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Sadler B, Christopherson PA, Perry CL, Bellissimo DB, Haberichter SL, Haller G, Antunes L, Flood VH, Di Paola J, Montgomery RR. Characterization of copy-number variants in a large cohort of patients with von Willebrand disease reveals a relationship between disrupted regions and disease type. Res Pract Thromb Haemost 2023; 7:102232. [PMID: 38077814 PMCID: PMC10704516 DOI: 10.1016/j.rpth.2023.102232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/13/2023] [Accepted: 10/01/2023] [Indexed: 02/12/2024] Open
Abstract
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.
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Affiliation(s)
- Brooke Sadler
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | | | - Daniel B. Bellissimo
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sandra L. Haberichter
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Pediatric Hematology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gabe Haller
- Department of Neurosurgery, Washington University, St. Louis, Missouri, USA
| | - Lilian Antunes
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Veronica H. Flood
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Pediatric Hematology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jorge Di Paola
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert R. Montgomery
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Pediatric Hematology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Zimmerman Program Investigators
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Pediatric Hematology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Department of Neurosurgery, Washington University, St. Louis, Missouri, USA
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Jalal MM, Mir R, Hamadi A, Altayar MA, Elfaki I, Barnawi J, Alkayyal AA, Amr M, Hadeel J, Moawadh MS, Alsaedi BSO, Alhelali MH, Yousif A. Association of Genetic and Allelic Variants of Von Willebrand Factor (VWF), Glutathione S-Transferase and Tumor Necrosis Factor Alpha with Ischemic Stroke Susceptibility and Progression in the Saudi Population. Life (Basel) 2023; 13:life13051200. [PMID: 37240845 DOI: 10.3390/life13051200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Stroke is a key cerebrovascular disease and important cause of death and disability worldwide, including in the kingdom of Saudi Arabia (KSA). It has a large economic burden and serious socioeconomic impacts on patients, their families and the community. The incidence of ischemic stroke is probably increased by the interaction of GSTT1 and GSTM1 null genotypes with high blood pressure, diabetes and cigarette smoking. The roles of VWF, GSTs and TNF-alpha gene variations in the induction of stroke are still uncertain and require further examination. In the current study, we studied the associations of SNPs in the genes VWF, GSTs and TNF-alpha with stroke in the Saudi population. Genotyping was performed using the ARMS -PCR for TNF-alpha, AS-PCR for VWF and multiplex PCR for GSTs. The study included 210 study subjects: 100 stroke cases and 110 healthy controls. We obtained significant distributions of VWF rs61748511 T > C, TNF-alpha rs1800629 G > A and GST rs4025935 and rs71748309 genotypes between stroke cases and the healthy controls (p < 0.05). The results also indicated that the TNF-alpha A allele was associated with risk of stroke with odd ratio (OR) = 2.22 and risk ratio = RR 2.47, p < 0.05. Similarly, the VWF-TC genotype and C allele were strongly linked with stroke with OR = 8.12 and RR 4.7, p < 0.05. In addition, GSTT1 and GSTT1 null genotype was strongly associated with stroke predisposition with OR = 8.30 and RR = 2.25, p < 0.0001. We conclude that there is a possible strong association between the VWF-T > C, TNF-alpha G > A, GSTT1 gene variants and ischemic stroke susceptibility in the Saudi population. However, future well-designed and large-scale case-control studies on protein-protein interactions and protein functional studies are required to verify these findings and examine the effects of these SNPs on these proteins.
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Affiliation(s)
- Mohammed M Jalal
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
- Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Rashid Mir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
- Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdullah Hamadi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
- Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Malik A Altayar
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
- Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Jameel Barnawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
- Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Mouminah Amr
- Neuroscience Center, King Abdullah Medical Complex, Jeddah 23816, Saudi Arabia
| | - Jabali Hadeel
- Department of Radiology, King Abdullah Medical Complex, Jeddah 23816, Saudi Arabia
| | - Mamdoh S Moawadh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Basim S O Alsaedi
- Department of Statistics, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Marwan H Alhelali
- Department of Statistics, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Aadil Yousif
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
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Manderstedt E, Lind-Halldén C, Lethagen S, Halldén C. Common and Rare Variants in Genes Associated with von Willebrand Factor Level Variation: No Accumulation of Rare Variants in Swedish von Willebrand Disease Patients. TH OPEN 2020; 4:e322-e331. [PMID: 33145474 PMCID: PMC7603419 DOI: 10.1055/s-0040-1718885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/15/2020] [Indexed: 10/31/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified genes that affect plasma von Willebrand factor (VWF) levels. ABO showed a strong effect, whereas smaller effects were seen for VWF , STXBP5 , STAB2 , SCARA5 , STX2 , TC2N , and CLEC4M . This study screened comprehensively for both common and rare variants in these eight genes by resequencing their coding sequences in 104 Swedish von Willebrand disease (VWD) patients. The common variants previously associated with the VWF level were all accumulated in the VWD patients compared to three control populations. The strongest effect was detected for blood group O coded for by the ABO gene (71 vs. 38% of genotypes). The other seven VWF level associated alleles were enriched in the VWD population compared to control populations, but the differences were small and not significant. The sequencing detected a total of 146 variants in the eight genes. Excluding 70 variants in VWF , 76 variants remained. Of the 76 variants, 54 had allele frequencies > 0.5% and have therefore been investigated for their association with the VWF level in previous GWAS. The remaining 22 variants with frequencies < 0.5% are less likely to have been evaluated previously. PolyPhen2 classified 3 out of the 22 variants as probably or possibly damaging (two in STAB2 and one in STX2 ); the others were either synonymous or benign. No accumulation of low frequency (0.05-0.5%) or rare variants (<0.05%) in the VWD population compared to the gnomAD (Genome Aggregation Database) population was detected. Thus, rare variants in these genes do not contribute to the low VWF levels observed in VWD patients.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Christina Lind-Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Stefan Lethagen
- Department for Coagulation Disorders, University Hospital, Malmö, Sweden.,National Hemophilia Center, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.,Sobi, Stockholm, Sweden
| | - Christer Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
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In silico features of ADAMTS13 contributing to plasmatic ADAMTS13 levels in neonates with congenital heart disease. Thromb Res 2020; 193:66-76. [PMID: 32531546 DOI: 10.1016/j.thromres.2020.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/24/2020] [Accepted: 05/26/2020] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Risk factors contributing to heightened thrombosis in pediatric congenital heart disease (CHD) patients are not fully understood. Among the neonatal CHD population, those presenting with single ventricular physiology are at the highest risk for perioperative thrombosis. The von Willebrand factor and ADAMTS13 interactions have emerged as causative risk factors for pediatric stroke and could contribute to heightened thrombosis in CHD neonates. METHODS This study investigates a cohort of children with single ventricle physiology and undergoing cardiac surgery, during which some patients developed thrombosis. In this cohort, we analyzed the relationship of several molecular features of ADAMTS13 with the plasma and activity levels in patients at risk of thrombosis. Additionally, in light of the natural antithrombotic activity of ADAMTS13, we have sequenced the ADAMTS13 gene for each patient and evaluated the role of genetic variants in determining the plasma ADAMTS13 levels using a series of in silico tools including Hidden Markov Models, EVmutation, and Rosetta. RESULTS Lower ADAMTS13 levels were found in patients that developed thrombosis. A novel in silico analysis to assess haplotype effect of co-occurring variants identified alterations in relative surface area and solvation energy as important contributors. Our analysis suggested that beneficial or deleterious effect of a variant can be reasonably predicted by comprehensive analysis of in silico assessment and in vitro and/or in vivo data. CONCLUSION Findings from this study add to our understanding the role of genetic features of ADAMTS13 in patients at high risk of thrombosis related to an imbalanced relation between VWF and ADAMTS13.
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