Characterization of copy-number variants in a large cohort of patients with von Willebrand disease reveals a relationship between disrupted regions and disease type

Background

Genetic analysis for von Willebrand disease (VWD) commonly utilizes DNA sequencing to identify variants in the von Willebrand factor (VWF) gene; however, this technique cannot always detect copy-number variants (CNVs). Additional mapping of CNVs in patients with VWD is needed.

Objectives

This study aimed to characterize CNVs in a large sample of VWF mutation-negative VWD patients.

Methods

To determine the role of CNVs in VWD, a VWF high-resolution comparative genomic hybridization array was custom-designed to avoid multiple sequence variations, repeated sequences, and the VWF pseudogene. This was performed on 204 mutation-negative subjects for whom clinical variables were also available.

Results

Among the 204 patients, 7 unique CNVs were found, with a total of 24 CNVs (12%). Of the 7 unique CNVs, 1 was novel, 1 was found in a VWF database, and 5 were previously reported. All patients with type 1C VWD and a CNV had the same exon 33 and 34 in-frame deletion. Certain clinical variables were also significantly different between those with and without CNVs.

Conclusion

The in-frame deletion in patients with type 1C VWD exactly matches the D4N module of the D4 domain, a region where mutations and deletions are known to affect clearance. We observed significantly higher VWF-to-ristocetin cofactor levels in patients with type 1C VWD and a CNV than in patients without a CNV, suggesting a relationship between CNVs and the increased clearance observed in patients with type 1C VWD. Glycoprotein IbM activity was significantly lower in patients with type 1 VWD and a CNV than in patients without a CNV, suggesting that platelet binding is more affected by CNVs than single base pair mutations. This work elucidates some of the underlying genetic mechanisms of CNVs in these patients.

Molecular pathogenesis and heterogeneity in type 3 VWD families in U.S. Zimmerman program

BACKGROUND

Type 3 von Willebrand Disease (VWD) is a rare and severe form of VWD characterized by the absence of von Willebrand factor (VWF).

OBJECTIVES

As part of the Zimmerman Program, we sought to explore the molecular pathogenesis, correlate bleeding phenotype and severity, and determine the inheritance pattern found in type 3 VWD families.

PATIENTS/METHODS

62 index cases with a pre-existing diagnosis of type 3 VWD were analyzed. Central testing included FVIII, VWF:Ag, VWF:RCo, and VWFpp. Bleeding symptoms were quantified using the ISTH bleeding score. Genetic analysis included VWF sequencing, comparative genomic hybridization and predictive computational programs.

RESULTS

75% of subjects (46) had central testing confirming type 3, while 25% were re-classified as type 1-Severe or type 1C. Candidate VWF variants were found in all subjects with 93% of expected alleles identified. The majority were null alleles including frameshift, nonsense, splice site, and large deletions, while 13% were missense variants. Additional studies on 119 family members, including 69 obligate carriers, revealed a wide range of heterogeneity in VWF levels and bleeding scores, even amongst those with the same variant. Co-dominant inheritance was present in 51% of families and recessive in 21%, however 28% were ambiguous.

CONCLUSION

This report represents a large cohort of VWD families in the U.S. with extensive phenotypic and genotypic data. While co-dominant inheritance was seen in approximately 50% of families, this study highlights the complexity of VWF genetics due to the heterogeneity found in both VWF levels and bleeding tendencies amongst families with type 3 VWD.

Common VWF sequence variants associated with higher VWF and FVIII are less frequent in subjects diagnosed with type 1 VWD

BACKGROUND

Genetic variation in the VWF gene is associated with von Willebrand factor (VWF) and factor VIII (FVIII) levels in healthy individuals.

OBJECTIVES

We hypothesized that VWF sequence variants associated with higher VWF or FVIII could impact the diagnosis of type 1 von Willebrand disease (VWD).

METHODS

We examined VWF antigen (VWF:Ag), VWF ristocetin cofactor activity (VWF:RCo), VWF propeptide (VWFpp), and FVIII levels along with VWF gene sequencing in 256 healthy control and 97 type 1 VWD subjects as part of a cross-sectional study.

RESULTS

We found several VWF sequence variants (VWF c.2880G>A and VWF c.2365A>G(;)c.2385T>C, found in linkage disequilibrium) associated with higher VWF and FVIII levels in healthy controls (P < .001 for both variants). In addition, these variants were significantly more common in controls than in subjects diagnosed with type 1 VWD and VWF:Ag <30 (P < .005). The decreased variant frequencies in type 1 VWD was not seen in other VWD types. VWF:Ag, VWF:RCo, and FVIII were not statistically different in type 1 VWD subjects who had these VWF variants compared to type 1 VWD patients without them. There was no difference in ABO blood group, VWF propeptide levels (excluding subjects with known VWF clearance defects), or bleeding score using the ISTH bleeding assessment tool.

CONCLUSIONS

These data suggest that certain VWF sequence variants associated with elevated FVIII and VWF levels may protect against reduced VWF levels. These findings were independent of other pathogenic sequence variants in VWF, suggesting a possible independent effect of c.2880G>A and c.2365A>G(;)c.2385T>C on VWF levels.

Critical von Willebrand factor A1 domain residues influence type VI collagen binding

BACKGROUND

von Willebrand factor (VWF) binds to subendothelial collagen at sites of vascular injury. Laboratory testing for von Willebrand disease (VWD), however, does not always include collagen binding assays (VWF:CB) and standard VWF:CB assays use type I and/or type III collagen rather than type VI collagen.

OBJECTIVES

We report here on several mutations that exclusively alter binding to type VI collagen.

PATIENTS/METHODS

Healthy controls and index cases from the Zimmerman Program for the Molecular and Clinical Biology of VWD were analyzed for VWF antigen (VWF:Ag), VWF ristocetin cofactor activity and VWF:CB with types I, III and VI collagen. VWF gene sequencing was performed for all subjects.

RESULTS

Two healthy controls and one type 1 VWD subject were heterozygous for an A1 domain sequence variation, R1399H, and displayed a selective decreased binding to type VI collagen but not types I and III. Expression of recombinant 1399H VWF resulted in absent binding to type VI collagen. Two other VWF A1 domain mutations, S1387I and Q1402P, displayed diminished binding to type VI collagen. An 11 amino acid deletion in the A1 domain also abrogated binding to type VI collagen.

CONCLUSIONS

VWF:CB may be useful in diagnosis of VWD, as a decreased VWF:CB/VWF:Ag ratio may reflect specific loss of collagen binding ability. Mutations that exclusively affect type VI collagen binding may be associated with bleeding, yet missed by current VWF testing.

Von Willebrand disease in the United States: a perspective from Wisconsin

Von Willebrand disease (VWD) is a common bleeding disorder with prevalence in the United States of 0.01 to 1% and a prevalence in the region around Milwaukee, Wisconsin, of at least 0.025%. Care of local patients with VWD primarily occurs through our comprehensive treatment centers, although some patients are managed solely by their primary care physician or community hematologist. Type 1 VWD is the most common subtype, with more females carrying this diagnosis than males. Diagnosis and treatment in general follows guidelines outlined by the National Institutes of Health. An ongoing study, the Zimmerman Program for the Molecular and Clinical Biology of VWD, is currently enrolling patients with all VWD subtypes across the United States to better delineate the extent of VWD and correlate bleeding symptoms with laboratory findings and VWF ( Von Willebrand factor) sequence variations. Results so far have shown that VWF gene polymorphisms are common, particularly in African Americans, and may affect laboratory assays of VWF function.

Assay of the von Willebrand factor (VWF) propeptide to identify patients with type 1 von Willebrand disease with decreased VWF survival

Type 1 von Willebrand disease (VWD) is characterized by a partial quantitative deficiency of von Willebrand factor (VWF). Few VWF gene mutations have been identified that cause dominant type 1 VWD. The decreased survival of VWF in plasma has recently been identified as a novel mechanism for type 1 VWD. We report 4 families with moderately severe type 1 VWD characterized by low plasma VWF:Ag and FVIII:C levels, proportionately low VWF:RCo, and dominant inheritance. A decreased survival of VWF in affected individuals was identified with VWF half-lives of 1 to 3 hours, whereas the half-life of VWF propeptide (VWFpp) was normal. DNA sequencing revealed a single (heterozygous) VWF mutation in affected individuals, S2179F in 2 families, and W1144G in 2 families, neither of which has been previously reported. We show that the ratio of steady-state plasma VWFpp to VWF:Ag can be used to identify patients with a shortened VWF half-life. An increased ratio distinguished affected from unaffected individuals in all families. A significantly increased VWFpp/VWF:Ag ratio together with reduced VWF:Ag may indicate the presence of a true genetic defect and decreased VWF survival phenotype. This phenotype may require an altered clinical therapeutic approach, and we propose to refer to this phenotype as type-1C VWD.

Genetic mutations in von Willebrand disease identified by DHPLC and DNA sequence analysis

Von Willebrand disease (VWD) is a common inherited bleeding disorder caused by quantitative (types 1 and 3) and qualitative (type 2) defects in von Willebrand factor (VWF). The VWF gene is a large gene containing 52 exons; except for type 2 VWD, the majority of mutations causing VWD are not localized to specific exons. We have used denaturing high performance liquid chromatography (DHPLC) to scan the coding region of the VWF gene for sequence variations. Primers were designed to amplify all 52 exons while avoiding amplification of the VWF pseudogene. Exon-specific primers were designed with sequencing primers, allowing direct sequencing of each VWF exon. Sequence variations in 33 previously characterized von Willebrand disease (VWD) samples were all detected using DHPLC demonstrating the high sensitivity of this technique. In addition, we analyzed 42 patients or family members with VWD. Thirty-two novel sequence variations were identified (2 deletions, 2 nonsense, 15 missense, 6 silent, and 7 intronic), some with clear functional consequences. A previously described deletion in exon 18, 2435delC, was also found in two unrelated type 3 patients. This DHPLC and DNA sequencing technique will enable the full length assessment of the VWF gene necessary to detect mutations causing types 1 and 3 VWD.

Technical standards and guidelines: Venous thromboembolism (Factor V Leiden and prothrombin 20210G>A testing): A disease-specific supplement to the standards and guidelines for clinical genetics laboratories

These standards and guidelines are designed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to this statement does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical molecular geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the laboratory record the rationale for any significant deviation from these standards and guidelines.

Incidence of weak D in blood donors typed as D positive by the Olympus PK 7200

The incidence of weak D has been reported to be between 0.23 and 0.5 percent in Europe and 3.0 percent in the United States. All studies were performed before the introduction of monoclonal anti-D reagents. Using current commercial reagents, this study evaluated D+ samples for the presence of weak D. D+ donors, typed by the Olympus PK 7200, using diluted monoclonal blend anti-D and diluted polyclonal anti-D, were selected by sampling batches of 100 to 200 samples from the previous day's collection. Anti-D reagents used on the Olympus PK 7200 are required to detect RBCs with the weak D phenotype which do not agglutinate at immediate spin (IS) when tested with polyclonal anti-D by manual tube methods. More than 95 percent of donors tested were Caucasian. Using tube tests with two different monoclonal blend anti-D reagents and one polyclonal anti-D typing reagent, the presence or absence of the D antigen was evaluated after the IS reading. Donors found negative or weakly positive (< 2+) at IS were further typed for weak D by the IAT. The weak D samples were RHD genotyped by allele-specific PCR. Of 1,005 donors tested, 4 (0.4%) were classified as weak D by one or more anti-D reagents. Polyclonal anti-D reagent demonstrated weaker reactions when compared with the monoclonal blends. All weak D samples were found positive for exon 4, intron 4, and exon 10, a finding consistent with most D+ samples. The incidence of weak D found in this study is not significantly different from that found in earlier studies using polyclonal anti-D reagents.

Quantitative evaluation of post-bone marrow transplant engraftment status using fluorescent-labeled variable number of tandem repeats

BACKGROUND

The analysis of highly polymorphic variable number of tandem repeat (VNTR) loci is useful for the estimation of donor-host chimerism in bone marrow transplant recipients.

METHODS AND RESULTS

A rapid and sensitive engraftment assay has been developed in which the VNTR loci, D1S80, D17S5, D1S111, and apoB, are amplified with fluorescent-labeled (Cy5.5) oligonucleotide primers, followed by analysis using the Visible Genetics, Inc, OpenGene System. The degree of chimerism is then calculated by determining the percentage of host contribution to the total informative allele peak area. Reconstitution experiments and analysis of 383 posttransplantation DNA samples, isolated from 71 different bone marrow transplant recipients, were evaluated as part of assay development. Reconstitution studies showed assay linearity and sensitivity of at least 1%. Patient results were compared with a previous analysis in which unlabeled PCR products were quantified on silver-stained polyacrylamide gels. High concordance was observed between fluorescent analysis and silver-staining method in all 71 patients.

CONCLUSIONS

Fluorescent analysis offers many advantages over previous methods, including faster turnaround time, decreased DNA requirements, greater resolution and/or sensitivity, and objective interpretation.

The sensitivity of allele-specific polymerase chain reaction can obviate concern of maternal contamination when fetal samples are genotyped for immune cytopenic disorders

OBJECTIVE

Fetuses at risk for immune cytopenic disorders can be identified by molecular genotyping assays. To better understand the impact of maternal contamination on genotyping results, the levels of contamination that are routinely encountered during prenatal testing of fetal samples and the sensitivity of allele-specific polymerase chain reaction in detecting paternal alloalleles were examined.

STUDY DESIGN

Reconstitution experiments were performed to define the sensitivity of allele-specific polymerase chain reaction assays. The sensitivities of allele-specific polymerase chain reactions and polymerase chain reaction-restriction fragment length polymorphism were compared for detection of the factor V Leiden mutation.

RESULTS

A quantitative analysis of variable-number tandem repeat loci revealed maternal contamination in 4 of 56 fetal samples. Contaminating deoxyribonucleic acid compromised genotyping results when it comprised between 94% and 99% of the total deoxyribonucleic acid. Allele-specific polymerase chain reaction was found to be the more sensitive technique (0.8% sensitivity vs 13% sensitivity).

CONCLUSION

These results illustrate that allele-specific polymerase chain reaction is well suited for reliable prenatal identification of fetuses at risk of immune cytopenic disorders.

Expression of spinach nitrite reductase in Escherichia coli: site-directed mutagenesis of predicted active site amino acids

Spinach ferredoxin-nitrite reductase is a chloroplast enzyme that contains a coupled [Fe4S4]-siroheme-active site and catalyzes the six-electron reduction of nitrite to ammonia. An expression system which produced enzymatically active spinach nitrite reductase (NiR) in Escherichia coli was developed in order to study the structure-function relationships of the coupled active site using site-directed mutagenesis. The spinach NiR cDNA, without the sequences encoding the chloroplast transit peptide, was expressed as a beta-galactosidase fusion containing five additional amino acids at the N-terminus. The expressed NiR in aerobic cultures was mostly insoluble and inactive. After optimizing growth conditions, active NiR represented 0.5-1.0% of the total protein. E. coli-expressed NiR was purified approximately 200-fold to homogeneity as indicated by SDS-polyacrylamide gel electrophoresis. The expressed NiR enzyme was recognized by rabbit anti-spinach NiR antibody as visualized by Western blot analysis. The absorption spectrum of the E. coli-expressed NiR was identical to authentic spinach NiR with a Soret and alpha band at 386 and 573 nm, respectively, and a A278/A386 = 1.9. The addition of nitrite to the oxidized enzyme preparation produced the characteristic shifts in the spectrum. The specific activity for the methyl viologen-dependent reduction of nitrite of E. coli-expressed NiR was 100 U/mg and the Km determined for nitrite was 0.3 mM, which are in agreement with reported values for this enzyme. These results indicate that the E. coli-expressed NiR is fully comparable to spinach NiR in purity, catalytic activity, and physical state.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular cloning of human liver sulfite oxidase

A 2.4 kilobase cDNA clone of human sulfite oxidase was isolated from a human liver cDNA library in lambda gt10. Comparison of three sulfite oxidase sequences to several plant and fungal nitrate reductase sequences reveals a single conserved cysteine with highly conserved flanking sequences. The conserved cysteine is postulated to be a ligand of molybdenum in sulfite oxidase and nitrate reductase.

Rapid determination of platelet alloantigen genotypes by polymerase chain reaction using allele-specific primers

BACKGROUND

The technique of allele-specific polymerase chain reaction (PCR) amplification has been adapted for DNA-based human platelet alloantigen typing.

STUDY DESIGN AND METHODS

Sequence-specific primers were used to discriminate between the alleles encoding the six major human platelet alloantigens in a series of patients and normal blood donors.

RESULTS

This technique allows the direct determination of platelet antigen genotypes from genomic DNA after PCR amplification and agarose gel electrophoresis. It offers significant advantages over previously described techniques for alloantigen identification, as the additional analytical steps of restriction enzyme digestion or dot blot hybridization are not required. The results obtained with this technique correlated precisely with those derived from serologic typing and allele-specific oligonucleotide hybridization.

CONCLUSION

The use of allele-specific PCR for platelet alloantigen typing should facilitate the development of DNA-based typing in other regional blood centers and clinical laboratories.

Rat sulfite oxidase antibodies cross-react with two gene family-related proteins: albumin and vitamin D-binding protein

Screening lambda cDNA libraries from rat liver with antibody to native rat liver sulfite oxidase (RLSO) showed cross-reaction with two proteins that belong to the same gene family: serum albumin and vitamin D-binding protein. Antibodies raised against native RLSO or sodium dodecyl sulfate-denatured protein cross-reacted with these proteins by Western blot analysis. The relative effectiveness of RLSO antibody binding was estimated to be 1/5 for rat serum albumin and 1/10 for rat vitamin D-binding protein. This result was not caused by contaminating proteins in the RLSO used for immunization as the RLSO preparation did not react with rat serum albumin antibody. RLSO antibodies, selected for their ability to bind rat serum albumin immobilized on nitrocellulose, recognized both rat serum albumin and RLSO. RLSO antibody, with albumin-reactive antibody removed, still recognized vitamin D-binding protein, suggesting that multiple determinants specific to each protein are involved in the cross-reaction. Comparison of RLSO antibody binding to the rat and human proteins indicated that the determinants were species-specific. cDNA clones identified by screening cDNA libraries with RLSO antibody demonstrated that these determinants reside in the C-terminal domain of these proteins. These results suggest that these proteins contain some common immunological features and may be evolutionarily related.

L-tryptophan injection fails to alter nutrient selection by rats

Nutritional studies on rats given a choice between two diets differing in protein content have led to the proposal that brain 5-HT content regulates protein intake [2]. Pharmacologic studies under similar conditions of dietary self-selection suggest that brain 5-HT controls carbohydrate intake [41]. We tested the effect of elevating brain 5-HT via tryptophan injection (100 mg/kg) on short-term food intake and selection by rats choosing between two diets differing in protein and carbohydrate content. Under these conditions neither total food intake nor protein and carbohydrate selection were affected despite increases of 50% in brain concentrations of 5-HT and 5-HIAA. The effect of Trp administration was selective to serotonin metabolism as brain concentrations of NE, DA and DOPAC were not affected. These results suggest that alterations in brain 5-HT content which may occur following meal ingestion may not be of physiological importance in regulating nutrient intake and selection.