A novel polymorphism in the factor XIII B-subunit (His95Arg): relationship to subunit dissociation and venous thrombosis.

BACKGROUND: Factor (F)XIII B-subunit, which plays a carrier role for zymogen FXIIIA, is highly polymorphic, but the molecular basis for these polymorphisms and their relationship to disease remains unknown. OBJECTIVES: To screen the FXIIIB gene coding region for common variation and analyze possible functional effects. METHODS AND RESULTS: We examined the FXIIIB gene by PCR-SSCP and identified three common single nucleotide polymorphisms: A8259G, C29470T and A30899G. A8259G results in substitution of His95Arg in the second Sushi domain. An FXIII tetramer ELISA was developed to analyze B-subunit dissociation from A-subunit (leading to access to the catalytic site of FXIII). Increased subunit dissociation, 0.51 vs. 0.45 (fraction of total tetramer), was found in plasma from subjects possessing the Arg-allele. However, when the variants were purified to homogeneity and binding was analyzed by steady-state kinetics, no difference was observed. The relationship between His95Arg and venous thrombosis was investigated in 214 patients and 291 controls from Leeds. His/Arg + Arg/Arg genotypes were more frequent in patients than controls (22.4% vs. 15.1%). His95Arg was also investigated in the Leiden Thrombophilia Study, in which a similar difference was observed for 471 patients vs. 472 controls (18.5% vs. 14.0%), for a pooled odds ratio (OR) of 1.5 (CI95 1.1-2.0). CONCLUSIONS: We have identified three FXIIIB polymorphisms, one of which codes for substitution of His95Arg. The Arg95 variant associates with a moderately increased risk for venous thrombosis, and with increased dissociation of the FXIII subunits in plasma, although in vitro steady-state binding between purified subunits was not affected.

Characterization of allelic and nucleotide variation between the RAGE gene on chromosome 6 and a homologous pseudogene sequence to its 5' regulatory region on chromosome 3: implications for polymorphic studies in diabetes.

Activation of the receptor for advanced glycation end products (RAGE) appears to be a key mechanism in the pathogenesis of diabetic vascular disease, making RAGE a candidate gene for investigation. RAGE is located in the major histocompatibility complex locus on chromosome 6, which contains a multitude of overlapping and duplicated genes involved predominantly in inflammatory and immune responses. The RAGE 5' flanking region from -505 in a 5' direction overlaps with PBX2, a gene that has a pseudogene copy on chromosome 3, making any studies of polymorphisms in this duplicated region potentially fraught with error. In this study we have addressed these issues by confirming RAGE as a predominantly single-copy gene and PBX2 to have two gene copies in the haploid human genome. We have characterized the gene:pseudogene differences between RAGE/PBX2 on chromosome 6 and PsiPBX2 on chromosome 3, which include a change from C to A at position -1139 RAGE/+2298 PBX2, previously reported as a polymorphism. Single chromosome-specific DNA amplification of the duplicated region has clarified five polymorphisms to be on chromosome 3 and one (at -1202 RAGE/+2234 PBX2) to be on chromosome 6. In conclusion, this study provides essential data for the study of RAGE and its genetics.

Human endothelial cell-derived nuclear proteins that recognise polymorphic DNA elements in the von Willebrand factor gene promoter include YY1.

Four common base-change polymorphisms have been found in the von Willebrand factor gene promoter: (-1793 C/G, -1234 T/C, -1185 G/A and -1051 A/G). All four polymorphisms are in strong linkage disequilibrium and recent reports have indicated these polymorphisms are associated with plasma vWF:Ag levels suggesting that one or more of these elements influence regulation of the vWF gene. We report that human endothelial cell-derived trans-acting factors display allelic preferences in binding activity to each polymorphic site. The common A allele variant of the -1051 polymorphism and the rarer A allele variant of the -1185 polymorphism provided specific binding of nuclear proteins. The G allele counterpart of these two variants did not produce any complex formation indicating that the nucleotide substitution at these positions alters the DNA binding ability of nuclear factors. The two alleles of the -1234 polymorphism produced two complexes with a similar migration pattern however stronger binding was found to the common T variant of this allele. Two specific complexes associated with the rarer G allele of the -1793 polymorphism, but only one associated with the C allele. Supershift experiments revealed that the trans-acting factor YYI recognised the slower migrating complex formed on the -1234 T/C and the -1051 A polymorphic sites with a strong binding preference for the -1234 T allele variant. The identification of YY1 as a component of the factors that recognise these elements suggests that this ubiquitous nuclear protein may play a role in the regulation of the vWF promoter.

Effects of novel polymorphisms in the RAGE gene on transcriptional regulation and their association with diabetic retinopathy.

Interactions between advanced glycation end products (AGEs) and the receptor for AGE (RAGE) are implicated in the vascular complications in diabetes. We have identified eight novel polymorphisms, of which the -1420 (GGT)n, -1393 G/T, -1390 G/T, and -1202 G/A were in the overlapping PBX2 3' untranslated region (UTR), and the -429 T/C (66.5% TT, 33.5% TC/CC), -407 to -345 deletion (99% I, 1% I/D, 0% D), -374 T/A (66.4% TT, 33.6% TA/AA), and +20 T/A were in the RAGE promoter. To evaluate the effects on transcriptional activity, we measured chloramphenicol acetyl transferase (CAT) reporter gene expression, driven by variants of the -738 to +49 RAGE gene fragment containing the four polymorphisms identified close to the transcriptional start site. The -429 C, -374 A, and 63-bp deletion alleles resulted in a mean increase of CAT expression of twofold (P < 0.0001), threefold (P < 0.001), and fourfold (P < 0.05), respectively, with the -374 T and A alleles yielding highly differential binding of nuclear protein extract from both monocyte- and hepatocyte-derived cell lines. The prevalence of the functional polymorphisms were investigated in subjects with type 2 diabetes (106 with and 109 without retinopathy), with the -429 C allele showing an increase in the retinopathy group (P < 0.05). These data suggest that the polymorphisms involved in differences in RAGE gene regulation may influence the pathogenesis of diabetic vascular complications.

Analysis of the tissue factor pathway inhibitor gene and antigen levels in relation to venous thrombosis.

Tissue factor pathway inhibitor (TFPI) inhibits tissue factor-induced coagulation. The major part of TFPI is releasable by heparin. We recently found eight patients with thrombosis and low levels of heparin-releasable TFPI in whom we investigated the TFPI gene for mutations. A transition of G to A coding for Valine264Methionine in the heparin-binding domain was found. The Val264Met polymorphism had an allele frequency of 3% in 96 healthy individuals. A silent polymorphism was identified in TFPI exon IV (T-->C), which does not alter Tyrosine 56. Apart from Val264Met, which was detected in one out of the eight patients, no other mutations in the TFPI gene were found in patients with low heparin-releasable TFPI. Analysis of Val264Met in 317 patients with deep vein thrombosis (DVT) and 292 controls showed no association between Val264Met and DVT. However, a study of total TFPI antigen levels in 122 DVT patients and 126 controls demonstrated an association between TFPI levels and venous thrombosis (P = 0.0001). These results provide evidence for a relationship between venous thrombosis and total TFPI level as a possible risk factor, whereas they do not support a link between DVT and mutations in the nine exons of the TFPI gene.

FXII (46C-->T) polymorphism and in vivo generation of FXII activity--gene frequencies and relationship in patients with coronary artery disease.

Increased Factor XIIa concentrations have been found in association with coronary artery disease. Recently, a common 46 C to T point mutation in exon I of the factor XII gene has been described which is associated with lower FXII clotting activity and lower zymogen levels in relation to possession of the T allele. It is not known whether this polymorphism relates to the phenotypes of FXIIa in vivo or to coronary artery disease. The aim of the study was to investigate the interaction of this polymorphism with FXIIa plasma levels and to study the prevalence of the polymorphism in 266 patients with suspected coronary artery disease characterised by angiography and in 185 healthy controls. FXIIa levels were strongly associated with FXII genotype with lower levels with increasing numbers of T alleles (p <0.0001). There was no difference between the prevalence of this polymorphism in patients with M1 compared to those without MI and controls and between all patients and controls (p > or =0.2, chi-square test). There was no association between extent of coronary artery disease (0, 1, 2, and 3 vessel disease) and FXII genotype. In conclusion, the common 46 C to T point mutation is strongly associated with FXIIa but the present study did not show an association with coronary artery disease. The role of this polymorphism in other thrombotic disorders such as ischemic stroke and venous thrombosis and its clinical significance in FXII deficient states remains to be investigated.

Prevalence of three common polymorphisms in the A-subunit gene of factor XIII in patients with coronary artery disease.

Activated blood coagulation factor XIII has an important role in the final stage of the clotting cascade by the covalent crosslinking of alpha- and gamma-fibrin chains. We have recently shown that a functional polymorphism in exon 2. codon 34 of the FXIII A-subunit gene is protective against myocardial infarction. To investigate the prevalence of three other common point mutations in the A-subunit gene (codon 564, C to T, 650 G to A and 651 G to C) and their association with FXIII activity and antigen levels, 275 patients with coronary artery disease and 196 controls were studied. There was no difference in the prevalence of the polymorphisms between patients and controls or between patients with or without MI. Only genotype at codon 564 was associated with FXIII activity with lower activities in subjects possessing the T allele. There was evidence of linkage disequilibrium between codon 34 and codon 564. These results suggest that FXIIIVal34Leu is the only common polymorphism in the coding region of the A-subunit gene of FXIII associated with coronary artery disease.

Detection of common viruses using the polymerase chain reaction to assess levels of viral presence in type 1 (insulin-dependent) diabetic patients.

The polymerase chain reaction was used to detect a range of common viruses in the peripheral blood of Type 1 diabetic and non-diabetic control patients in order to identify any abnormal viral presence, with possible roles in the pathogenesis of Type 1 diabetes. Peripheral blood from 17 newly diagnosed Type 1 diabetic patients, 38 Type 1 diabetic patients with disease of longer duration, and 43 age and sex matched non-diabetic controls was obtained. Samples were screened for cytomegalovirus, Epstein-Barr virus, enterovirus (including coxsackie), and mumps virus. Cytomegalovirus was detected in control patients only (5%), Epstein-Barr virus was detected equally in newly diagnosed and control patients (12%), and enterovirus was detected slightly more frequently in diabetic than non-diabetic patients (41% and 31%, respectively). Mumps virus was not detected in any of the samples. It is concluded that Type 1 diabetic individuals are neither more prone to persistence of common viruses nor to more frequent acute infections with the viruses tested for than non-diabetic individuals. If common viruses are involved in the pathogenesis of Type 1 diabetes then they act either as non-specific agents to which the host has abnormal immune responses, or, the diabetogenic viruses are eliminated from the body by the time of disease diagnosis.

Sequence analysis of two tandemly linked Em genes from wheat.

DNA sequences are presented for two members of the wheat Em gene family. The sequences correspond to the two linked genes at the Xem-1AL locus. Comparisons of these sequences with that of another wheat Em gene and two Em cDNA clones reveals substantial homology within the protein-coding regions, and the presence in the 5'-flanking regions of the genomic sequences of motifs characteristic of ABA-responsive cis-acting elements.

Genetic analysis of a mutant class of Physcomitrella patens in which the polarity of gravitropism is reversed.

In the moss Physcomitrella patens, single-cell protonemata and multicellular gametophores respond to reorientation relative to the gravity vector by growing negatively gravitropically. A mutant class in which the protonemata, but not the gametophores, respond by growing towards gravity has been identified. In this paper, we describe the isolation of additional mutants of this class. Complementation and segregation ratio analyses were carried out on these mutants, which indicate that a single gene may mutate to switch the polarity of gravitropism.

Molecular cloning and chromosomal location of genes encoding the "Early-methionine-labelled" (Em) polypeptide of Triticum aestivum L. var. Chinese Spring.

The "Early-methionine-labelled" (Em) polypeptide is the most abundant cytosolic polypeptide found in mature wheat embryos. Using a near full-length cDNA clone as a hybridisation probe to detect genomic sequences by Southern blotting of electrophoretic separations of genomic DNA derived from Triticum aestivum L. var. Chinese Spring and a series of its aneuploid derivatives, we demonstrate that the Em polypeptide is the product of a small multigene family in which the copies are located on each of the long arms of the homoeologous group 1 chromosomes. Screening of a variety of genotypes additionally reveals a number of restriction fragment length polymorphisms associated with these loci. Screening of a library of genomic DNA cloned in the vector λEMBL 4 has resulted in the isolation of a genomic fragment containing two closely linked Em genes. These are separated by ca. 2.5 kb. Analysis of restriction enzyme digests of this clones fragment has identified it as originating from chromosome 1A.