Association between intronic SNP in urate-anion exchanger gene, SLC22A12, and serum uric acid levels in Japanese

Serum uric acid levels are maintained by urate synthesis and excretion. URAT1 (coded by SLC22CA12) was recently proposed to be the major absorptive urate transporter protein in the kidney regulating blood urate levels. Because genetic background is known to affect serum urate levels, we hypothesized that genetic variations in SLC22A12 may predispose humans to hyperuricemia and gout. We investigated rs893006 polymorphism (GG, GT and TT) in SLC22A12 in a total of 326 Japanese subjects. Differences in clinical characteristics among the genotype groups were tested by the analysis of variance (ANOVA). In male subjects, mean serum uric acid levels were significantly different among the three genotypes. Levels in the GG genotype subjects were the highest, followed by those with the GT and TT genotypes. However, no differences between the groups were seen in the distributions of creatinine, Fasting plasma glucose (FPG), HbA(1c), total cholesterol, triglyceride, HDL cholesterol levels or BMI. A single nucleotide polymorphism (SNP) in the urate transporter gene SLC22CA12 was found to be associated with elevated serum uric acid levels among Japanese subjects. This SNP may be an independent genetic marker for predicting hyperuricemia.     

Association of FcRn Heavy Chain Encoding Gene (FCGRT) Polymorphisms with IgG Content in Bovine Colostrum

In this study, we evaluated haplotypes of the bovine FCGRT (encoding the FcRn heavy chain) and their relationship to the IgG concentration in bovine colostrum. Four single nucleotide polymorphism (SNP), classified into five haplotypes, were identified in a total of 49 Holstein-Frisians cows. Haplotype 5 was found to be significantly associated with a high IgG level ([OR] = 9.90, 95%CI = 1.11–88.34, p = 0.016) and haplotype 2 exhibited a similar trend ([OR] = 2.89, 95%CI = 1.17–7.11, p = 0.019).     

Polymorphisms in the promoter region of ESR2 gene and breast cancer susceptibility

Genetic variations like single nucleotide polymorphisms (SNPs) in genes involved in estrogen biosynthesis, metabolism and signal transduction have been suggested to affect breast cancer susceptibility. In this study we tested the hypothesis that polymorphisms in the promoter of ESR2 gene may be associated with increased risk for breast cancer. We analyzed three SNPs in the promoter region of human ESR2 gene by means of allele-specific tetra-primer PCR. A total of 318 sporadic breast cancer cases and 318 age-matched controls were included in the study. With regard to homozygous genotypes, women with sporadic breast cancer more frequently carried the CC genotype of ESR2 promoter SNP rs2987983 (OR 1.99, p = 0.005). Calculation of allele positivity demonstrated that presence of T allele of this SNP was more frequent in healthy women. Our data suggest that a SNP in the promoter region of ESR2 gene might be able to affect breast cancer risk. These results further support the emerging hypothesis that ERβ is an important factor in breast cancer development.     

葡萄糖转运体9(GLUT9)基因启动子区的rs13124007(G/C)及rs6850166(G/A)位点的单核苷酸多态性(SNP)与汉族女性痛风相关性研究

目的:探讨葡萄糖转运体9(GLUT9)基因启动子区的rs13124007(C/G)及rs6850166(A/G)位点的单核苷酸多态性(SNP)与中国汉族女性人群痛风易感性之间的相关性.方法:选取185例痛风患者和300例正常对照者,提取基因组DNA,采用聚合酶链式反应(PCR技术),特异性扩增GLUT9基因所需要的目的片段,对扩增的目的片段进行测序后,比较痛风组和正常对照组的基因型频率及等位基因频率分布情况.结果:女性痛风组中GLUT9基因的启动子区rs13124007和rs6805116两个位点的基因型频率分布与正常对照组相比,统计学上无明显的差异(X2=0.906,P=0.636;X2=3.335,P=0.189),rs13124007 SNP位点的C等位基因频率和rs6850166SNP位点的A的等位基因频率与正常对照组相比也无明显的统计学差异(X2=0.506,P=0.477;X=3.268,P=0.071).结论:葡萄糖转运体9(GLUT9)基因启动子区的rs 13124007(C/G)及rs6850166(A/G)位点的单核苷酸多态性(SNP)与中国汉族女性人群痛风易感性无明显的相关性.     

The rs9939609 polymorphism in the fat mass and obesity associated (FTO) gene is associated with obesity in Tunisian population

Abstract

Context: Variations in the fat mass and obesity-associated gene (FTO) has been associated with obesity in many populations, but the results are conflicting.

Objective: The aim of this study was to evaluate the effect of the rs9939609 polymorphism in the FTO gene on obesity risk and plasma leptin, adiponectin, insulin and lipid concentrations in Tunisians.

Materials and methods: Four hundred and ninety-four subjects with obesity and 334 non-obese participated in this study. The rs9939609 (T/A) genotype was determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Results: Significant differences in genotype frequencies were observed between cases and controls. In the separate analysis by gender, the association between the AA genotype and obesity was statistically significant in women but not in men. After stratification by obesity class this association remains only with obesity class III.

Discussion: Our study is in agreement with studies on Caucasian, Portuguese and Cebu Filipino populations where a gender-specific association was found between rs9939609 polymorphism and obesity. It is also in agreement with studies on Mexican, Spanish and European populations, where an association was found with obesity class III.

Conclusion: The rs9939609 polymorphism of FTO gene is associated with obesity, especially obesity class III in women.     

High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene

We have sequenced 2,388 bp of the European rabbit sex determining region Y (SRY) gene. These data provide a 10-fold increase in the coverage of the Y chromosome in this species, including the entire open reading frame of the SRY, the polyadenylation signal, and two repetitive sequences in the 5' -region. A survey of 2021 bp of this gene in eight domestic breeds and four wild individuals revealed a total of nine single nucleotide polymorphisms and one indel, defining two deeply divergent lineages. The resulting estimation of nucleotide diversity (pi=1.34 x10(-3)) is very high when compared with other species, but no variability was detected among the domestic breeds. This study represents a first step in the characterization of the European rabbit Y chromosome and its variability. These sequences can be used in additional phylogeographical analyses of the European rabbit and other Leporid species, as well as in evolutionary studies of sex determination and the Y chromosome in wild species.     

Polycystic ovary syndrome is linked with the fat mass obesity (FTO) gene variants rs17817449 and rs1421085 in western Saudi Arabia

Polycystic ovary syndrome (PCOS) is characterised by infertility, obesity, insulin resistance and clinical and/or biochemical signs of hyperandrogenism. Obesity is known to be correlated with PCOS causing ovulatory dysfunction and hormone imbalances. Moreover, fat mass and the obesity gene (FTO) were linked with obesity and PCOS. Therefore, it is of interest to determine the genotype and allele frequency for three FTO variants - rs17817449 (G/T), rs1421085 (C/T) and rs8050136 (A/C) -in western Saudi population. 95 PCOS patients and 94 controls were recruited for this study. The genetic variants were assayed using real-time polymerase chain reaction using TaqMan genotyping assays. The chi-squared test was applied to investigate the difference between single nucleotide polymorphisms on PCOS and control subjects, and binary logistic regression was used to determine the association of FTO variants with PCOS symptoms. Variants rs17817449 and rs1421085 were significantly linked with PCOS susceptibility in the study population. Rs17817449 and rs8050136 were significantly associated with hair loss in the PCOS group. Furthermore, rs1421085 and rs8050136 were associated with a high body mass index (BMI>30 kg/m2). Risk alleles in our population associated with hair loss and elevated BMI in women with PCOS were homozygous C for rs8050136. This data will help in defining the genetic predisposition of PCOS among women in western Saudi Arabia.     

Screening the human serum proteome for genotype-phenotype associations: an analysis of the IL6 -174G>C polymorphism

Interleukin (IL)-6 is a circulatory, pleiotropic cytokine with multiple roles in the immune system. Both IL-6 and the IL6 -174G>C promoter polymorphism have been linked to various diseases associated with inflammation. However, the mechanism by which the polymorphism influences disease risk is unclear. We postulated that serum proteome analysis of individuals with different IL6 -174G>C genotypes would provide insight on genotype-phenotype associations of this polymorphism and its role in disease susceptibility. Serum from a random sample of control participants in an ongoing population-based case-control study of non-Hodgkin lymphoma was pooled by IL6 genotype and used to screen for the optimal SELDI-TOF MS arrays for analysis. We report differences in serum protein expression of individuals with specific genotypes based on pooled and individual sample analysis. In particular, we report an association of the -174C allele with increased apolipoprotein C-I (ApoC-I). Additionally, we corroborate previous findings of an association of the -174C allele with lower autoantibodies to heat shock protein 60 and confirm the absence of any association between the IL6 -174G>C genotype and serum IL-6 levels. This study illustrates that proteome analysis can enhance our understanding of genotype-phenotype relationships. Additional studies are needed to clarify the interaction between the IL6 -174G>C polymorphism and ApoC-I.     

Molecular identification of the strains of the domestic silkworm,Bombyx mori (Lepidoptera: Bombycidae), which are endemic to Korea,based on single nucleotide polymorphisms in mitochondrial genome sequences

The domestic silkworm, Bombyx mori (Lepidoptera: Bombycidae), has been diversified into various strains over a long period. However, methods to distinguish silkworm strains remain limited partially owing to the genetic similarity caused by the long history of domestication. In this study, we developed molecular identification methods to distinguish three domestic silkworm strains, which are endemic to Korea. By comparing publicly available complete mitochondrial genome (mitogenome) sequences of five endemic strains and 34 stock silkworm strains analyzed in a previous study, we detected 15 single nucleotide polymorphisms (SNPs; SNP1–SNP15), which distinguished the following three endemic strains: Sun7ho (SN7), Sandongsammyeon (SDS), and Sammyeonhonghoeback (SMH). We used two SNPs for each strain to identify the three endemic strains. To distinguish each SN7 and SDS from the remaining four endemic and 34 stock strains, the PCR-restriction fragment length polymorphism method was employed using Acu I and Hpa I restriction enzymes, which recognize SNP1 and SNP8, respectively. Additionally, the tetra-primer amplification refractory mutation system PCR method was used to determine the regions containing SNP3, SNP11, and both SNP14 and SNP15 to distinguish SN7, SDS, and SMH, respectively, from the remaining strains. A validation test with additional individuals showed that each target strain was clearly recognized, suggesting that mitogenome SNP-based methods can be used to identify three endemic silkworm strains during culture and breeding.     

Susceptibility of mice genetically deficient in the surfactant protein (SP)-A or SP-D gene to pulmonary hypersensitivity induced by antigens and allergens of Aspergillus fumigatus

Lung surfactant protein A (SP-A) and D (SP-D) are innate immune molecules which are known to interact with allergens and immune cells and modulate cytokine and chemokine profiles during host hypersensitivity response. We have previously shown therapeutic effects of SP-A and SP-D using a murine model of lung hypersensitivity to Aspergillus fumigatus (Afu) allergens. In this study, we have examined the susceptibility of SP-A (AKO) or SP-D gene-deficient (DKO) mice to the Afu allergen challenge, as compared with the wild-type mice. Both AKO and DKO mice exhibited intrinsic hypereosinophilia and several-fold increase in levels of IL-5 and IL-13, and lowering of IFN-gamma to IL-4 ratio in the lungs, suggesting a Th2 bias of immune response. This Th2 bias was reversible by treating AKO or DKO mice with SP-A or SP-D, respectively. The AKO and DKO mice showed distinct immune responses to Afu sensitization. DKO mice were found more susceptible than wild-type mice to pulmonary hypersensitivity induced by Afu allergens. AKO mice were found to be nearly resistant to Afu sensitization. Intranasal treatment with SP-D or rhSP-D (a recombinant fragment of human SP-D containing trimeric C-type lectin domains) was effective in rescuing the Afu-sensitized DKO mice, while SP-A-treated Afu-sensitized AKO mice showed several-fold elevated levels of IL-13 and IL-5, resulting in increased pulmonary eosinophilia and damaged lung tissue. These data reaffirm an important role for SP-A and SP-D in offering resistance to pulmonary allergenic challenge.     

Oxidized LDL receptor gene (OLR1) is associated with the risk of myocardial infarction

Lectin-like oxidized low-density lipoprotein receptor (LOX-1/OLR1) has been suggested to play a role in the progression of atherogenesis. We analyzed the OLR1 gene and found a single nucleotide polymorphism (SNP), G501C, in patients with ischemic heart disease from a single family, which resulted in the missense mutation of K167N in LOX-1 protein. We compared the group of patients with myocardial infarction (MI) (n=102) with a group of clinically healthy subjects (n=102), and found that the MI group had a significantly high frequency of 501G/C+501C/C (38.2%) compared with the healthy group (17.6%; p<0.002). The odds ratio for the risk of MI associated with the 501G/C+501C/C genotype was 2.89 (95% CI, 1.51-5.53). These findings suggest that OLR1 or a neighboring gene linked with G501C SNP is important for the incidence of MI. Manipulating LOX-1 activity might be a useful therapeutic and preventative approach for coronary artery disease, especially for individuals with the G501C genotype of OLR1.     

Polymorphisms of the insulin-like growth factor-binding protein 3 gene (IGFBP3) in gayal (Bos frontalis)

The gene coding for insulin-like growth factor-binding protein 3 (IGFBP3) is important for regulation of growth, development and metabolism in mammals. The present investigation was conducted to study nucleotide polymorphism of the IGFBP3 in gayal (Bos frontalis) and to compare the variations with those which occur in other ruminants. A fragment of 645 base pairs of the IGFBP3 covering a part of exon 2, the complete intron 2 and exon 3 and a part of intron 3 was amplified, sequenced (n=46) and digested (n=79) with HaeIII restriction enzyme from 125 collected gayal samples. Nine single nucleotide polymorphisms (SNPs) [C14T, A122C, C137T, G144C, C155T, G213A, C279A, G334A and G460A] were identified and located in intron 2, revealing high genetic variability. The alignment of nucleotide sequences was found to be very similar to those for other bovid species. Sequencing and HaeIII digestion showed that frequency of alleles C and A [consisting of fragments of sizes 56, 64, 228, 264, 282, 298 and 497 bp (CC genotype)] was 0.96 and 0.04 for the SNP C279A. Moreover, the genotype frequency of the SNP C279A in gayal was compared with that in other ruminants and it appears that this polymorphism may be associated with low fat content and rapid growth in this rare species.     

Association of interleukin-(IL)10 haplotypes and serum IL-10 levels in the progression of childhood immune thrombocytopenic purpura

Derangement of genetic and immunological factors seems to have a pivotal role in the pathophysiology of immune thrombocytopenic purpura (ITP). We investigated interleukin(IL)-10 genetically determined expression in children with an acute progression of ITP (n=41) compared to young patients with chronic ITP (n=44) and healthy controls (n=60), and attempted to correlate IL-10 production with the course of the disease. We genotyped our study population for three single nucleotide polymorphisms at positions -1082 (A/G), -819 (C/T) and -592 (C/A) in the promoter region of the IL-10 gene. IL-10 levels were measured by enzyme-linked immunoassay. The IL-10 production in our study population was significantly higher in patients carrying the GCC haplotype than those bearing ACC and ATA haplotypes (6.9 ± 1.5 vs 3.6 ± 0.8 vs 3.3 ± 0.3, p=0.03). The serum concentration of IL-10 was significantly higher in patients with an acute course of their disease, who mainly carried the GCC haplotype (92%), compared to chronic subjects, bearing the non-GCC haplotypes, and controls [17 pg/mL (1.7-18) vs 3.5 pg/mL (0.6-11) vs 3 pg/mL (1-7), p<0.01)]. Our findings show that patients carrying the GCC-high producer IL-10 haplotype have an acute development of ITP and that IL-10 levels might represent a useful predictive biomarker of the disease course.     

Single Nucleotide Polymorphisms in the Coding Region of the Developmental Gene Gcyc in Natural Populations of the Relict Ramonda myconi (Gesneriaceae)

Abstract: Gcyc is a developmental gene, present in the Gesneriaceae family, that has both highly conserved and highly variable regions. Ramonda myconi (Gesneriaceae) is a paleoendemic plant restricted to mountainous areas of NE Spain. In this study we examine the population variation in the coding region of Gcyc in R. myconi. The fast-evolving nature of the coding regions of the Gcyc gene plus the ancient history of R. myconi together provide an appropriate background to obtain the first insights into population-level variation in developmental genes of flowering plants. One locus of Gcyc was specifically amplified and sequenced. Four single nucleotide polymorphisms (SNPs) were detected in the 420 sequenced bases of the gene in two R. myconi populations. The Pyrenean population had only one SNP while all four SNPs were present in the southern population. Three out of four SNPs were non-synonymous. Such novel results indicate that the detection of SNPs in R. myconi over its entire distribution area could be used as an aid to reconstructing the population history of the species, as well as to investigate the relationship between developmental genes and morphological traits.     

Molecular implications of the human glutathione transferase A-4 gene (hGSTA4) polymorphisms in neurodegenerative diseases

Several lines of evidence, including an increased level of lipid peroxidation and the depletion of antioxidant molecules like as glutathione (GSH), indicate that oxidative stress plays an important role in the pathogenesis of several neurodegenerative disorders, such as Parkinson's disease (PD) and Alzheimer's disease (AD). We previously observed a significant increased level of DNA oxidative damage in peripheral blood cells of PD patients, with respect to controls, moreover, the activity of glutathione transferases (GSTs) measured in circulating plasma was higher in controls than in PD patients, suggesting a lower enzymatic protection in PD individuals. Among human GSTs, glutathione transferase A4-4 displays a high catalitic activity towards 4-hydroxy-2-nonenal (HNE), a marker of lipid peroxidation whose levels have been found significantly increased in the substantia nigra of Parkinson's disease patients, in respect to controls. We performed this study to determine the presence of allelic variants of functional interest in the coding region of the hGSTA4 gene on 60 PD patients and 60 healthy controls. By the combined effort of polymerase chain reaction/single-strand conformation polymorphisms (PCR/SSCP) techniques, we observed a single nucleotide polymorphism (SNP) G351A leading to the silent mutation Gln117Gln. No significant difference was observed in the distribution of this polymorphism between PD individuals and controls, moreover, we did not observe any other polymorphism in the hGSTA4 gene in our population. Further studies are required to test the role played by both factors regulating the level of the expression of the hGSTA4 gene and any possible post-translational modification of the protein, in the protection against oxidative damage in neuronal cells.     

The first report of polymorphisms and genetic characteristics of the prion protein gene (PRNP) in horses

ABSTRACT

Prion diseases have a wide host range, but prion-infected cases have never been reported in horses. Genetic polymorphisms that can directly impact the structural stability of horse prion protein have not been investigated thus far. In addition, we noticed that previous studies focusing on horse-specific amino acids and secondary structure predictions of prion protein were performed for limited parts of the protein. In this study, we found genetic polymorphisms in the horse prion protein gene (PRNP) in 201 Thoroughbred horses. The identified polymorphism was assessed to determine whether this polymorphism impedes stability of protein using PolyPhen-2, PROVEAN and PANTHER. In addition, we evaluated horse-specific amino acids in horse and mouse prion proteins using same methods. We found only one single nucleotide polymorphism (SNP) in the horse prion protein, and three annotation tools predicted that the SNP is benign. In addition, horse-specific amino acids showed different effects on horse and mouse prion proteins, respectively.

Abbreviations: PRNP: prion protein gene; SNP: single nucleotide polymorphism; CJD: Creutzfeldt-Jakob disease; CWD: chronic wasting disease; TME: transmissible mink encephalopathy; FSE: feline spongiform encephalopathy; MD: molecular dynamics; ER: endoplasmic reticulum; GPI: glycosylphosphatidylinositol; NMR: nuclear magnetic resonance; ORF: open reading frame; GWAS: genome-wide association study; NAPA: non-adaptive prion amplification; HMM: hidden Markov model; NCBI: National Center for Biotechnology Information     

Development of Genotyping Methods for Single Nucleotide Polymorphism in the Human Pancreatic Ribonuclease Gene (RNASE1) and Their Application to Population Studies

Two potential single nucleotide polymorphisms [SNPs; rs1804215 (G979T) and rs11545379 (G1169T)] have been identified in the human pancreatic ribonuclease, RNase 1, gene (RNASE1) that could give rise to an amino acid substitution in the protein, but relevant population data are not available. We have developed genotyping methods for each SNP using the mismatched PCR-restriction fragment length polymorphism technique. These methods are advantageous in comparison with other SNP genotyping methods because they are technically simpler and do not require specialized instruments. We applied these genotyping methods to examine the genotype distribution of each SNP in four populations, including Japanese populations living in two prefectures, an Ovambo population, and a Turkish population. In all the populations studied, however, only a single genotype for each SNP was found. Therefore, irrespective of differences in ethnic groups, RNASE1 might show markedly low heterogeneity in its genetic structure with regard to these SNPs.     

Evidence for the effect of serotonin receptor 1A gene (HTR1A) polymorphism on tractability in Thoroughbred horses

Tractability, or how easily animals can be trained and controlled, is an important behavioural trait for the management and training of domestic animals, but its genetic basis remains unclear. Polymorphisms in the serotonin receptor 1A gene (HTR1A) have been associated with individual variability in anxiety‐related traits in several species. In this study, we examined the association between HTR1A polymorphisms and tractability in Thoroughbred horses. We assessed the tractability of 167 one‐year‐old horses reared at a training centre for racehorses using a questionnaire consisting of 17 items. A principal components analysis of answers contracted the data to five principal component (PC) scores. We genotyped two non‐synonymous single nucleotide polymorphisms (SNPs) in the horse HTR1A coding region. We found that one of the two SNPs, c.709G>A, which causes an amino acid change at the intracellular region of the receptor, was significantly associated with scores of four of five PCs in fillies (all Ps < 0.05) and one PC in colts (P < 0.01). Horses carrying an A allele at c.709G>A showed lower tractability. This result provides the first evidence that a polymorphism in a serotonin‐related gene may affect tractability in horses with the effect partially different depending on sex.