UTR Haplotypes Research Articles

Large-Scale Evaluation of Candidate Genes Identifies Associations between VEGF Polymorphisms and Bladder Cancer Risk

Common genetic variation could alter the risk for developing bladder cancer. We conducted a large-scale evaluation of single nucleotide polymorphisms (SNPs) in candidate genes for cancer to identify common variants that influence bladder cancer risk. An Illumina GoldenGate assay was used to genotype 1,433 SNPs within or near 386 genes in 1,086 cases and 1,033 controls in Spain. The most significant finding was in the 5′ UTR of VEGF (rs25648, p for likelihood ratio test, 2 degrees of freedom = 1 × 10−5). To further investigate the region, we analyzed 29 additional SNPs in VEGF, selected to saturate the promoter and 5′ UTR and to tag common genetic variation in this gene. Three additional SNPs in the promoter region (rs833052, rs1109324, and rs1547651) were associated with increased risk for bladder cancer: odds ratio (95% confidence interval): 2.52 (1.06–5.97), 2.74 (1.26–5.98), and 3.02 (1.36–6.63), respectively; and a polymorphism in intron 2 (rs3024994) was associated with reduced risk: 0.65 (0.46–0.91). Two of the promoter SNPs and the intron 2 SNP showed linkage disequilibrium with rs25648. Haplotype analyses revealed three blocks of linkage disequilibrium with significant associations for two blocks including the promoter and 5′ UTR (global p = 0.02 and 0.009, respectively). These findings are biologically plausible since VEGF is critical in angiogenesis, which is important for tumor growth, its elevated expression in bladder tumors correlates with tumor progression, and specific 5′ UTR haplotypes have been shown to influence promoter activity. Associations between bladder cancer risk and other genes in this report were not robust based on false discovery rate calculations. In conclusion, this large-scale evaluation of candidate cancer genes has identified common genetic variants in the regulatory regions of VEGF that could be associated with bladder cancer risk.

Evidence for a functional haplotype in the 3′UTR of the hAQP5 gene

Aquaporin 5 (AQP5) is a water channel expressed in mammalian airways and alveolar epithelium. Mice deficient in AQP5 are hyperresponsive to cholinergic-stimulated bronchoconstriction, a hallmark of clinical asthma. A genetic mutation screen of the hAQP5 gene identified two A to G SNPs in the 3′UTR that occur in linkage disequilibrium. The most common A-A haplotype is conserved in mouse, human, and rat. To address the significance of the A to G nucleotide variation in human, we compared the 3′UTR of the AQP5 gene to monkey, macaque, gorilla, orangutan, and chimpanzee. Interestingly, the rare G-G 3′UTR haplotype found in humans, as well as A-G and G-A combinations which do not occur in humans, were detected in primates. To determine the effects of the A to G variations on mRNA expression, 634 ntds of the hAQP5 gene including the A-A (WT) or G-G (SNP) 3′UTR haplotypes, or A-G/G-A chimeric haplotypes were fused to a green fluorescent protein reporter cassette. Plasmid constructs were transfected into MLE-15 cells and total RNA isolated. Real-time quantitative PCR identified a greater than 80% reduction in mRNA expression of the AG and GA chimeric constructs as compared to both WT and SNP haplotype constructs (p<0.01). These data suggest that the A-A and G-G AQP5 3′UTR haplotypes are subject to functional genetic selection in humans. This research is supported by NIH R15#HL077290-01.

Tryptophan hydroxylase-2 gene polymorphisms in rhesus monkeys: association with hypothalamic–pituitary–adrenal axis function and in vitro gene expression

Tryptophan hydroxylase-2 (TPH2) is a newly identified second form of TPH responsible for serotonin synthesis in the brain and has been increasingly implicated as a contributor to the etiology of various psychiatric disorders. In this study, we have identified the constellation of polymorphisms in rhesus monkey TPH2 and investigated genotype/phenotype association as well as gene expression effects of specific polymorphisms. Genomic DNA was obtained from 247 rhesus monkeys, among which 24 had been previously examined for plasma cortisol level, dexamethasone suppression, and combined dexmethasone/ACTH challenge. Polymorphisms in all exons, splicing junctions and approximately 2 kb of the 5'-flanking region (5'-FR) of TPH2 were identified by sequencing. We identified 17 single nucleotide polymorphisms (SNPs) including two that are predictive of amino-acid change (25Pro>His and 75Gly>Ser, respectively), two mononucleotide repeats, one dinucleotide repeat, and one 159-bp insertion polymorphism. The 3'-UTR polymorphisms were significantly associated with hypothalamic-pituitary-adrenal (HPA) axis activity, especially 2051A>C, which was strikingly correlated with plasma cortisol level in the morning only (F=10.203, P=0.001). Luciferase reporter gene assays showed that the 3'-UTR polymorphisms and haplotypes had a profound effect on in vitro gene expression. Accordingly, these investigations revealed that polymorphisms in 3'-UTR of rhesus monkey TPH2 modulate HPA axis function, presumably by affecting levels of TPH2 expression.

Association between SLC11A1 polymorphisms and susceptibility to different clinical forms of tuberculosis in the Peruvian population

Polymorphism in SLC11A1 has been implicated in host susceptibility to tuberculosis. We have studied associations between INT4, D543N, and 3′UTR polymorphisms of SLC11A1 and different clinical forms of TB. Analysis used 507 patients with pulmonary TB, 123 with extra pulmonary TB and 513 controls. INT4 and D543N showed allelic association with pulmonary TB ( P = 0.02 and 0.03 respectively). INT4–D543N–3′UTR haplotypes showed an association with pulmonary TB ( P = 0.03). No association of SLC11A1 with miliary TB was observed, and a possible association of D543N to the pleural form ( P = 0.08) was suggested. These results support association between SLC11A1 and TB, particularly to the common pulmonary form.

Vitamin D receptor 3′-untranslated region polymorphisms: lack of effect on mRNA stability

Allelic variation at the 3′-end of the vitamin D receptor (VDR) gene has been associated with a 3–5-fold increased risk of developing prostate cancer and with differences in bone mineralization. This genetic diversity does not alter the VDR protein structurally, but instead may be a marker(s) of other, nearby polymorphisms that influence message stability or translation. The work reported here was instigated to identify additional VDR 3′-UTR polymorphisms that may have functional significance and to then test whether these genetic variants alter message stability. Initially, four novel, frequently occurring sequence variants were identified that associated with two common haplotypes that were described previously. These common sequence variants were not found within three message-destabilizing elements that we mapped within the 3′-UTR of the vitamin D receptor mRNA. Furthermore, the two VDR 3′-UTR haplotypes conferred an identical half-life on a heterologous β-globin reporter gene, in an in vitro assay. We therefore conclude that common polymorphisms within the VDR 3′-UTR do not influence message stability.