Screened Single Nucleotide Polymorphisms Research Articles

Causal effects of noise and air pollution on multiple diseases highlight the dual role of inflammatory factors in ambient exposures

BackgroundNoise and air pollution are significant environmental threats with proven adverse health effects. However, the causality between these ambient exposures and disease is still largely unknown. This study aims to provide genetic evidence for this gap and investigates the dual role of inflammatory factors, emphasizing the need for integrated public health strategies. MethodsWe included noise and air pollution as exposures, 91 inflammatory factors as mediators, and 26 diseases as outcomes. We explored causal relationships using Mendelian randomization. To ensure the reliability, we screened single nucleotide polymorphisms (SNPs) closely associated with exposure as instrumental variables (IVs), and assessed the pleiotropy and heterogeneity of these IVs. ResultsOur results suggest that “Hearing difficulty/problems with background noise” increases the risk of hypertension, bronchitis, and menopause; loud music exposure frequency increases the risk of bronchitis; noisy workplace raises the risk of hypertension, coronary heart disease, narcolepsy, and irritable bowel syndrome; NO2 increases the risk of myocardial infarction and chronic heart failure; NOx increases the risk of pneumonia and inflammatory diseases of female pelvic organs; and PM10 increases the risk of myocardial infarction, narcolepsy, and type 2 diabetes; PM2.5–10 increases the risk of developing pneumonia and type 2 diabetes. Furthermore, we found that nine inflammatory factors play a mediating role, of which four play a mediating role in increasing the risk of morbidity and eight play a mediating role in protection against ambient exposures. Finally, we selected SNPs significantly associated with exposure and outcome for enrichment analysis. ConclusionsThis study provides the first genetic evidence linking noise and air pollution to various diseases, highlighting the dual mediating role of inflammatory factors. Our findings align with the “One Health” framework, emphasizing the interconnectedness of environmental and human health. Integrated public health strategies considering these complex biological responses are essential for promoting overall well-being.

Socioeconomic traits and the risk of Barrett's esophagus and gastroesophageal reflux disease: A Mendelian randomization study.

Previous observational studies have shown that the prevalence of gastroesophageal reflux disease (GERD) and Barrett's esophagus (BE) is associated with socioeconomic status. However, due to the methodological limitations of traditional observational studies, it is challenging to definitively establish causality. To explore the causal relationship between the prevalence of these conditions and socioeconomic status using Mendelian randomization (MR). We initially screened single nucleotide polymorphisms (SNPs) to serve as proxies for eight socioeconomic status phenotypes for univariate MR analysis. The inverse variance weighted (IVW) method was used as the primary analytical method to estimate the causal relationship between the eight socioeconomic status phenotypes and the risk of GERD and BE. We then collected combinations of SNPs as composite proxies for the eight socioeconomic phenotypes to perform multivariate MR (MVMR) analyses based on the IVW MVMR model. Furthermore, a two-step MR mediation analysis was used to examine the potential mediation of the associations by body mass index, major depressive disorder (MDD), smoking, alcohol consumption, and sleep duration. The study identified three socioeconomic statuses that had a significant impact on GERD. These included household income [odds ratio (OR): 0.46; 95% confidence interval (95%CI): 0.31-0.70], education attainment (OR: 0.23; 95%CI: 0.18-0.29), and the Townsend Deprivation Index at recruitment (OR: 1.57; 95%CI: 1.04-2.37). These factors were found to independently and predominantly influence the genetic causal effect of GERD. Furthermore, the mediating effect of educational attainment on GERD was found to be mediated by MDD (proportion mediated: 10.83%). Similarly, the effect of educational attainment on BE was mediated by MDD (proportion mediated: 10.58%) and the number of cigarettes smoked per day (proportion mediated: 3.50%). Additionally, the mediating effect of household income on GERD was observed to be mediated by sleep duration (proportion mediated: 9.75%). This MR study shed light on the link between socioeconomic status and GERD or BE, providing insights for the prevention of esophageal cancer and precancerous lesions.

Genetic polymorphisms linked to extreme postorthodontic external apical root resorption in Koreans

BackgroundExternal apical root resorption (EARR) is a common undesirable outcome of orthodontic treatment, this study aimed to identify genetic polymorphisms associated with the susceptibility to extreme orthodontic-induced EARR in a Korean population using extreme phenotype analysis sampling.MethodsGenomic DNA was isolated from the saliva of 77 patients who underwent orthodontic treatment involving two maxillary premolar extractions. The patients were divided into two groups based on EARR values measured on periapical radiographs: The significant resorption group (SG, EARR ≥ 4 mm) and the normal group (NG, EARR < 2 mm). In the NG group, patients with EARR < 1 mm were named the non-resorption group (NonG). Targeted next-generation sequencing was performed using the screened single nucleotide polymorphisms (SNPs), and firth logistic regression analysis was used to determine genetic associations with EARR. Haplotype-based association analysis was performed for specific SNPs.ResultsSNPs related to genes TNFSF11, TNFRSF11B, WNT3A, SFRP2, LRP6, P2RX7, and LRP1 were found to be significantly associated with severe EARR (p < 0.05, pre-Bonferroni correction p-values). Additionally, the haplotype CCA of rs17525809, rs208294, and rs1718119 P2RX7 had a higher frequency in the SG group.ConclusionExtreme phenotype analysis has identified eleven SNPs related to genes TNFSF11, TNFRSF11B, WNT3A, SFRP2, LRP6, P2RX7, and LRP1 that are associated with severe root resorption in the Korean population. These findings will contribute to the development of predictive diagnostic tools for identifying severe root resorption that may occur during orthodontic treatment.

Evaluation for causal effects of socioeconomic traits on risk of female genital prolapse (FGP): a multivariable Mendelian randomization analysis

BackgroundAlthough observational studies have established some socioeconomic traits to be independent risk factors for pelvic organ prolapse (POP), they can not infer causality since they are easily biased by confounding factors and reverse causality. Moreover, it remains ambiguous which one or several of socioeconomic traits play predominant roles in the associations with POP risk. Mendelian randomization (MR) overcomes these biases and can even determine one or several socioeconomic traits predominantly accounting for the associations.ObjectiveWe conducted a multivariable Mendelian randomization (MVMR) analysis to disentangle whether one or more of five categories of socioeconomic traits, “age at which full-time education completed (abbreviated as “EA”)”, “job involving heavy manual or physical work (“heavy work”)”, “average total household income before tax (income)”, “Townsend deprivation index at recruitment (TDI)”, and “leisure/social activities” exerted independent and predominant effects on POP risk.MethodsWe first screened single-nucleotide polymorphisms (SNPs) as proxies for five individual socioeconomic traits and female genital prolapse (FGP, approximate surrogate for POP due to no GWASs for POP) to conduct Univariable Mendelian randomization (UVMR) analyses to estimate causal associations of five socioeconomic traits with FGP risk using IVW method as major analysis. Additionally, we conducted heterogeneity, pleiotropy, and sensitivity analysis to assess the robustness of our results. Then, we harvested a combination of SNPs as an integrated proxy for the five socioeconomic traits to perform a MVMR analysis based on IVW MVMR model.ResultsUVMR analyses based on IVW method identified causal effect of EA (OR 0.759, 95%CI 0.629–0.916, p = 0.004), but denied that of the other five traits on FGP risk (all p > 0.05). Heterogeneity analyses, pleiotropy analyses, “leave-one-out” sensitivity analyses and MR-PRESSO adjustments did not detect heterogeneity, pleiotropic effects, or result fluctuation by outlying SNPs in the effect estimates of six socioeconomic traits on FGP risk (all p > 0.05). Further, MVMR analyses determined a predominant role of EA playing in the associations of socioeconomic traits with FGP risk based on both MVMR Model 1 (OR 0.842, 95%CI 0.744–0.953, p = 0.006) and Model 2 (OR 0.857, 95%CI 0.759–0.967, p = 0.012).ConclusionOur UVMR and MVMR analyses provided genetic evidence that one socioeconomic trait, lower educational attainment, is associated with risk of female genital prolapse, and even independently and predominantly accounts for the associations of socioeconomic traits with risk of female genital prolapse.

Natural Selection on Exonic SNPs Shapes Allelic Expression Imbalance (AEI) Adaptability in Lung Cancer Progression.

Tumors are driven by a sequence of genetic and epigenetic alterations. Previous studies have mostly focused on the roles of somatic mutations in tumorigenesis, but how germline variants act is largely unknown. In this study, we hypothesized that allelic expression imbalance (AEI) participated in the process of germline variants on tumorigenesis. We screened single-nucleotide polymorphisms (SNPs) as representative germline variants. By using 127 patients’ RNA sequencing data from paired lung cancer and adjacent normal tissues from public databases, we analyzed the effects of the functional consequence of SNPs, function and conservativeness on genes with AEI. We found that natural selection can affect AEI. Functional adaptability of genes with a high frequency of AEI and a correlation of the incidence of AEI with conservativeness were observed in both adjacent tissues and tumor tissues. Moreover, we observed a higher incidence of AEI in genes with non-synonymous SNPs than in those with synonymous SNPs. However, we also found that AEI was affected by allele expression noise, especially in tumor tissues, which led to an increased proportion of AEI, weakened the effect of natural selection and eliminated the influence of the functional consequence of SNPs on AEI. We unveiled a previously unknown adaptive regulatory mechanism in which the effect of natural selection on SNPs can be reflected in allelic expression, which provides insight into a better understanding of cancer evolution.

The CXCL9 Polymorphism rs884304 Associates with Early CXCL9 Reconstitution and with Severe Chronic Graft-Versus-Host Disease (cGVHD) in Human Allograft Recipients

Introduction: CXCL9 is a CXCR3 ligand that was shown to be implicated in the pathomechanism of cGVHD after allogeneic stem cell transplantation (alloSCT). In the present study, we screened single nucleotide polymorphisms (SNPs) inside the CXCL9 locus, and measured peritransplant CXCL9 serum levels kinetics to further determine the role of CXCL9 in cGVHD pathogenesis. Patients and methods: Patients surviving at least 6 months after alloSCT with available DNA or sera were eligible for this study. 317 patients who were allografted at the University of Heidelberg and did not receive statin-based endothelial prophylaxis (SEP) constituted the no-SEP training cohort, 424 patients from Heidelberg who received SEP constituted the SEP cohort. The no-SEP validation cohort consisted of 211 patients who were allografted at an independent institution (Charite Berlin). Patients were retrospectively graded for cGVHD based on the NIH consensus criteria. Prospectively collected serum samples taken once weekly before alloSCT until day+28 were analyzed for CXCL9 serum levels in n=132 / n=331 patients (no SEP/SEP resp.). CXCL9 serum levels dropped within two weeks after conditioning therapy and normalized until day+28. Minimal serum concentrations measured between days 0-14 and recovery serum values measured on day+28 were used to calculate the slope of CXCL9 recovery in the context of calcineurin inhibitors. Four SNPs (rs4282209, rs3733236, rs2276885 and rs884304) in CXCL9 locus were selected based on linkage disequilibrium (LD) and tagging SNP approach. The SNPs were genotyped in recipient DNA and analyzed for association with severe cGVHD. Hazard ratios (HR) with 95% confidence interval (CI) were estimated using Cox regression. Multivariate analysis included age, diagnosis, matched vs. mismatched donor, sex of donor and recipient and usage of ATG as covariates. Functionality of the regulatory SNP rs884304 was investigated using luciferase reporter assay in HEK293T cells. A total of 5 reporter constructs were generated with Quik-change site-directed mutagenesis kit (Invitrogen). In addition to the wildtype construct, three constructs carried variant alleles for each of the three SNPs, and one construct carried variant alleles for all the three SNPs. The constructs were transfected using lipofectamine 2000 reagent and incubated for 24h without treatment or treated with IFN- γ and/or cyclosporine (CsA) or tacrolimus. Cells were subsequently lysed and assayed for luciferase activity. Results: Overall, 60 of 317 patients (19%) in the no-SEP training cohort, 54 of 424 patients (13%) in the SEP cohort, and 50 of 211 patients (24%) in the validation cohort developed at least one episode of severe cGVHD. Out of the four SNPs, only the AA/AG genotypes for the rs884304G&amp;gt;A polymorphism associated with significantly higher risk of severe cGVHD in the no-SEP training cohort (HR: 2.01, 95%CI 1.04-3.90, P=0.04). The effect was also reproduced in the no-SEP validation cohort (HR: 1.88, 95%CI 1.06-3.32, P=0.04). In contrast, no significant effect was observed for high risk genotypes in the SEP cohort (HR 0.77, 95% CI 0.41-1.46, P=0.43). In reporter assays in the context of IFN- γ activation, significantly reduced suppressive effects of CsA on the promoter activity in the constructs with variant alleles of SNP rs884304 (P&amp;lt;0.001) and rs884004 (P&amp;lt;0.001) was observed compared to the wildtype construct (Figure 1). The slope of CXCL9 serum level increase until day+28 significantly correlated with the incidence of severe cGVHD (every 1 unit, HR 1.007, 95%CI 1.001-1.014, P=0.03) and was higher in high risk genotypes of rs884304 (Kruskal-Wallis test p=0.02). Conclusion: Rapidly rising CXCL9 serum levels after alloSCT are associated with an increased risk of developing severe cGVHD. CXCL9 SNPs rs884304 and rs884004 alter CXCL9 suppression in response to calcineurin inhibitors, representing one possible mechanism for enhanced CXCL9 expansion and subsequent cGVHD promotion. Figure 1: Reduced suppressive effect of CsA on CXCL9 promoter activity with HR SNPs in the context of IFN- γ activation. Disclosures Dreger: AbbVie, AstraZeneca, Gilead, Janssen, Novartis, Riemser, Roche: Consultancy; AbbVie, Gilead, Novartis, Riemser, Roche: Speakers Bureau; Neovii, Riemser: Research Funding; MSD: Membership on an entity's Board of Directors or advisory committees, Other: Sponsoring of Symposia. Luft:JAZZ: Research Funding; Neovii: Research Funding.

Association between vitamin D receptor gene polymorphism and ankylosing spondylitis in Han Chinese.

To investigate whether vitamin D receptor (VDR) gene polymorphisms confer susceptibility to aankylosing spondylitis (AS) and study its polymorphisms in Han Chinese. We screened single nucleotide polymorphisms (SNPs) in the VDR region through genome-wide genotyping chips in AS cases and healthy controls, then used the exome sequencing result to analyze all the potential AS-associated SNPs in the VDR gene. Thirty-two SNPs were found in the VDR gene in the genome-wide genotyping chips and the logistic regression result showed no significant difference between AS cases and controls. A total of 46 SNPs in the VDR region were genotyped through exome sequencing, including four functional SNPs (rs731236 [TaqI], rs2228570 [FokI], rs7975232 [ApaI], rs1544410 [BsmI]) and two newly discovered SNPs (12:48259222 and 12:48276730). To note, rs731236 and rs2228570 locate in the exons of VDR, which cause synonymous and missense mutation. The association test showed there was no significant difference between AS cases and controls in the allele frequency distribution, but haplotype analysis of rs11168266-rs11168267 show nominal significance (P = 0.01268). Our preliminary study indicates the haplotypes (TG) of rs11168266-rs11168267 in the VDR gene confers susceptibility to AS, which is worth further research.

Polymorphisms in the Perilipin Gene May Affect Carcass Traits of Chinese Meat-type Chickens.

Improved meat quality and greater muscle yield are highly sought after in high-quality chicken breeding programs. Past studies indicated that polymorphisms of the Perilipin gene (PLIN1) are highly associated with adiposity in mammals and are potential molecular markers for improving meat quality and carcass traits in chickens. In the present study, we screened single nucleotide polymorphisms (SNPs) in all exons of the PLIN1 gene with a direct sequencing method in six populations with different genetic backgrounds (total 240 individuals). We evaluated the association between the polymorphisms and carcass and meat quality traits. We identified three SNPs, located on the 5′ flanking region and exon 1 of PLIN1 on chromosome 10 (rs315831750, rs313726543, and rs80724063, respectively). Eight main haplotypes were constructed based on these SNPs. We calculated the allelic and genotypic frequencies, and genetic diversity parameters of the three SNPs. The polymorphism information content (PIC) ranged from 0.2768 to 0.3750, which reflected an intermediate genetic diversity for all chickens. The CC, CT, and TT genotypes influenced the percentage of breast muscle (PBM), percentage of leg muscle (PLM) and percentage of abdominal fat at rs315831750 (p<0.05). Diplotypes (haplotype pairs) affected the percentage of eviscerated weight (PEW) and PBM (p<0.05). Compared with chickens carrying other diplotypes, H3H7 had the greatest PEW and H2H2 had the greatest PBM, and those with diplotype H7H7 had the smallest PEW and PBM. We conclude that PLIN1 gene polymorphisms may affect broiler carcass and breast muscle yields, and diplotypes H3H7 and H2H2 could be positive molecular markers to enhance PEW and PBM in chickens.

FcγRIIB Gene Polymorphisms Are Associated with Disease Risk and Clinical Manifestations of Systemic Lupus Erythematosus in Koreans.

Systemic lupus erythematosus (SLE) is chronic autoimmune disease with various autoantibodies, which are involved in tissue damage. Fc gamma receptors (FcγRs) bind the constant region of the immunoglobulin G and transmit stimulatory or inhibitory signal to immune cells. The FcγR genes map to 1q23, a susceptible locus for SLE. We have screened single nucleotide polymorphisms (SNPs) in one of FcγR gene, FcγRIIB, which is the only inhibitory receptor, after considering gene map and reported SNPs. There were 3 SNPs in FcγRIIB: 10849 T>C (rs1050501) in exon 5 and 10950 T>G (rs6666965) and 11045 G>T (rs12117530) in intron 5 in Koreans. The frequency of the minor allele (T) of rs12117530 was significantly higher in SLE patients (50 patients, 20.4%) than healthy controls (17 patients, 12%, p = 0.041). Leukopenia occurred more frequently in SLE patients carrying the minor allele (T) of rs12117530 (p = 0.032). Among 5 haplotypes, the frequency of decreased complement was significantly lower in SLE patients with haplotype 1 [TTG] (p = 0.045). Nephritis, lymphopenia and anti-dsDNA antibody were significantly less frequent in SLE patients with haplotype 2 [TGG] (p = 0.046, p = 0.018, p = 0.002, respectively). The frequency of thrombocytopenia and anti-dsDNA antibody was significantly higher in SLE patients with haplotype 3 [CTG] (p < 0.001, p = 0.04, respectively). These data reveal that genetic polymorphisms within FcγRIIB are associated with disease susceptibility and phenotypes of SLE in Koreans. Furthermore, FcγRIIB rs12117530 polymorphism (T allele) may be an important risk factor in SLE.

Identification and association of single-nucleotide polymorphisms in gonadotropin-inhibitory hormone (GnIH) gene with egg production traits in Erlang mountainous chickens.

Gonadotropin-inhibitory hormone (GnIH) gene is an important gene in reproduction. In this study, we screened single-nucleotide polymorphisms (SNPs) in the chicken GnIH gene among 204 individuals in Erlang mountainous chickens. We then analyzed the associations between polymorphisms of the GnIH gene and 5 egg production traits in chickens. Five SNPs (T3305C, T3310C, G3403C, G3411A, and T3591C) were detected. Associations between polymorphic loci and age at first egg, body weight at first egg, weight at first egg, egg weight in 300 days, and egg production in 300 days were analyzed using analysis of covariance. The results showed that SNP1, SNP3, and SNP4 had large effects on age at first egg, while SNP5 had a large effect on body weight at first egg; of the effect of the TT genotype was significantly higher than that of CT (P < 0.01). Further analysis show that the highest frequency (0.2353) haplotype H1H1 was associated with the latest age at first egg. The H4H5 haplotype had a positive effect on egg production in 300 days and a negative effect on weight at first egg. We observed no association between the H3H3 haplotype and body weight at first egg.

Comprehensive Variant Screening of the UGT Gene Family

PurposeUGT1A1, UGT2B7, and UGT2B15 are well-known pharmacogenes that belong to the uridine diphosphate glucuronyltransferase gene family. For personalized drug treatment, it is important to study differences in the frequency of core markers across various ethnic groups. Accordingly, we screened single nucleotide polymorphisms (SNPs) of these three genes and analyzed differences in their frequency among five ethnic groups, as well as attempted to predict the function of novel SNPs.Materials and MethodsWe directly sequenced 288 subjects consisting of 96 Korean, 48 Japanese, 48 Han Chinese, 48 African American, and 48 European American subjects. Subsequently, we analyzed genetic variability, linkage disequilibrium (LD) structures and ethnic differences for each gene. We also conducted in silico analysis to predict the function of novel SNPs.ResultsA total of 87 SNPs were detected, with seven pharmacogenetic core SNPs and 31 novel SNPs. We observed that the frequencies of UGT1A1 *6 (rs4148323), UGT1A1 *60 (rs4124874), UGT1A1 *93 (rs10929302), UGT2B7 *2 (rs7439366), a part of UGT2B7 *3 (rs12233719), and UGT2B15 *2 (rs1902023) were different between Asian and other ethnic groups. Additional in silico analysis results showed that two novel promoter SNPs of UGT1A1 -690G>A and -689A>C were found to potentially change transcription factor binding sites. Moreover, 673G>A (UGT2B7), 2552T>C, and 23269C>T (both SNPs from UGT2B15) changed amino acid properties, which could cause structural deformation.ConclusionFindings from the present study would be valuable for further studies on pharmacogenetic studies of personalized medicine and drug response.

Polymorphism of MyoD1 and Myf6 genes and associations with carcass and meat quality traits in beef cattle

Myogenic determination factor 1 (MyoD1) and myogenic factor 6 (Myf6) genes belong to the myogenic differentiation (MyoD) gene family, which play key roles in growth and muscle development. The study aimed to investigate the effects of variants in cattle MyoD1 and Myf6 on carcass and meat traits. We screened single nucleotide polymorphisms (SNPs) of both genes in 8 cattle populations, including Simmental, Angus, Hereford, Charolais, Limousin, Qinchuan, Luxi, and Jinnan by sequencing. The G782A locus was identified in exon 1 of MyoD1 (MyoD1-BglI) as well as the T186C locus in exon 1 of Myf6 (Myf6-ApaLI). For the two SNPs, the A allele was significantly more frequent than the B allele in the populations tested. The χ(2) test showed that the MyoD1-BglI locus conformed to Hardy-Weinberg equilibrium in the 8 populations, as did the Myf6-ApaLI locus, with the exception of the Simmental population (P > 0.05). Association analysis revealed that the MyoD1-BglI locus was significantly associated with loin muscle area (LMA) (P < 0.05), and the Myf6-ApaLI locus was significantly associated with carcass length (CL) (P < 0.05). Animals with BB and AB genotypes for the MyoD1-BglI locus had larger LMAs compared to animals with AA genotype. Individuals with BB genotype had longer CLs compared to those with AA and AB genotypes. We conclude that the two SNPs might provide useful genetic markers, opening up new possibilities for cattle breeding and improvements in gene-assisted selection.

Genetic variation in a miR-335 binding site in BIRC5 alters susceptibility to lung cancer in Chinese Han populations

Polymorphisms in 3′ untranslated region (UTR) of cancer-related genes might affect their regulation by microRNAs (miRNAs) and thereby contribute to carcinogenesis. In this study, we screened single nucleotide polymorphisms (SNPs) in 3′ UTR of cancer-related genes and investigated their effects on risk of lung cancer. First, we genotyped seven SNPs in a Chinese Han population with 600 lung cancer patients and 600 matched healthy controls and found that compared with the TT genotype of rs2239680 in 3′ UTR of baculoviral IAP repeat containing 5 (BIRC5), C allele was associated with a significantly increased risk of lung cancer and advanced pathologic stage, with the odds ratio for participants carrying the CT or CC genotype being 1.50 [95% confidence interval (CI) 1.20–1.89, P<0.01] and 2.29 (95% CI 1.64–3.18, P<0.01), respectively. These results were further replicated and confirmed in another independent population with 1000 lung cancer cases and 1000 matched healthy controls. In support of the postulation that the 3′ UTR SNP may directly affect miRNA-binding site, reporter gene assays indicated BIRC5 was a direct target of miR-335, and the rs2239680 T>C change resulted in altered regulation of BIRC5 expression. Moreover, BIRC5 was over expressed in lung cancer tissues compared with the normal lung tissues, and the protein levels of BIRC5 correlated with SNP genotypes in normal lung tissues. Our findings defined a 3′ UTR SNP in human BIRC5 oncogene that may increase individual susceptibility to lung cancer probably by attenuating the interaction between miR-335 and BIRC5.

Toll-like Receptor 1 Polymorphisms Affect Innate Immune Responses and Outcomes in Sepsis

Polymorphisms affecting Toll-like receptor (TLR)-mediated responses could predispose to excessive inflammation during an infection and contribute to an increased risk for poor outcomes in patients with sepsis. To identify hypermorphic polymorphisms causing elevated TLR-mediated innate immune cytokine and chemokine responses and to test whether these polymorphisms are associated with increased susceptibility to death, organ dysfunction, and infections in patients with sepsis. We screened single-nucleotide polymorphisms (SNPs) in 43 TLR-related genes to identify variants affecting TLR-mediated inflammatory responses in blood from healthy volunteers ex vivo. The SNP associated most strongly with hypermorphic responses was tested for associations with death, organ dysfunction, and type of infection in two studies: a nested case-control study in a cohort of intensive care unit patients with sepsis, and a case-control study using patients with sepsis, patients with sepsis-related acute lung injury, and healthy control subjects. The SNP demonstrating the most hypermorphic effect was the G allele of TLR1(-7202A/G) (rs5743551), which associated with elevated TLR1-mediated cytokine production (P < 2 x 10(-20)). TLR1(-7202G) marked a coding SNP that causes higher TLR1-induced NF-kappaB activation and higher cell surface TLR1 expression. In the cohort of patients with sepsis TLR1(-7202G) predicted worse organ dysfunction and death (odds ratio, 1.82; 95% confidence interval, 1.07-3.09). In the case-control study TLR1(-7202G) was associated with sepsis-related acute lung injury (odds ratio, 3.40; 95% confidence interval, 1.59-7.27). TLR1(-7202G) also associated with a higher prevalence of gram-positive cultures in both clinical studies. Hypermorphic genetic variation in TLR1 is associated with increased susceptibility to organ dysfunction, death, and gram-positive infection in sepsis.

A Systematic Single Nucleotide Polymorphism Screen to Fine-Map Alcohol Dependence Genes on Chromosome 7 Identifies Association With a Novel Susceptibility Gene ACN9

Chromosome 7 has shown consistent evidence of linkage with a variety of phenotypes related to alcohol dependence in the Collaborative Study on the Genetics of Alcoholism (COGA) project. With a sample of 262 densely affected families, a peak logarithm of odds (LOD) score for alcohol dependence of 2.9 was observed at D7S1799. The LOD score in the region increased to 4.1 when a subset of the sample was genotyped with the Illumina Linkage III panel for the Genetic Analysis Workshop 14 (GAW14). To follow up on this linkage region, we systematically screened single nucleotide polymorphisms (SNPs) across a 2 LOD support interval surrounding the alcohol dependence peak. The SNPs were selected from the HapMap Phase I CEPH data to tag linkage disequilibrium bins across the region. Across the 18-Mb region, genotyped by the Center for Inherited Disease Research (CIDR), 1340 SNPs were analyzed. Family-based association analyses were performed on a sample of 1172 individuals from 217 Caucasian families. Eight SNPs showed association with alcohol dependence at p < .01. Four of the eight most significant SNPs were located in or very near the ACN9 gene. We conducted additional genotyping across ACN9 and identified multiple variants with significant evidence of association with alcohol dependence. These analyses suggest that ACN9 is involved in the predisposition to alcohol dependence. Data from yeast suggest that ACN9 is involved in gluconeogenesis and the assimilation of ethanol or acetate into carbohydrate.

The GSTP1 Gene Is a Susceptibility Gene for Childhood Asthma and the GSTM1 Gene Is a Modifier of the GSTP1 Gene

Background: Bronchial asthma is a chronic airway disorder characterized by bronchial inflammation. Oxidative stress is a key component of inflammation. Glutathione S-transferase P1 (GSTP1), the abundant isoform of glutathione S-transferases (GSTs) in lung epithelium, plays a key role in cellular protection against oxidative stress. Several studies have shown that the GSTP1 geneis involved in the pathogenesis of asthma and a gene-gene interaction may occur within the GST gene superfamily. Methods: We screened single-nucleotide polymorphisms (SNPs) at the GSTP1 locus and performed an association study in the Japanese population using two independent case-control groups (group 1: 391 pediatric patients with asthma, 462 adult patients with asthma, and 639 controls, and group 2: 115 pediatric patients with asthma and 184 controls). The effect of GSTM1 null/present genotype on the association between GSTP1 Ile105Val and asthma was also investigated. Results: We identified 20 SNPs at this locus and found this region consisted of one linkage disequilibrium block represented by four SNPs (tag SNPs). The association between the Ile105Val polymorphism in the GSTP1 gene and childhood asthma was significant in both groups (p = 0.047 in group 1, and p = 0.021 in group 2). This association was only significant in patients with GSTM1-positive genotype in both groups (group 1: GSTM1 present p = 0.013 and GSTM1 null p = 0.925, and group 2: GSTM1 present p = 0.015 and GSTM1 null p = 0.362). Conclusions: These findings suggest that the GSTP1 gene is a childhood asthma susceptible gene, and the GSTM1 gene is a modifier gene of GSTP1 for the risk of childhood asthma in the Japanese population.

Leukotriene-related Gene Polymorphisms in Patients with Aspirin-intolerant Urticaria and Aspirin-intolerant Asthma: Differing Contributions of ALOX5 Polymorphism in Korean Population

The pathogenesis of aspirin (acetylsalicylic acid, ASA)-intolerant urticaria (AIU) is still poorly understood but it has recently been suggested that it is associated with the overproduction of leukotriene (LT). This is supported by evidence that cyclooxygenase 2 inhibitor is given safely to patients with AIU. The present study was designed to investigate the role of genetic polymorphism of LT related genes in the pathogenesis of AIU via a case-control study. We screened single nucleotide polymorphisms (SNPs) in genes encoding enzymes involved in leukotriene synthesis in the Korean population with AIU (n=101), ASA-intolerant asthma (AIA, n=95) and normal healthy controls (n=123). Genotype was determined by primer extension reactions using the SNapShot ddNTP primer extension kit. Among 8 SNPs of four LT related genes, the polymorphism of ALOX5 at positions of -1708 G>A showed significant difference in genotype frequency between AIU and AIA (p=0.01). Furthermore, there were significant differences observed in the frequencies of two ALOX5 haplotypes between the AIU group and AIA group (p<0.05). However, there were no differences in allele, genotype, or haplotype frequencies of ALOX5 between the AIU group and the normal control group. These results suggested that ALOX5 has a differing contribution in two major clinical pathogenesis related to ASA-sensitivity.

Leukotriene-related gene polymorphisms in ASA-intolerant asthma: an association with a haplotype of 5-lipoxygenase.

A recent study has demonstrated the possible involvement of a leukotriene C4 synthase (LTC4S) gene polymorphism in ASA-intolerant asthma (AIA) in a Polish population, whereas no significant association was noted in other populations. To investigate the role of genetic polymorphism in AIA development, we screened single nucleotide polymorphisms (SNPs) of the key enzymes involved in arachidonate metabolism, and the cysteinyl leukotriene receptor 1 (CYSLTR1) in a large Korean population with AIA: 93 AIA and 181 ASA-tolerant asthma (ATA) patients, and 123 normal controls. The single-base extension method was used to genotype SNPs in 5-lipoxygenase (ALOX5, -1708G-->A, 21C-->T, 270G-->A, 1728G-->A), ALOX5-activating protein (ALOX5AP, 218A-->G), prostaglandin-endoperoxide synthase 2 (PTGS2, COX2, -162C-->G, 10T-->G, R228H, V511A), LTC4S (-444A-->C), and CYSLTR1 (927T-->C). Haplotype analyses were undertaken for the SNPs in ALOX5. No significant differences in allele and genotype frequencies of single SNPs were observed between the patient groups ( P>0.05). However, the frequency of the ALOX5-ht1[G-C-G-A] haplotype in the AIA group was significantly higher than its frequency in the ATA group with a probability ( P) of 0.01, odds ratio (OR) of 5.0, and 95% confidence interval (95%CI) of 1.54-17.9, and in the normal controls ( P=0.03, OR=4.5, 95%CI=1.1-18.4), by using a dominant model. These results suggest a lack of association between the ALOX5AP, PTGS2, LTC4S, and CYSLTR1 gene polymorphisms and the AIA phenotype in the Korean population. However, the possible involvement of ALOX5-ht1[G-C-G-A] in AIA development is suggested.

Variants in TNFRSF5 locus and association analysis with Hepatitis B virus (HBV) infection.

Human TNFRSF5, a key signaling molecule expressed by antigen-presenting cells of the immune system, might have associations with autoimmune diseases and various infectious diseases. In the present study, we screened single-nucleotide polymorphisms (SNPs) in TNFRSF5 and examined whether they are risk factors for persistent HBV infection or disease severity. We resequenced all 9 exons, the promoter and splicing regions of all introns for 186 Chinese individuals, and identified 11 SNPs. Haplotypes and their frequencies were estimated. The linkage disequilibrium (LD) pattern was also evaluated. Neutrality tests indicated that the variation pattern at TNFRSF5 locus departs from neutrality and may be maintained by positive selection or demography factors such as population growth. Three SNPs (g.53031T>C, g.54068T>C and g.64493A>G) were determined as haplotype-tag SNPs (htSNPs). Furthermore, computer analyses indicated that sequences surrounding g.53031T>C and g.53824T>C were potential binding sites for transcription factors Sp1 and H4TF-2, respectively. We then genotyped these four SNPs for 603 persistent HBV infection patients and 384 spontaneously recovered subjects by PCR direct sequencing. No statistically significant associations were observed between any of the SNPs or haplotypes and persistent HBV infection or disease severity. The information from this study of the TNFRSF5 would be useful for genetic studies of other common diseases.

Polymorphism analysis of the upstream region of the human N-methyl- d-aspartate receptor subunit NR1 gene ( GRIN1): implications for schizophrenia

Dysfunction of the gene for the NR1 subunit of the N-methyl- d-aspartate (NMDA) receptor ( GRIN1) has been implicated in the pathogenesis of schizophrenia. In support of this hypothesis are behavioral abnormalities reminiscent of schizophrenia in mice with an attenuated expression of the NR1 subunit receptor and the reduced level of NR1 mRNA in postmortem brains of patients with schizophrenia. We screened single nucleotide polymorphisms (SNPs) in the upstream region between +51 and −941 from the translation initiation codon of GRIN1 and identified 17 SNPs, 10 of which were located within the region containing the Sp1 motif and the GSG motifs. As genotyping of 191–196 Japanese patients with schizophrenia and 202–216 controls revealed no significant association between schizophrenia and the SNPs in the upstream region of GRIN1, these SNPs apparently do not play a critical role in the pathogenesis of schizophrenia in the Japanese population.