Identification and functional characterization of a polymorphic oestrogen response element in the human coagulation factor IX gene promoter.

The liver expressed procoagulant factor IX (FIX) shows inter-individual variation in levels, some of which is heritable. Raised levels of FIX are associated with a thrombotic tendency. This study demonstrated that, in females but not males, part of this variation in FIX levels is due to polymorphic genotype at a locus in the factor IX gene (F9) promoter 698 bp upstream of the major transcription initiation site (-698C/T). The -698C allele (associated with higher FIX level) shows closer homology to a canonical ORE sequence and a higher binding affinity for oestrogen receptor alpha than the -698T allele. Reporter gene vectors were constructed with elements spanning residues -738 to +50 of the F9 promoter corresponding to wild type -698C and -698T alleles. A related series of vectors comprising three copies of the F9 ORE driving expression of a minimal synthetic promoter were also created. Transfection into the liver-derived HepG2 and erythroleukaemic K562 cell lines demonstrated increased levels of expression in the presence of oestrogenic factors when compared to those found in their absence; this stimulation was more pronounced in the non-liver derived K562 cell line and from the reporter vectors containing promoter elements corresponding to the -698C allele.

The -1185 A/G and -1051 G/A dimorphisms in the von Willebrand factor gene promoter and risk of myocardial infarction.

Elevated plasma von Willebrand factor (VWF) levels are associated with coronary artery disease, although the precise mechanism for this is unclear. Recently, four linked dimorphisms in the VWF gene promoter were demonstrated to influence plasma VWF level. We conducted a case-control study of 525 acute myocardial infarction (MI) cases and 451 control subjects, all aged < or = 75 years, to assess the potential contribution of two of these dimorphisms (-1185 G/A and -1051 A/G) to the risk of MI. The frequency of the -1185A/-1051G haplotype, associated with elevated VWF levels, was similar in the case and control groups, yielding a haplotypic odds ratio for MI of 0.93 (95% CI 0.77, 1.12, P = 0.43), and there was no significant association between the -1185A/-1051G haplotype and the risk of MI in any subgroup analysed. We therefore conclude that possession of the -1185A/-1051G haplotype does not confer an increased risk for MI.

FLT3 internal tandem duplication mutations in adult acute myeloid leukaemia define a high-risk group.

Genomic DNA from 106 cases of adult de novo acute myeloid leukaemia (AML) was screened by polymerase chain reaction (PCR) and gel electrophoresis for FLT3 internal tandem duplication (ITD) mutations within the juxtamembrane (JM) domain. FLT3 mutations were detected in 14 cases (13.2%) and occurred in FAB types M1 (4 out of 14 cases), M3 (1 out of 10 cases), M4 (5 out of 37 cases) and M5 (4 out of 11 cases). Sequence analysis of four cases with abnormal PCR electrophoretic patterns revealed in frame duplications in the region of exon 11 of between 27 and 111 base pairs. Three are predicted to result in the tandem duplication of adjacent amino acid residues and one to result in a tandem duplication plus insertion of a novel amino acid motif. Statistical analysis showed the FLT3 mutations to be a strong prognostic factor, with patients lacking the mutation surviving significantly longer from diagnosis (mean 29.1 months) than those with an ITD (mean 12.8 months; P = 0.0002). Thirteen of the 14 patients with FLT3 mutations died within 18 months of diagnosis. FLT3 mutations were of prognostic significance in good risk disease (P = 0.04), as well as in patients with standard risk disease (P = 0.0096). This study demonstrates that the FLT3 ITD mutation occurs in a significant percentage of adult AML cases and is an important adverse prognostic factor that appears independent of conventional karyotypic findings.

A rapid method for haemophilia B mutation detection using conformation sensitive gel electrophoresis.

Conformation sensitive gel electrophoresis (CSGE) was confirmed as an effective procedure for screening the factor IX (FIX) gene by detecting 10/10 previously known FIX gene mutations. The FIX genes of a further 11 haemophilia B patients with unknown mutations were then screened and an abnormal CSGE profile was identified in all cases. Subsequent DNA sequencing demonstrated one of these to be a novel mutation (31133insT, Arg338Fs), the remaining 10 having been previously reported on the haemophilia B database. Mutation screening of the FIX gene using CSGE was demonstrated to be a rapid and efficient means of carrier analysis in families with haemophilia B.

Identification of different gene expression patterns in low and high grade non-Hodgkin's lymphomas by differential display.

We have compared the patterns of gene expression in non-Hodgkin's lymphoma (NHL) biopsy samples from patients with either low grade or high grade disease, by the polymerase chain reaction (PCR) based technique of differential display. By using a combination of 30 primer pairs we estimate that we were able to survey over 3,000 genes expressed in these tissues. In this study we compared a group of three low grade follicular centre lymphomas with a group of two high grade diffuse large cell lymphomas and scored only those PCR products that were represented in all samples of each group. In doing so we were able to avoid many of the problems associated with the occurence of false PCR-positives. 139 differences were then scored as representing genes which may be differentially expressed during the transformation from low to high grade disease. However, as many of these might simply reflect changing populations of cells, we focused on only those genes which appeared to be expressed exclusively in either low grade or high grade disease. We have identified 14 such genes, of which 10 were low grade specific and 4 were high grade specific. This approach therefore appears to offer a systematic method for the identification and characterisation of differentially expressed genes, which are characteristic of different NHL sub-types.

Promoter studies in hemostasis.

In recent years the technique of gene cloning, coupled with the application of polymerase chain reaction (PCR)-based procedures, has greatly facilitated the production of cloned genomic material encompassing the putative promoter regions of genes involved in the hemostatic process. These recombinant vectors provide the raw material for reporter gene studies and DNA footprinting analysis; two of the three most frequently used in vitro procedures to study promoter function. The third of these methods to be described in this chapter, band shift or electrophoretic mobility shift assay (EMSA), normally uses synthetically produced double-stranded oligonucleotide sequences corresponding to specific areas of interest within the promoter region.

A Gly --> Ser change causes defective folding in vitro of calcium-binding epidermal growth factor-like domains from factor IX and fibrillin-1.

The calcium-binding epidermal growth factor-like (cbEGF) domain is a common motif found in extracellular proteins. A mutation that changes a highly conserved Gly residue to Ser in this domain has been identified both in the factor IX (FIX) and fibrillin-1 genes, where it is associated with relatively mild variants of hemophilia B and Marfan syndrome, respectively. We have investigated the structural consequences in vitro of this amino acid change when introduced into single cbEGF domains from human FIX (G60S) and human fibrillin-1 (G1127S), and a covalently linked pair of cbEGF domains from fibrillin-1. High pressure liquid chromatography analysis, mass spectrometry, and 1H NMR analysis demonstrate that wild-type cbEGF domains purified in the reduced form and refolded in vitro adopt the native fold. In contrast, the Gly --> Ser change causes defective folding of FIX and fibrillin-1 cbEGF domains. However, in the case of the factor IX mutant domain, a Ca2+-dependent change in conformation, identified by NMR in a proportion of the refolded material, suggests that some material refolds to a native-like structure. This is consistent with enzyme-linked immunosorbent assay analysis of FIX G60S from a hemophilia B patient Oxford d2, which demonstrates that the mutant protein is partially recognized by a monoclonal antibody specific for this region of FIX. NMR analysis of a covalently linked pair of fibrillin cbEGF domains demonstrates that the C-terminal domain adopts the native epidermal growth factor fold, despite the fact that the adjacent mutant domain is misfolded. The implications of these results for disease pathogenesis are discussed.

Precise carrier diagnosis in families with haemophilia A: use of conformation sensitive gel electrophoresis for mutation screening and polymorphism analysis.

Causative mutations in the factor VIII gene of seven unrelated patients with severe haemophilia A were identified using the mutation screening procedure conformation sensitive gel electrophoresis (1) and characterised by direct sequencing. Female family members of all patients had requested either carrier status determination or prenatal diagnosis. However, lack of the factor VIII gene inversion, a prior family history or informative polymorphisms prevented diagnosis in these families. Identification of a mutation in each family enabled female carrier status to be determined in all cases. Six mutations were previously unreported. One Afro-Caribbean patient had two sequence changes; A670 2G and A6769G. The latter, resulting in Met2238Val and previously reported as a FVIII mutation, was shown to be polymorphic with a 42% heterozygosity rate in an Afro-Caribbean population. Conformation sensitive gel electrophoresis was found to be technically simple and efficient at locating previously unknown FVIII gene mutations.

A-793 G to A transition in the factor IX gene promoter is polymorphic in the Caucasian population.

We report the incidence of a prevalent polymorphism at position -703 in the promoter region of the factor IX gene in caucasian individuals. This DNA change was originally reported as one of two changes in the factor IX gene of a severely affected haemophilia B patient from Japan. We confirm the neutral nature of this change and demonstrate that, despite showing linkage disequilibrium with the previously reported Msel RFLP < 100 bp distant, the use of these two loci together in a carrier screening strategy significantly increases the level of informativity over the achieved using either polymorphism alone.

The high frequency of the -6G-->A factor IX promoter mutation is the result both of a founder effect and recurrent mutation at a CpG dinucleotide.

We report a new Liverpool family with a mild haemophilia B Leyden phenotype caused by a -6G-->A mutation in a CpG dinucleotide in the promoter of the clotting factor IX gene. This mutation had previously been identified in three other U.K. pedigrees and six others worldwide. To investigate whether these mutations were of independent origin, the haplotype was determined for eight polymorphic loci, within or immediately adjacent to the factor IX gene, for nine of the 10 existing patients. Six probands had identical haplotypes, including all four U.K. probands, suggesting that they arose from a common founder. The other three probands differed in haplotype from the common haplotype, and from each other, suggesting that they were independent mutations at this CpG dinucleotide.

A single base pair deletion in the promoter region of the factor IX gene is associated with haemophilia B.

Patients with the haemophilia B Leyden phenotype show a distinct pattern of factor IX expression characterized by a post-pubertal increase in FIX levels and the remission of clinical symptoms in adult life. This phenotype has previously been linked to single base mutations within transcription factor binding sites in a region of approximately 40 bp around the major start point of transcription of the FIX gene. Here we report a novel mutation in this region within the transcription factor C/EBP binding site at +1 to +18. The mutation is a single base pair deletion from a triplet of thymine residues at +6 to +8. We show that the extent to which this mutation disrupts the binding of C/EBP to its binding site is less marked than the disruption caused by the +13 A-->G mutation of FIX Norwich (1). This correlates with age-matched phenotypic data we have available for the patient reported here and that of FIX Norwich.

An MseI RFLP in the 5' flanking region of the factor IX gene: its use for haemophilia B carrier detection in Caucasian and Thai populations.

We have identified an MseI restriction fragment length polymorphism (RFLP) in the 5' flanking region of the factor IX gene. RFLPs in the factor IX locus are routinely used as linkage markers to track defective factor IX genes through affected pedigrees, allowing diagnosis of the haemophilia B carrier state in female members of the kindred. Currently, seven intragenic polymorphic loci have been characterized allowing carrier diagnosis in 89% of cases in the Caucasian population. Additional screening with the MseI RFLP reported in this publication increases this figure to 94% of cases. In Asian populations only one of these RFLPs (HhaI) is present at any significant frequency. Hence, carrier detection rates are much reduced in comparison to the corresponding figure of 89% in Caucasians. We report that this MseI RFLP is also present in the Thai population. Indeed, when used in combination with the HhaI polymorphism, the MseI RFLP should significantly improve the carrier detection rate in the Thai population from 11% to 40% of cases.

Key residues involved in calcium-binding motifs in EGF-like domains.

Many extracellular proteins with diverse functions contain domains similar to epidermal growth factor (EGF), a number of which have a consensus Asp/Asn, Asp/Asn, Asp*/Asn*, Tyr/Phe (where the asterisk denotes a beta-hydroxylated residue). These include the coagulation factors IX and X, proteins with two EGF-like domains, the first of which contains the consensus residues. The first EGF-like domain of human factor IX contains a calcium-binding site, which is believed to be responsible for one of the high-affinity sites detected in this protein. Similar results have been obtained for bovine factor X. We have now used protein engineering and 1H-NMR techniques to investigate the importance of individual consensus residues for ligand binding. Measurement of a calcium-dependent Tyr 69 shift in the isolated first EGF-like domain from human factor IX demonstrates that Asp 47, Asp 49, and Asp 64 are directly involved in this binding. Gln 50, whose importance has previously been overlooked, is also involved in this binding. Two mutations in this domain, Asp 47----Glu, and Asp 64----Asn, present in patients with haemophilia B, reduce calcium binding to the domain greater than 4-fold and greater than 1,000-fold, respectively. Furthermore, the defective calcium binding of Asn 64 can be partially rescued by the compensatory mutation Gln 50----Glu. This latter mutation, when introduced singly more than doubles the affinity of the domain for calcium. This study thus defines residues involved in a new type of calcium-binding site and provides strong circumstantial evidence for calcium-binding motifs in many extracellular proteins, including the developmentally important proteins of Drosophila, notch, delta and crumbs.

Protein engineering of the propeptide of human factor IX.

Vitamin-K-dependent plasma proteins contain a highly conserved propeptide sequence located between the classical hydrophobic leader sequence and the N-terminus of the mature protein. This acts as a recognition sequence for the vitamin-K-dependent carboxylase which catalyses the conversion of specific glutamate residues to gamma-carboxyglutamate (Gla) residues in the adjacent Gla domain. Protein engineering of the 18 residue propeptide from human factor IX has highlighted the importance of residues -16Phe and -10Ala with respect to carboxylase recognition. In addition, studies of haemophilia B patients have shown that C-terminal propeptide residues -4Arg and -1Arg are required for proteolysis of the propeptide from the mature protein. To extend these previous studies we have introduced two novel mutations into the propeptide of human factor IX at positions -17(Val----Asp) and -6(Leu----AsP), and studied the effect of these changes on gamma-carboxylation and proteolytic processing. Both mutations reduce the expression of a calcium-dependent epitope in the Gla domain; however, only -6Leu----Asp shows reduced binding to barium sulphate. In addition, this latter mutation prevents proteolytic processing of the propeptide. These data support the current hypothesis that the propeptide contains two recognition elements: one for carboxylase recognition located towards the N-terminus, and one for propeptidase recognition located near the C-terminus.

Identification of haemophilia B patients with mutations in the two calcium binding domains of factor IX: importance of a beta-OH Asp 64----Asn change.

The polymerase chain reaction procedure (PCR) coupled with direct sequencing has been used to screen a panel of haemophilia B patients. This analysis has identified, amongst others, several mutations in the functionally important gla and type B EGF domains of factor IX, both of which are known to bind calcium. Type B EGF domains are widely distributed in proteins; located within these domains are highly conserved amino acid residues important for the formation of a high-affinity calcium binding site. One prominent feature of these domains is a highly conserved beta-hydroxylated Asp or Asn residue. Of particular interest is the identification of one patient, with a substitution of the beta-hydroxy Asp-64 residue normally present in factor IX for Asn. This change results in a functionally defective factor IX molecule with altered calcium binding properties. To explain the functional abnormality caused by this substitution of one amino acid residue for another which is commonly found at the equivalent position in other proteins with type B EGF domains, we propose the existence of additional conserved residues within this domain, which are important for calcium binding, and which correlate with whether the beta-hydroxylated residue is Asp or Asn.