526C) effects on serum lipids and risk of coronary artery disease in southern Chinese Hakka population

ObjectiveTo analyze the relationship of Apolipoprotein E (APOE) and solute carrier organic anion transporter family member 1B1 (SLCO1B1) gene polymorphisms with coronary artery disease (CAD).Methods1,129 CAD patients and 1,014 non‐CAD controls were included in the study, and relevant information and medical records were collected. The single‐nucleotide polymorphisms (SNPs) were analyzed, including rs429358, rs7412 in APOE gene and rs2306283, rs4149056 in SLCO1B1 gene.ResultsThe CAD patients’ average age was 66.3 ± 10.7 years, while 65.5 ± 12.0 years in controls. The frequencies of APOE allele ɛ3, ɛ4, and ɛ2 were 83.01%, 10.08%, and 6.91% respectively. There were statistically significant differences in genotype ɛ3/ɛ4 (χ² = 8.077, p = 0.005) in CAD patients compared with the controls. The SLCO1B1 genotype *1b/*1b and haplotype *1b showed the highest frequency in the study sample. Moreover, ε4 carriers had significantly lower HDL‐C, Apo‐A1 levels than ε3 carriers among CAD patients, while ε2 carriers showed lower LDL‐C, Apo‐B level, and higher Apo‐A1/Apo‐B level than ε3 and ε4 carriers. In controls, ε2 carriers showed lower LDL‐C and Apo‐B level, higher Apo‐A1, and Apo‐A1/Apo‐B level than ε4 carriers. Logistic regression analysis showed that high LDL‐C and Apo‐B level, low HDL‐C level, smoking, and the ε4 allele were risks for the presence of CAD.ConclusionsAPOE ε4 allele may be associated with susceptibility to CAD in southern Chinese Hakka population. It indicated that the APOE SNPs rs429358 and rs7412 are associated with CAD, but not SNPs rs2306283 and rs4149056 of SLCO1B1 gene.     

Interleukin-33 gene polymorphisms and chronic obstructive pulmonary disease in the Chinese Han population

ObjectiveTo investigate the relationship between interleukin (IL)-33 gene polymorphisms rs928413 and rs7044343 with chronic obstructive pulmonary disease (COPD) in the Chinese Han population.MethodWe assessed IL-33 rs928413 and rs7044343 polymorphisms by Sanger sequencing of PCR products amplified from the genomic DNA of 160 COPD patients and 123 healthy controls.ResultsThere was no significant difference in the distribution of rs928413 AA, AG, or AA genotypes or rs7044343 CC, CT, or TT genotypes between the two groups. However, COPD patients had a significantly higher frequency of the rs928413 G allele G (14.1% vs 7.3%, respectively). This allele was significantly associated with susceptibility to COPD (odds ratio [OR]: 2.04, 95% confidence interval [CI]: 1.12–3.57). The rs928413 dominant inheritance model was associated with COPD susceptibility (OR: 2.08, 95%CI: 1.09–4.04).ConclusionThe G allele of rs928413 and the rs928413 dominant inheritance model were associated with susceptibility to COPD in the Chinese Han population.     

Analysis of rs1864182 and rs1864183 variants in ATG10 gene and antineutrophil cytoplasmic autoantibody‐associated vasculitis in Chinese Guangxi population

ObjectivesTo investigate the association of autophagy‐associated gene 10 (ATG10) gene polymorphisms (rs1864182 and rs1864183) with antineutrophil cytoplasmic autoantibody (ANCA)‐associated vasculitis (AAV) in Chinese Guangxi population.MethodsThe single nucleotide polymorphisms (SNPs) of ATG10 rs1864182 and rs1864183 in 395 participants (195 AAVs and 200 healthy controls) were genotyped. Generalized multiple dimensionality reduction (GMDR) was used to analyze the SNP‐SNP interactions among two SNPs of ATG10 gene and other SNPs of autophagy gene previously studied by our research team.ResultsIn this study, we found that the two ATG10 SNPs were not associated with AAV risk in Chinese Guangxi population. However, there were statistically significant differences in the incidence of hemoptysis, hematuria, and proteinuria among the three genotypes of ATG10 rs1864182 and rs1864183 (p < 0.05). Moreover, permutation test of GMDR suggested that immunity‐related GTPase M(IRGM) rs4958847, autophagy‐associated gene 7 (ATG7) rs6442260, ATG7 rs2594966, ATG10 rs1864183, protein kinase B(AKT2) rs3730051, and AKT2 rs11552192 might interact with each other in the process of developing AAV (p < 0.05).ConclusionsOur results indicated that there existed no association between ATG10 SNPs and AAV, and SNP‐SNP interactions among IRGM rs4958847, ATG7 rs6442260, ATG7 rs2594966, ATG10 rs1864183, AKT2 rs3730051, and AKT2 rs11552192 may confer AAV risk in the Chinese Guangxi population.     

TLR4 polymorphisms as potential predictors of atopic dermatitis in Chinese Han children

BackgroundToll‐like receptor 4 (TLR4) is considered to be involved in the pathogenesis and progression of atopic dermatitis (AD). In the present study, we evaluated the relationship between TLR4 gene polymorphisms and the susceptibility or severity of AD among Chinese Han children.MethodsA total of 132 AD patients and 100 healthy controls were enrolled in this study. Four single‐nucleotide polymorphisms (rs19277914, rs11536891, rs7869402, and rs11536889) of the TLR4 gene were genotyped by multiplex PCR combined with next‐generation sequencing.ResultsOur results showed that a significantly reduced risk for AD was associated with C allele [p = 0.008; odds ratio (OR) = 0.41, C vs. T], TC genotype (p = 0.022; OR = 0.41, TC vs. TT), and TC + CC genotype (p = 0.010; OR = 0.39, TC + CC vs. TT) of TLR4 rs11536891. The frequency of the haplotype GCCG (rs1927914–rs11536891–rs7869402–rs11536889) in AD patients was lower than that in the controls (p = 0.010; OR = 0.38). Moreover, the results indicated that a higher risk of severe AD was related to the T allele (p = 0.019; OR = 2.97, T vs. C) and the TC genotype (p = 0.021; OR = 3.34, TC vs. CC) of TLR4 rs7869402. A risk haplotype of TLR4 (GTTG) was found in severe AD patients (p = 0.010; OR = 5.26).ConclusionsOur data suggested that TLR4 rs11536891 polymorphism was associated with the susceptibility to AD in Chinese Han children. And TLR4 rs7869402 might confer the severity of pediatric AD patients.     

Assessment of Association between Common Variants at 17q12 and Prostate Cancer Risk—Evidence from Serbian Population and Meta‐Analysis

This study aimed to evaluate possible association between genotypes and alleles of two 17q12 polymorphisms (rs3760511 and rs7501939) and prostate cancer (PCa) risk and progression. Two hundred seventy‐one patients with PCa, 261 patients with benign prostatic hyperplasia (BPH), and 171 controls were included in the study. Single nucleotide polymorphisms (SNPs) were genotyped by using PCR followed by restriction fragment length (PCR‐RFLP) analysis. We conducted meta‐analysis of published studies regarding association of these SNPs with PCa risk. Evidence of positive association between the AC genotype of the SNP rs3760511 and BPH risk for the best‐fitting overdominant model of association (BPH vs. controls comparison, p = 0.026; odds ratio [OR] = 1.58; 95% confidence interval [95%CI] 1.05–2.36) were obtained. The association between T allele of rs7501939 and PCa risk was determined in PCa versus controls comparison (p = 0.0032; OR = 0.66, 95%CI 0.50–0.87) with the best‐fitting model of inheritance being log‐additive. This variant was also found to be associated with the risk of BPH (p = 0.0023; OR = 0.65, 95%CI 0.49–0.86). We found no association between parameters of PCa progression and the analyzed SNPs. Meta‐analysis showed strong association between these variants and PCa risk. Our study shows association between SNPs at locus 17q12 and the risk of prostatic diseases in Serbian population. At the same time, results of meta‐analysis suggest the association of these SNPs with PCa risk.     

A polymorphism in the 3′-untranslated region of the matrix metallopeptidase 9 gene is associated with susceptibility to idiopathic calcium nephrolithiasis in the Chinese population

ObjectiveTo investigate whether single nucleotide polymorphisms (SNPs) in the 3′ untranslated region (UTR) of the matrix metallopeptidase 9 gene (MMP9) are associated with susceptibility to calcium oxalate stones.MethodsA total of 428 patients with kidney stone disease (KSD) and 450 control individuals were enrolled. Three MMP9 SNPs (rs20544, rs9509, and rs1056628) were genotyped, and MMP9 mRNA and protein expression was determined in patients and controls. The dual luciferase reporter gene assay was conducted by transfecting HEK293 cells with miR-491-5p mimics and plasmids containing MMP9 with rs1056628 AA/CC genotypes.ResultsThe rs1056628 CC genotype was significantly increased in KSD patients compared with controls (CC vs AA: odds ratio [OR] = 2.279, 95% confidence interval [CI] = 1.048–4.956). The rs1056628 C allele frequency was higher in KSD patients than controls. The increased KSD risks associated with rs1056628 were more evident in individuals aged <30 years (OR = 3.504, 95% CI = 1.102–11.139) and men (OR = 2.522, 95% CI = 1.004–6.334). mRNA and protein levels of MMP9 were significantly higher in KSD patients with the CC genotype than in those with the AA genotype.ConclusionThis study demonstrates that MMP9 SNP rs1056628 is associated with a significant KSD risk in Chinese Han individuals.     

Mannose-binding lectin 2 gene polymorphisms and predisposition to allergic bronchial asthma in a western Romanian children population: an observational study

ObjectivesTo analyse: (1) the associations between different mannose-binding lectin 2 (MBL2) genotypes and susceptibility to bronchial asthma (BA) in Romanian children; and (2) the correlations between several patient sociodemographic variables and MBL2 polymorphisms.MethodsThis prospective observational case–control study included paediatric patients with symptomatic BA and healthy controls. Participants were genotyped for two MBL2 single-nucleotide polymorphisms (SNPs): exon 1 codon 54 A/B variant rs1800450, and -550 promoter H/L variant rs11003125 (GenBank accession). Associations between MBL2 genotypes and susceptibility to BA were determined by calculated odds ratios, and Kendall Tau’s correlations were used to investigate the associations between sociodemographic variables and SNPs.ResultsAmong 59 patients with BA and 65 healthy controls, associations between MBL2 polymorphisms and susceptibility to BA were not found to be statistically significant. Statistically significant weak positive correlations were found between age at diagnosis and A/B genotype, and between the smoking status of biologically male and female parents. A statistically significant weak inverse association was found between male parent smoking status and family history of BA.ConclusionThese results may help guide future research into paediatric BA in Romania and Eastern Europe. Due to study limitations, the results require validation in future large-scale studies.     

Association of FAM13A polymorphisms with COPD and COPD-related phenotypes in Han Chinese

ObjectivesGenome-wide association studies (GWAS) and integrative genomics approaches have demonstrated significant associations between chronic obstructive pulmonary disease (COPD) and FAM13A polymorphisms in non-Asian populations. The aim of this study was to investigate whether FAM13A polymorphisms would be associated with COPD susceptibility and COPD-related phenotypes in a Chinese Han population.MethodsSeven single nucleotide polymorphisms (SNPs) (rs7671167, rs10007590, rs2869966, rs2869967, rs2045517, rs1903003, rs6830970) in FAM13A gene were genotyped in a case–control study (680 COPD patients and 687 controls). Allele frequencies and genotype distributions were compared between patients and controls. To estimate the strength of association, odds ratios (OR) (with 95% CI) were calculated and potential confounding variables were tested by using logistic regression analysis.ResultsStatistical analysis revealed that SNP rs7671167 was associated with COPD in former smokers with adjusted P-value of 0.026. Five SNPs (rs7671167, rs2869966, rs2869967, rs2045517, and rs6830970) were associated with FEV1/FVC ratio in the entire cohort and rs6830970 was associated with FEV1/FVC ratio in COPD cases (P range 0.003–0.034). Borderline associations with FEV1/FVC ratio were found for rs2869966, rs2869967 and rs2045517 among cases (P = 0.05). Six SNPs (rs7671167, rs2869966, rs2869967, rs2045517, rs1903003, rs6830970) showed strong linkage disequilibrium (r² ≥ 0.9). Four major haplotypes were observed but showed no significant difference between case and control groups (P = 0.2356, 0.1273, 0.6266 and 0.3006 respectively).ConclusionsThe current study suggests that the FAM13A locus might be a contributor to COPD susceptibility in Chinese Han population.     

Identification of haplotype tag single nucleotide polymorphisms within the nuclear factor-κB family genes and their clinical relevance in patients with major trauma

IntroductionNuclear factor-κB (NF-κB) family plays an important role in the development of sepsis in critically ill patients. Although several single nucleotide polymorphisms (SNPs) have been identified in the NF-κB family genes, only a few SNPs have been studied.MethodsA total of 753 patients with major blunt trauma were included in this study. Tag SNPs (tSNPs) were selected from the NF-κB family genes (NFKB1, NFKB2, RELA, RELB and REL) through construction of haplotype blocks. The SNPs selected from genes within the canonical NF-κB pathway (including NFKB1, RELA and REL), which played a critical role in innate immune responses were genotyped using pyrosequencing method and analyzed in relation to the risk of development of sepsis and multiple organ dysfunction (MOD) syndrome. Moreover, the rs842647 polymorphism was analyzed in relation to tumor necrosis factor α (TNF-α) production by peripheral blood leukocytes in response to bacterial lipoprotein stimulation.ResultsEight SNPs (rs28362491, rs3774932, rs4648068, rs7119750, rs4803789, rs12609547, rs1560725 and rs842647) were selected from the NF-κB family genes. All of them were shown to be high-frequency SNPs in this study cohort. Four SNPs (rs28362491, rs4648068, rs7119750 and rs842647) within the canonical NF-κB pathway were genotyped, and rs842647 was associated with sepsis morbidity rate and MOD scores. An association was also observed between the rs842647 A allele and lower TNF-α production.Conclusionsrs842647 polymorphism might be used as relevant risk estimate for the development of sepsis and MOD syndrome in patients with major trauma.

Electronic supplementary material

The online version of this article (doi:10.1186/s13054-015-0836-6) contains supplementary material, which is available to authorized users.     

Associations between ATG16L1 gene polymorphism and antineutrophil cytoplasmic antibody‐associated vasculitis in the Chinese Guangxi population: A case–control study

BackgroundAntineutrophil cytoplasmic antibody (ANCA)‐associated vasculitis (AAV) is an autoimmune disease often accompanied by rapidly progressive renal failure, and the genetic background is still unknown. Our study was performed to test whether autophagy‐related 16 like 1 (ATG16L1) rs4663402 and rs4663396 single nucleotide polymorphisms (SNPs) were associated with AAV in the Chinese Guangxi population.MethodsOne hundred seventy seven unrelated AAV patients and 216 healthy controls were included in this case–control study. Multiplex polymerase chain reaction combined with high‐throughput sequencing was used for typing, and SNPStats and SHEsis were used for association analysis, pairwise linkage disequilibrium, and haplotype analysis.Resultsrs4663402 and rs4663396 were in Hardy–Weinberg equilibrium in AAV and control groups. The frequencies of rs4663402 AA, AT, and TT genotypes were 82.5%, 16.9%, and 0.6%, respectively, in patients with AAV, and 83.5%, 16.2%, and 0.5%, respectively, in controls. The frequencies of rs4663396 CC, CT, and TT genotypes were 63.8%, 33.9%, and 2.3%, respectively, in patients with AAV, and 69.2%, 26.6%, and 4.2%, respectively, in controls. Haplotype analysis revealed two SNPs in a single haplotype block (D′ = 1.0). Our logistic regression adjusted for sex and age showed no association between rs4663402 and rs4663396 and the risk for AAV in genetic models (p > 0.05). However, ATG16L1 rs4663396 CC and CT + TT genotypes exhibited statistically significant differences in the incidence of arthralgia (p = 0.03).ConclusionsOur results indicated that ATG16L1 rs4663402 and rs4663396 polymorphisms were not associated with AAV in the Chinese Guangxi population. ATG16L1 rs4663396 CT + TT genotype may be associated with arthralgia.     

Association between the TAP1 gene polymorphisms and recurrent respiratory papillomatosis in patients from Western Mexico: A pilot study

BackgroundRecurrent respiratory papillomatosis (RRP) is a respiratory tract disease that affects children and adults and is characterized by the recurrent proliferation of multiple papillomas. The etiologic agent is the human papillomavirus, mainly genotypes 6 and 11. Furthermore, polymorphisms in TAP1 appear to influence the selection of antigenic peptides and the transport process to the rough endoplasmic reticulum, for their subsequent presentation to T lymphocytes, an essential process against viral diseases and tumor processes. Previous studies have shown that individuals with those polymorphisms are susceptible to immune, infectious, and tumor‐related diseases. The present study aimed to determine the association between the TAP1 rs1057141 (c.1177A>G) and rs1135216 (c.2090A>G) single nucleotide polymorphisms (SNPs) and RRP.MethodsA case–control study was carried out on a group of 70 individuals (35 controls and 35 patients). RRP diagnosis, HPV genotyping, and viral load were determined through histology and PCR. SNPs rs1057141 and rs1135216 were identified through allelic discrimination, using real‐time PCR. The haplotypic analyses were performed using the Arlequin 3.5 program.ResultsHPV‐6 and HPV‐11 were the genotypes found in the samples. In the polymorphism analysis, rs1057141 showed no significant differences (p = 0.049, CI = 0.994–7.331). In contrast, a significant difference was found in rs1135216 (p = 0.039, OR = 2.4) in the allelic analysis, as well as in the dominant (p = 0.027, OR = 3.06), codominant (p = 0.033, OR = 3.06), and additive model (p = 0.043, OR = 2.505) in subjects with the G allele.ConclusionThe G allele in rs1135216 was associated with a genetic risk of susceptibility for RRP in a population in Western Mexico.