Contribution Of Single Nucleotide Polymorphisms Research Articles

The nonsynonymous single nucleotide polymorphisms of DNA repair geneXRCC1and susceptibility to the development of cervical carcinoma and high‐risk human papillomavirus infection

To evaluate contribution of single nucleotide polymorphisms (SNPs) of X-ray repair cross-complementing group 1 (XRCC1) gene to the risk of cervical carcinoma, we conducted a case-control study of 1012 patients including 539 carcinoma and 473 cervical intraepithelial neoplasia (CIN) and 800 normal women controls and genotyped three XRCC1 SNPs (Arg194Trp, Arg280His, and Arg399Gln). We found that compared with the Arg399Gln (GG), subjects carrying the homozygous Gln399Gln (AA) genotype had a significantly 2.32-fold increased risk of cervical carcinoma (95% CI 1.47–3.65), heterozygous Arg399Gln (GA) genotype were also associated with a significantly increased risk of cervical carcinoma, with the adjusted odds ratio (OR) being 1.58 (95% CI 1.24–2.00). Similarly, compared with Arg194Arg (CC) wild-type genotype, elevated risks were associated with the Trp194Trp (TT) for carcinoma (ORs and 95% CIs being 2.09 [1.45–3.02]) but not for heterozygote Arg194Trp (CT). In addition, three common haplotypes were found to be associated with an increased risk of cervical carcinoma. Using 194Arg-280Arg-399Arg as the reference, the OR and 95% confidence interval for 194Arg-280Arg-399Gln, 194Arg-280His-399Arg, 194Trp-280Arg-399Arg were 2.30 (1.86–2.85), 1.85 (1.41–2.41), 1.98 (1.62–2.40), respectively. The significantly increased risk associated with the haplotypes was also observed in squamous cell carcinoma (SCC) for all three common haplotypes using 194Arg-280Arg-399Arg as the reference. Neither difference was found for adenocarcinoma and CIN. All three SNPs and haplotypes did not confer more risk of high-risk human papillomavirus infection in carcinoma, CIN, and normal subgroup. Our findings suggest thatXRCC1polymorphisms including genotypes and haplotypes contribute to susceptibility to the development of cervical SCC, and the increased susceptibility is probably not through increasing susceptibility to human papillomavirus infection.

Contribution of single nucleotide polymorphisms of the IL1A gene to the cleavage of precursor IL-1α and its transcription activity

We previously demonstrated the association of IL1A gene single nucleotide polymorphisms (SNPs) with susceptibility to systemic sclerosis (SSc) patients. In this study, we explored the effects of SNP on the transcriptional activity and processing of the precursor IL-1alpha (pre-IL-1alpha) in skin fibroblasts. Two kinds of promoter regions of the IL1A gene were prepared including C or T at -889, referred to C/IL1A and T/IL1A, and inserted into a luciferase reporter vector (pGL3). Skin fibroblasts were explanted from two SSc patients whose genomic DNA contained GG and TT genotypes at +4845 of the IL1A gene, respectively. Cell lysates were collected and reacted with various concentrations of calpain, and then the processing of pre-IL-1alpha was analyzed by Western blotting using monoclonal anti-IL-1alpha antibody. A SNP was determined by the allelic discrimination method using fluorescence-labeled Taq-Man probes. Significant differences in the luciferase activities were not detected between pGL3 (C/IL1A) and pGL3 (T/IL1A) in SSc fibroblasts. Calpain required a 100-fold higher concentration to process the pre-IL-1alpha containing Ala at the 114th amino acid than that to do containing Ser. The frequency of the GG genotype was significantly higher in SSc patients than that in healthy donors, whereas the frequency of TT genotype was significantly higher in RA patients than that in healthy donors. Our observation showed that the SNP at +4845 affected the enzymatic efficiency of the protease in cleaving pre-IL-1alpha. Pre-IL-1alpha with Ala, which was high in frequency in SSc patients, was more resistant to be cleaved by proteases in human sera than pro-IL-1alpha with Ser.

Association between SNP and haplotypes in PPARGC1 and adiponectin genes and bone mineral density in Chinese nuclear families

To assess the contribution of single nucleotide polymorphisms (SNP) and haplotypes in the peroxisome proliferators-activated receptor-gamma co-activator-1 (PPARGC1) and adiponectin genes to normal bone mineral density (BMD) variation in healthy Chinese women and men. We performed population-based (ANOVA) and family-based (quantitative trait locus transmission disequilibrium test) association studies of PPARGC1 and adiponectin genes. SNP in the 2 genes were genotyped. BMD was measured using dual-energy X-ray absorptiometry in the lumbar spine and hip in 401 nuclear families with a total of 1260 subjects, including 458 premenopausal women, 20-40 years of age; 401 postmenopausal women (mothers), 43-74 years of age; and 401 men (fathers), 49-76 years of age. Significant within-family association was found between the Thr394Thr polymorphism in the PPGAGC1 gene and peak BMD in the femoral neck (P=0.026). Subsequent permutations were in agreement with this significant within-family association result (P=0.016), but Thr394Thr SNP only accounted for 0.7% of the variation in femoral neck peak BMD. However, no significant within-family association was detected between each SNP in the adiponectin gene and peak BMD. Although no significant association was found between BMD and SNP in the PPARGC1 and adiponectin genes in both men and postmenopausal women, haplotype 2 (T-T) in the adiponectin gene was associated with lumbar spine BMD in postmenopausal women (P=0.019). Our findings suggest that Thr394Thr SNP in the PPARGC1 gene was associated with peak BMD in the femoral neck in Chinese women. Confirmation of our results is needed in other populations and with more functional markers within and flanking the PPARGC1 or adiponectin genes region.

The nonsynonymous single nucleotide polymorphisms of DNA repair geneXRCC1and susceptibility to the development of cervical carcinoma and high-risk human papillomavirus infection

To evaluate contribution of single nucleotide polymorphisms (SNPs) of X-ray repair cross-complementing group 1 (XRCC1) gene to the risk of cervical carcinoma, we conducted a case-control study of 1012 patients including 539 carcinoma and 473 cervical intraepithelial neoplasia (CIN) and 800 normal women controls and genotyped three XRCC1 SNPs (Arg194Trp, Arg280His, and Arg399Gln). We found that compared with the Arg399Gln (GG), subjects carrying the homozygous Gln399Gln (AA) genotype had a significantly 2.32-fold increased risk of cervical carcinoma (95% CI 1.47-3.65), heterozygous Arg399Gln (GA) genotype were also associated with a significantly increased risk of cervical carcinoma, with the adjusted odds ratio (OR) being 1.58 (95% CI 1.24-2.00). Similarly, compared with Arg194Arg (CC) wild-type genotype, elevated risks were associated with the Trp194Trp (TT) for carcinoma (ORs and 95% CIs being 2.09 [1.45-3.02]) but not for heterozygote Arg194Trp (CT). In addition, three common haplotypes were found to be associated with an increased risk of cervical carcinoma. Using 194Arg-280Arg-399Arg as the reference, the OR and 95% confidence interval for 194Arg-280Arg-399Gln, 194Arg-280His-399Arg, 194Trp-280Arg-399Arg were 2.30 (1.86-2.85), 1.85 (1.41-2.41), 1.98 (1.62-2.40), respectively. The significantly increased risk associated with the haplotypes was also observed in squamous cell carcinoma (SCC) for all three common haplotypes using 194Arg-280Arg-399Arg as the reference. Neither difference was found for adenocarcinoma and CIN. All three SNPs and haplotypes did not confer more risk of high-risk human papillomavirus infection in carcinoma, CIN, and normal subgroup. Our findings suggest that XRCC1 polymorphisms including genotypes and haplotypes contribute to susceptibility to the development of cervical SCC, and the increased susceptibility is probably not through increasing susceptibility to human papillomavirus infection.

Identification of common polymorphisms in the promoter of the UGT1A9 gene: evidence that UGT1A9 protein and activity levels are strongly genetically controlled in the liver.

Polymorphisms in UDP-glucuronosyltransferases (UGTs) can influence detoxifying capacities and have considerable therapeutic implications in addition to influence various (patho)physiological processes. UGT1A9 plays a central role in the metabolism of various classes of therapeutic drugs in addition to carcinogens and steroids. The great interindividual variability of UGT1A9-mediated glucuronidation remains poorly explained, while evidence for its genetic origin exists. The proximal UGT1A9 promoter was screened for polymorphisms by sequencing and, the contribution of single nucleotide polymorphisms (SNPs) to the variability of UGT1A9 protein levels and activity was evaluated. We confirmed the presence of the -109 to -98 T10 polymorphism and found ten novel SNPs that generated a diversity of haplotypes in two independent populations. In a panel of 48 human liver microsomes, the UGT1A9 expression varied by 17-fold and was significantly correlated with SNPs -275, -331/-440, -665 and -2152. The base insertion T10 reported to increase reporter gene expression in HepG2 cells [] was not linked to -275 and -2152 SNPs and was not associated with changes in UGT1A9 protein levels. Compared to wild-type individuals, there were statistically significant higher glucuronidating activities in livers with the -275 and -2152 using mycophenolic acid and propofol as UGT1A9 substrates, indicating an extensive glucuronidator phenotype associated with these variants. This is the first study to demonstrate that naturally occurring sequence variations in the UGT1A9 promoter are informative in predicting the levels of protein and glucuronidating activity, providing a potential mechanism for interindividual variation in UGT1A9-mediated metabolism.

TNFA-TNFB haplotypes modify susceptibility to type I diabetes mellitus independently of HLA class II in a Moroccan population.

The contribution of single nucleotide polymorphisms in tumor necrosis factors (TNF) alpha and beta to autoimmune diseases, and to type 1 diabetes mellitus (T1DM) in particular, is not well established, and may be confounded by linkage disequilibrium to class II HLA genes. At least two polymorphisms seem to have functional relevance in the respective genes: TNFA-307 and TNFB+252. We have typed these two polymporphisms in samples of Moroccan T1DM patients and controls for which class II HLA genes had already been typed. Tumor necrosis factors and compound TNF-class II HLA haplotypes were inferred; it was the first time that such a design had been implemented. Independent of linkage disequilibrium with class II HLA, TNF haplotype TNFA-307*2 - TNFB+252*2 showed a significant protective effect (OR = 0.031), partly exacerbated by partial linkage to protective class II haplotypes. Such effect could be detected because Morocco shows the highest frequency of the TNFA-307*2 allele yet reported. This highlights the possible population differences in alleles contributing to autoimmune diseases.

Uncoupling Protein 3 and Peroxisome Proliferator-Activated Receptor γ2 Contribute to Obesity and Diabetes in Palauans

We examined the genetic contribution of single nucleotide polymorphisms (SNPs) of the energy metabolism-related genes, including beta 3 adrenergic receptor (β3AR), apolipoprotein E (apo-E), promoter of uncoupling protein 3 (UCP3-p), peroxisome proliferator-activated receptor gamma 2 (PPARγ2) and leptin receptor (LEPR) to metabolic disorders, in 118 inhabitants of Palau. The data were statistically analyzed and ethnically compared to correlate SNPs and their metabolic parameters. UCP3-p (P < 0.01) and PPARγ2 (p = 0.05) correlated with plasma HbA1c, and UCP3-p correlated with fasting blood glucose (P < 0.01) in males, but not in females. UCP3-p correlated with body fat (%) (P < 0.01) in females, but not in males. Plasma leptin levels and apo-E were correlated in both groups. The frequency of SNPs for PPARγ2, LEPR, and UCP3-p are significantly different between Palauans and Caucasians.