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Ramanan R, Verstraete A, Van Laer C, Freson K. Implementation and clinical utility of multigene panels for bleeding, platelet, and thrombotic disorders. J Thromb Haemost 2025:S1538-7836(25)00277-6. [PMID: 40345666 DOI: 10.1016/j.jtha.2025.04.026] [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: 02/24/2025] [Revised: 04/21/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025]
Abstract
High-throughput sequencing, with its capacity to simultaneously sequence large volumes of genomic data, has evolved from a research-focused technology to a clinical tool. This review outlines key steps in the development of a clinical hemostasis and thrombosis genetics service leveraging a multigene panel. We discuss its value across inherited bleeding, platelet, and thrombotic disorders (BPTDs) in the context of published studies utilizing multigene panels for these conditions. Benefits of sequencing include establishing a diagnosis through the simultaneous assessment of multiple candidate genes, exclusion of genocopies, and predictions of phenotype to deliver targeted therapy. The presence of concomitant variants may modify phenotype; however, predictions on disease course from oligogenic modifiers are not yet used to guide patient care or counseling. Limitations in the widespread roll-out of multigene panels for clinical diagnosis of BPTDs exist. These challenges relate to detection of structural variants, variable diagnostic hit rates, and management of incidental findings. Variants of uncertain significance also frustrate diagnostic yield. Family segregation studies, in vitro characterization, and protein modeling aid interpretation of variant pathogenicity. Although multigene panels offer substantial opportunities to improve BPTD diagnostics, their implementation should be guided by appropriate expertise and in conjunction with clinical research to ensure safe and ethical care.
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Affiliation(s)
- Radha Ramanan
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia; Department of Human Molecular Pathology, Alfred Hospital, Melbourne, Victoria, Australia.
| | - Andreas Verstraete
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Christine Van Laer
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; Clinical Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Kathleen Freson
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
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Tischer A, Moon-Tasson L, Auton M. Structure-resolved dynamics of type 2M von Willebrand disease. J Thromb Haemost 2025; 23:1215-1228. [PMID: 39756657 PMCID: PMC11972889 DOI: 10.1016/j.jtha.2024.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/22/2024] [Accepted: 12/20/2024] [Indexed: 01/07/2025]
Abstract
BACKGROUND Genetically determined amino acid substitutions in the platelet adhesive A1 domain alter von Willebrand factor's (VWF) platelet agglutination competence, resulting in both gain- (type 2B) and loss-of-function (type 2M) phenotypes of von Willebrand disease. Prior studies of variants in both phenotypes revealed defects in secondary structure that altered stability and folding of the domain. An intriguing observation was that loss of function arose from both misfolding of A1 and, in a few cases, hyperstabilization of the native structure. OBJECTIVES To fully understand the 2M phenotype, we thoroughly investigated the structure/function relationships of 15 additional type 2M variants and 2 polymorphisms in the A1 domain. METHODS These variants were characterized using circular dichroism, fluorescence, calorimetry, hydrogen-deuterium exchange mass spectrometry, surface plasmon resonance, and platelet adhesion under shear flow. RESULTS Six variants were natively folded, with 4 being hyperstabilized. Nine variants disordered A1, causing a loss in α-helical structure and unfolding enthalpy. GPIbα binding affinity and platelet adhesion dynamics were highly correlated to helical structure. Hydrogen-deuterium exchange resolved specific C-terminal secondary structure elements that differentially diminish the GPIbα binding affinity of A1. These localized structural perturbations were highly correlated to GPIbα binding affinity and shear-dependent platelet adhesion. CONCLUSION While hyperstabilized dynamics in A1 do impair stable platelet attachment to VWF under flow, variant-induced localized disorder in specific regions of the domain misfolds A1 and abrogates platelet adhesion. These 2 opposing conformational properties represent 2 structural classes of VWF that drive the loss-of-function phenotype that is type 2M von Willebrand disease.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Laurie Moon-Tasson
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.
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Kartal-Kaess M, Pinto F, Labarque V, de Kovel M, Nolan B, Carcao M, d'Oiron R, Mikkelsen TS, Ljung R, Andersson NG, Pediatric Network on Hemophilia Management (PedNet) Study Group. Hemophilia B Leyden: characteristics and natural history in the International Pediatric Network of Hemophilia Management Registry. J Thromb Haemost 2025; 23:921-927. [PMID: 39742973 DOI: 10.1016/j.jtha.2024.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Collaborators] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 11/20/2024] [Accepted: 12/23/2024] [Indexed: 01/04/2025]
Abstract
BACKGROUND A unique form of hemophilia B (HB) is HB Leyden. We evaluated the international Pediatric Network on Hemophilia Management Registry (PedNet) database to explore the natural history of HB Leyden, investigate genotype-phenotype associations, and guide clinical decision-making. OBJECTIVES To assess the association between genetic variants, endogenous factor (F)IX levels over time, treatment, and bleeding phenotype in children with HB Leyden. METHODS Data on genetic variants, FIX levels at diagnosis and over time, bleeding, and treatment details were extracted from the international PedNet in children with hemophilia born since 2000. RESULTS Of 457 individuals with HB, 24 showed an HB Leyden genotype. The most frequent F9 variant was c.-35G>A, affecting 14 individuals, followed by c.-35G>C (n = 4), c.-49T>A (n = 2), and c.-52C>T, c.-34A>G, and c.-22delT (n = 1 each). Major clinical differences in bleeding and treatment modality were observed when comparing c.-35G>A with non-c.-35G>A genotypes. For all children with a c.-35G>A genotype, FIX levels increased before the age of 4 years but did not normalize over time, irrespective of initial severity. In children with non-c.-35G>A genotypes, an increase in FIX was less common (4/9) and occurred later. CONCLUSION HB Leyden is caused by the variant c.-35G>A in >50% of cases in whom a FIX increase occurs at very young ages, which is associated with low bleeding rates. This contrasts with the phenotype of individuals with HB Leyden due to a non-c.-35G>A variant. Our study may thus help guide clinical decision-making in this rare HB entity.
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Affiliation(s)
- Mutlu Kartal-Kaess
- Division of Pediatric Hematology & Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
| | - Fernando Pinto
- Department of Haematology, Royal Hospital for Children, Glasgow, United Kingdom
| | - Veerle Labarque
- Department of Pediatrics, Pediatric Hemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | | | - Beatrice Nolan
- Department of Paediatric Haemtaology, Children's Coagulation Centre, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Manuel Carcao
- Division of Haematology, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roseline d'Oiron
- Centre de Référence de l'Hémophilie et des Maladies Hémorragiques Rares, Hôpital Bicêtre Assistance Publique-Hôpitaux de Paris, et INSERM Hémostase inflammation thrombose U1176, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | | | - Rolf Ljung
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Nadine G Andersson
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Department for Thrombosis and Hemostasis, Skåne University Hospital, Malmö, Sweden.
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Collaborators
Mt Alvarèz Román, O Benitez Hidalgo, J Blatny, M Bührlen, M Carvalho, H Chambost, A Rosa Cid, C Oudot, C Escuriola-Ettingshausen, K Fischer, V Labarque, H Knudsen, N Gretenkort Andersson, R Ljung, C Königs, M Koskenvuo, C Male, T Stamm Mikkelsen, A Molinari, J Motwani, B Nolan, R d'Oiron, J Oldenburg, M Olivieri, H Pergantou, F Pinto, S Ranta, M Kartal-Kaess, E Zápotocká, G Kenet, M Carcao, G Rivard,
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4
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Popp NA, Powell RL, Wheelock MK, Holmes KJ, Zapp BD, Sheldon KM, Fletcher SN, Wu X, Fayer S, Rubin AF, Lannert KW, Chang AT, Sheehan JP, Johnsen JM, Fowler DM. Multiplex, multimodal mapping of variant effects in secreted proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.04.01.587474. [PMID: 39975210 PMCID: PMC11838247 DOI: 10.1101/2024.04.01.587474] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Despite widespread advances in DNA sequencing, the functional consequences of most genetic variants remain poorly understood. Multiplexed Assays of Variant Effect (MAVEs) can measure the function of variants at scale, and are beginning to address this problem. However, MAVEs cannot readily be applied to the ~10% of human genes encoding secreted proteins. We developed a flexible, scalable human cell surface display method, Multiplexed Surface Tethering of Extracellular Proteins (MultiSTEP), to measure secreted protein variant effects. We used MultiSTEP to study the consequences of missense variation in coagulation factor IX (FIX), a serine protease where genetic variation can cause hemophilia B. We combined MultiSTEP with a panel of antibodies to detect FIX secretion and post-translational modification, measuring a total of 44,816 effects for 436 synonymous variants and 8,528 of the 8,759 possible missense variants. 49.6% of possible F9 missense variants impacted secretion, post-translational modification, or both. We also identified functional constraints on secretion within the signal peptide and for nearly all variants that caused gain or loss of cysteine. Secretion scores correlated strongly with FIX levels in hemophilia B and revealed that loss of secretion variants are particularly likely to cause severe disease. Integration of the secretion and post-translational modification scores enabled reclassification of 63.1% of F9 variants of uncertain significance in the My Life, Our Future hemophilia genotyping project. Lastly, we showed that MultiSTEP can be applied to a wide variety of secreted proteins. Thus, MultiSTEP is a multiplexed, multimodal, and generalizable method for systematically assessing variant effects in secreted proteins at scale.
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Affiliation(s)
- Nicholas A. Popp
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Rachel L. Powell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Melinda K. Wheelock
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kristen J. Holmes
- Division of Hematology and Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Brendan D. Zapp
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kathryn M. Sheldon
- Division of Hematology and Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Xiaoping Wu
- Cell Marker Laboratory, Seattle Children’s Hospital, Seattle, WA
| | - Shawn Fayer
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Alan F. Rubin
- Bioinformatics Division, WEHI, Parkville, VIC, AU
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, AU
| | - Kerry W. Lannert
- Division of Hematology and Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Alexis T. Chang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - John P. Sheehan
- Division of Hematology, Medical Oncology, and Palliative Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jill M. Johnsen
- Division of Hematology and Oncology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest, Seattle, WA, USA
- Washington Center for Bleeding Disorders, Seattle, WA
| | - Douglas M. Fowler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Bioengineering, University of Washington School of Medicine, Seattle, WA
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5
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Liu B, Zhou L, Cao L, Liu H, Tong L, Zhang Z, Shen H, Ruan C, Zhou Y, Jiang M. Optical genome mapping identified deletions, inversions, and insertions in hemophilia. Blood Adv 2025; 9:360-364. [PMID: 39602656 PMCID: PMC11787463 DOI: 10.1182/bloodadvances.2024014762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 11/08/2024] [Accepted: 11/08/2024] [Indexed: 11/29/2024] Open
Affiliation(s)
- Boyan Liu
- Hematology Department, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Lu Zhou
- Hematology Department, Affiliated Hospital of Nantong University, Nantong, China
| | - Lijuan Cao
- National Clinical Medical Research Center of Blood Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Haoning Liu
- Hematology Department, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Laigen Tong
- Hematology Department, Affiliated Hospital of Nantong University, Nantong, China
| | - Zichan Zhang
- Hematology Department, Affiliated Hospital of Nantong University, Nantong, China
| | - Hongjie Shen
- National Clinical Medical Research Center of Blood Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Changgeng Ruan
- National Clinical Medical Research Center of Blood Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yafeng Zhou
- Department of Cardiology, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
| | - Miao Jiang
- Hematology Department, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
- National Clinical Medical Research Center of Blood Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Cardiology, The Fourth Affiliated Hospital of Soochow University, Suzhou, China
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Bos MHA, van Diest RE, Monroe DM. Blood coagulation factor IX: structural insights impacting hemophilia B therapy. Blood 2024; 144:2198-2210. [PMID: 38996207 PMCID: PMC11600082 DOI: 10.1182/blood.2023023276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024] Open
Abstract
ABSTRACT Coagulation factor IX plays a central role in hemostasis through interaction with factor VIIIa to form a factor X-activating complex at the site of injury. The absence of factor IX activity results in the bleeding disorder hemophilia B. This absence of activity can arise either from a lack of circulating factor IX protein or mutations that decrease the activity of factor IX. This review focuses on analyzing the structure of factor IX with respect to molecular mechanisms that are at the basis of factor IX function. The proteolytic activation of factor IX to form activated factor IX(a) and subsequent structural rearrangements are insufficient to generate the fully active factor IXa. Multiple specific interactions between factor IXa, the cofactor VIIIa, and the physiological substrate factor X further alter the factor IXa structure to achieve the full enzymatic activity of factor IXa. Factor IXa also interacts with inhibitors, extravascular proteins, and cellular receptors that clear factor IX(a) from the circulation. Hemophilia B is treated by replacement of the missing factor IX by plasma-derived protein, a recombinant bioequivalent, or via gene therapy. An understanding of how the function of factor IX is tied to structure leads to modified forms of factor IX that have increased residence time in circulation, higher functional activity, protection from inhibition, and even activity in the absence of factor VIIIa. These modified forms of factor IX have the potential to significantly improve therapy for patients with hemophilia B.
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Affiliation(s)
- Mettine H. A. Bos
- Department of Internal Medicine, Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, The Netherlands
| | - Rianne E. van Diest
- Department of Internal Medicine, Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, The Netherlands
| | - Dougald M. Monroe
- Department of Medicine and UNC Blood Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
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Sacco M, Testa MF, Ferretti A, Basso M, Lancellotti S, Tardugno M, Di Gennaro L, Concolino P, Minucci A, Spoliti C, Branchini A, De Cristofaro R. An integrated multitool analysis contributes elements to interpreting unclassified factor IX missense variants associated with hemophilia B. J Thromb Haemost 2024; 22:2724-2738. [PMID: 39019441 DOI: 10.1016/j.jtha.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/10/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Dissection of genotype-phenotype relationships in hemophilia B (HB) is particularly relevant for challenging (mild HB) or for HB-associated but unclassified factor (F)IX missense variants. OBJECTIVE To contribute elements to interpret unclassified HB-associated FIX missense variants by a multiple-level approach upon identification of a reported, but uncharacterized, FIX missense variant associated with mild HB. METHODS Molecular modeling of wild-type and V92A FIX variants, expression studies in HEK293 cells with evaluation of protein (ELISA, western blotting) and activity (activated partial thromboplastin time-based/chromogenic assays) levels after recombinant expression, and multiple prediction tools. RESULTS The F9(NM_000133.4):c.275T>C (p.V92A) variant was found in a mild HB patient (antigen, 45.4 U/dL; coagulant activity, 23.6 IU/dL; specific activity, 0.52). Newly generated molecular models showed alterations in Gla/EGF1-EGF2 domain conformation impacting Ca++ affinity and protein-protein interactions with activated factor XI (FXIa). Multitool analysis indicated a moderate impact on protein structure/function of the valine-to-alanine substitution, in accordance with patient and modeling data. Expression studies on the V92A variant showed a specific activity (0.49 ± 0.07; wild-type, 1.0 ± 0.1) recapitulating that of the natural variant, and pointed toward a moderate activation impairment as the main determinant underlying the p.V92A defect. The validated multitool approach, integrated with evidence-based data, was challenged on a panel (n = 9) of unclassified FIX missense variants, which resulted in inferred protein (secretion/function) outputs and HB severity. CONCLUSION The rational integration of multitool and multiparameter analyses contributed elements to interpret genotype/phenotype relationships of unclassified FIX missense variants, with implications for diagnosis, management, and treatment of HB patients, and potentially translatable into other human disorders.
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Affiliation(s)
- Monica Sacco
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Antonietta Ferretti
- Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy
| | - Maria Basso
- Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy
| | - Stefano Lancellotti
- Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy
| | - Maira Tardugno
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy
| | - Leonardo Di Gennaro
- Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy
| | - Paola Concolino
- Molecular and Genomic Diagnostics Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Angelo Minucci
- Molecular and Genomic Diagnostics Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Claudia Spoliti
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Raimondo De Cristofaro
- Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy; Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy.
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Munkhuu P, Bazarragchaa M, Ichinkhorloo P, Yoo K, Ayush E, Batjargal O, Namjil E, Jav S, Purevdorj E, Lkhagvasuren S. The genetic analysis of eight families with hemophilia B in Mongolia: Identification of two novel mutation. Mol Genet Genomic Med 2024; 12:e2495. [PMID: 39268837 PMCID: PMC11393770 DOI: 10.1002/mgg3.2495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND This study aimed to conduct molecular diagnostics among individuals with hemophilia B (HB) and carriers of hemophilia in Mongolia. METHODS Eight patients (six severe, two mild) with HB and their 12 female relatives were enrolled from eight families. Sanger sequence was performed for mutation identification. The questionnaire survey was conducted to evaluate carrier symptoms in female relatives. RESULTS Two families had a history of HB. A total of five different variants (c.223C > T; c.344A > G; c.464G > C; c.187_188del; and c.1314_1314delA) were identified in six patients with severe HB. Of these, two (c.187_188del and c.1314_1314delA) were novel. No variant in the entire F9 was found in two patients with mild HB. Nonsense c.223C > T (p.Arg75*) mutation was detected in two unrelated patients. Carrier testing identified five mothers as carriers, while one younger sister was a non-carrier. The carrier status of six female relatives of the two mild patients remained undetermined. By questionnaire survey, only one of the five genetically identified carriers displayed noticeable symptoms of being a carrier. CONCLUSION The novel variants c.187_188del and c.1314_1314delA can cause severe hemophilia B. This study did not observe a significant association between symptoms and carrier status in the five carriers.
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Affiliation(s)
- Purevdorj Munkhuu
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Munkhtsetseg Bazarragchaa
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Purevdorj Ichinkhorloo
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Ki‐Young Yoo
- HematologyKorean Hemophilia FoundationSeoulSouth Korea
| | - Enkh‐Amar Ayush
- Department of Gastroenterology, School of MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Ochbadrakh Batjargal
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | | | - Sarantuya Jav
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Erkhembulgan Purevdorj
- Department of Molecular Biology and Genetics, School of Bio‐MedicineMongolian National University of Medical ScienceUlaanbaatarMongolia
| | - Sodnomtsogt Lkhagvasuren
- Division for Science and TechnologyMongolian National University of Medical SciencesUlaanbaatarMongolia
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Tonetto E, Cucci A, Follenzi A, Bernardi F, Pinotti M, Balestra D. DNA base editing corrects common hemophilia A mutations and restores factor VIII expression in in vitro and ex vivo models. J Thromb Haemost 2024; 22:2171-2183. [PMID: 38718928 DOI: 10.1016/j.jtha.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Replacement and nonreplacement therapies effectively control bleeding in hemophilia A (HA) but imply lifelong interventions. Authorized gene addition therapy could provide a cure but still poses questions on durability. FVIIIgene correction would definitively restore factor (F)VIII production, as shown in animal models through nuclease-mediated homologous recombination (HR). However, low efficiency and potential off-target double-strand break still limit HR translatability. OBJECTIVES To correct common model single point mutations leading to severe HA through the recently developed double-strand break/HR-independent base editing (BE) and prime editing (PE) approaches. METHODS Screening for efficacy of BE/PE systems in HEK293T cells transiently expressing FVIII variants and validation at DNA (sequencing) and protein (enzyme-linked immunosorbent assay; activated partial thromboplastin time) level in stable clones. Evaluation of rescue in engineered blood outgrowth endothelial cells by lentiviral-mediated delivery of BE. RESULTS Transient assays identified the best-performing BE/PE systems for each variant, with the highest rescue of FVIII expression (up to 25% of wild-type recombinant FVIII) for the p.R2166∗ and p.R2228Q mutations. In stable clones, we demonstrated that the mutation reversion on DNA (∼24%) was consistent with the rescue of FVIII secretion and activity of 20% to 30%. The lentiviral-mediated delivery of the selected BE systems was attempted in engineered blood outgrowth endothelial cells harboring the p.R2166∗ and p.R2228Q variants, which led to an appreciable and dose-dependent rescue of secreted functional FVIII. CONCLUSION Overall data provide the first proof-of-concept for effective BE/PE-mediated correction of HA-causing mutations, which encourage studies in mouse models to develop a personalized cure for large cohorts of patients through a single intervention.
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Affiliation(s)
- Elena Tonetto
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Alessia Cucci
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Antonia Follenzi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Novara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology and Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, Ferrara, Italy
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Rawal A, Kidchob C, Ou J, Sauna ZE. Application of machine learning approaches for predicting hemophilia A severity. J Thromb Haemost 2024; 22:1909-1918. [PMID: 38718927 DOI: 10.1016/j.jtha.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND Hemophilia A (HA) is an X-linked congenital bleeding disorder, which leads to deficiency of clotting factor (F) VIII. It mostly affects males, and females are considered carriers. However, it is now recognized that variants of F8 in females can result in HA. Nonetheless, most females go undiagnosed and untreated for HA, and their bleeding complications are attributed to other causes. Predicting the severity of HA for female patients can provide valuable insights for treating the conditions associated with the disease, such as heavy bleeding. OBJECTIVES To predict the severity of HA based on F8 genotype using a machine learning (ML) approach. METHODS Using multiple datasets of variants in the F8 and disease severity from various repositories, we derived the sequence for the FVIII protein. Using the derived sequences, we used ML models to predict the severity of HA in female patients. RESULTS Utilizing different classification models, we highlight the validity of the datasets and our approach with predictive F1 scores of 0.88, 0.99, 0.93, 0.99, and 0.90 for all the validation sets. CONCLUSION Although with some limitations, ML-based approaches demonstrated the successful prediction of disease severity in female HA patients based on variants in the F8. This study confirms previous research findings that ML can help predict the severity of hemophilia. These results can be valuable for future studies in achieving better treatment and clinical outcomes for female patients with HA, which is an urgent unmet need.
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Affiliation(s)
- Atul Rawal
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Christopher Kidchob
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jiayi Ou
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Zuben E Sauna
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA.
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11
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Mårtensson A, Letelier A, Manderstedt E, Glosli H, Ljung R. Origin of pathogenic variant and mosaicism in families with a sporadic case of haemophilia B. Haemophilia 2024; 30:774-779. [PMID: 38632836 DOI: 10.1111/hae.15019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
INTRODUCTION Of newly diagnosed cases of haemophilia B, the proportion of sporadic cases is usually 50% of severe cases and 25% of moderate/mild cases. However, cases presumed to be sporadic due to family history may not always be sporadic. Few case reports have been published on mosaicism in haemophilia B. AIM The present study aimed to trace the origin of the pathogenic variant in a well-defined cohort of sporadic cases of haemophilia B by haplotyping markers. It also aimed to determine the frequency of mosaicism in presumed non-carrier mothers. METHODS The study group was 40 families, each with a sporadic case of haemophilia B analysed in two-to-three generations by Sanger sequencing, haplotyping and using the sensitive droplet digital polymerase chain reaction (ddPCR) technique. RESULTS In 31/40 (78%) of the families, the mother carried the same pathogenic variant as her son, while Sanger sequencing showed that 9/40 (22%) of the mothers did not carry this variant. Of these variants, 2/9 (22%) were shown to be mosaics by using the ddPCR technique. 16/21 carrier mothers, with samples from three generations available, had a de novo pathogenic variant of which 14 derived from the healthy maternal grandfather. CONCLUSION The origin of the pathogenic variant in sporadic cases of haemophilia B is most often found in the X-chromosome derived from the maternal grandfather or, less often, from the maternal grandmother. Mosaic females seem to be found at the same frequency as in haemophilia A but at a lower percentage of the pathogenic variant.
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Affiliation(s)
- Annika Mårtensson
- Department of Clinical Sciences Lund - Paediatrics, Lund University, Lund, Sweden
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Anna Letelier
- Department of Clinical Sciences Lund - Paediatrics, Lund University, Lund, Sweden
| | - Eric Manderstedt
- Department of Clinical Sciences, Center for Primary Health Care Research, Lund University, Lund, Sweden
| | - Heidi Glosli
- Centre for Rare Disorders, Oslo University Hospital, Oslo, Norway
| | - Rolf Ljung
- Department of Clinical Sciences Lund - Paediatrics, Lund University, Lund, Sweden
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12
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Alzahrani HA, Warsi A, Mullah-Ali A, Alotaibi G, Abu-Riash M, Alshahrani M, Siddiqui M, Owaidah T, Hashmi S. Consensus-Based Expert Recommendations on the Management of Hemophilia A in the Gulf Region. Acta Haematol 2024; 148:91-104. [PMID: 38565097 PMCID: PMC11809456 DOI: 10.1159/000538400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Hemophilia A presents a significant health challenge in the Gulf region, where it has an especially high prevalence. There are several unmet needs associated with the management of hemophilia A in the region. The aim of this manuscript was to contextualize unmet management needs, provide recommendations to optimize care, and specify requirements for the establishment of gene therapy centers in the region. SUMMARY An expert panel was assembled comprising ten clinical hematologists from Kuwait, Oman, Saudi Arabia, and the UAE. The Delphi methodology was used to obtain a consensus on statements relating to several aspects of hemophilia A. A consensus was reached for all statements by means of an online, anonymized voting system. The consensus statements pertain to screening and diagnosis, treatment approaches, and requirements for the implementation of gene therapy. KEY MESSAGES There are significant challenges that hinder the optimal management of hemophilia A in the Gulf region. The consensus statements presented provide specific recommendations to improve diagnostic and treatment approaches, promote multidisciplinary care, and optimize regional data generation and reporting. These statements also delineate the requirements for the establishment of gene therapy centers for hemophilia A in the region. BACKGROUND Hemophilia A presents a significant health challenge in the Gulf region, where it has an especially high prevalence. There are several unmet needs associated with the management of hemophilia A in the region. The aim of this manuscript was to contextualize unmet management needs, provide recommendations to optimize care, and specify requirements for the establishment of gene therapy centers in the region. SUMMARY An expert panel was assembled comprising ten clinical hematologists from Kuwait, Oman, Saudi Arabia, and the UAE. The Delphi methodology was used to obtain a consensus on statements relating to several aspects of hemophilia A. A consensus was reached for all statements by means of an online, anonymized voting system. The consensus statements pertain to screening and diagnosis, treatment approaches, and requirements for the implementation of gene therapy. KEY MESSAGES There are significant challenges that hinder the optimal management of hemophilia A in the Gulf region. The consensus statements presented provide specific recommendations to improve diagnostic and treatment approaches, promote multidisciplinary care, and optimize regional data generation and reporting. These statements also delineate the requirements for the establishment of gene therapy centers for hemophilia A in the region.
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Affiliation(s)
- Hazzaa Abdulla Alzahrani
- Consultant Hematology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ashraf Warsi
- Department of Oncology, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Ali Mullah-Ali
- Consultant Pediatric Hematology, National Bank of Kuwait Specialized Hospital for Children, Shuwaikh Industrial, Kuwait
| | - Ghazi Alotaibi
- Department of Medicine (Oncology Center), King Saud University, Riyadh, Saudi Arabia
| | - Mahmoud Abu-Riash
- Senior Clinical Specialist Hematology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammad Alshahrani
- Consultant Pediatric Hematology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mustaqeem Siddiqui
- Consultant Hematology, Sheikh Shakhbout Medical City, Abu Dhabi, United Arab Emirates
| | - Tarek Owaidah
- Consultant Hemato-Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shahrukh Hashmi
- Consultant Hematology, Sheikh Shakhbout Medical City, Abu Dhabi, United Arab Emirates
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13
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Zhang H, Xin M, Lin L, Chen C, Balestra D, Ding Q. Pleiotropic effects of different exonic nucleotide changes at the same position contribute to hemophilia B phenotypic variation. J Thromb Haemost 2024; 22:975-989. [PMID: 38184202 DOI: 10.1016/j.jtha.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND The disease-causing effects of genetic variations often depend on their location within a gene. Exonic changes generally lead to alterations in protein production, secretion, activity, or clearance. However, owing to the overlap between proteins and splicing codes, missense variants can also affect messenger RNA splicing, thus adding a layer of complexity and influencing disease phenotypes. OBJECTIVES To extensively characterize a panel of 13 exonic variants in the F9 gene occurring at 6 different factor IX positions and associated with varying severities of hemophilia B (HB). METHODS Computational predictions, splicing analysis, and recombinant factor IX assays were exploited to characterize F9 variants. RESULTS We demonstrated that 5 (38%) of 13 selected F9 exonic variants have pleiotropic effects. Although bioinformatic approaches accurately classified effects, extensive experimental assays were required to elucidate and deepen the molecular mechanisms underlying the pleiotropic effects. Importantly, their characterization was instrumental in developing tailored RNA therapeutics based on engineered U7 small nuclear RNA to mask cryptic splice sites and compensatory U1 small nuclear RNA to enhance exon definition. CONCLUSION Overall, albeit a multitool bioinformatic approach suggested the molecular effects of multiple HB variants, the deep investigation of molecular mechanisms revealed insights into the HB phenotype-genotype relationship, enabling accurate classification of HB variants. Importantly, knowledge of molecular mechanisms allowed the development of tailored RNA therapeutics, which can also be translated to other genetic diseases.
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Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min Xin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Liya Lin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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14
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Gupta N, Dutta A, Ahmed B, Ross CR, S C, Dolan G, John MJ, Radhakrishnan N, Aggarwal S, Seth T, Kaul V, Shah V. Expert Opinions on the Management of Hemophilia A in India: The Role of Emicizumab. Cureus 2024; 16:e58941. [PMID: 38725780 PMCID: PMC11081140 DOI: 10.7759/cureus.58941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/12/2024] Open
Abstract
Hemophilia A (HA) is a genetic disorder of hemostasis associated with a deficiency or reduced activity of clotting factor VIII (FVIII). This disorder remains unacceptably underdiagnosed in India. Early diagnosis and appropriate management of HA can substantially prevent morbidity and mortality. Currently, HA is managed with regular replacement therapy using standard or extended half-life FVIII concentrates or non-factor drug products. The challenges associated with FVIII concentrates include plateauing of drug effect, issues with its administration and adherence to treatment, breakthrough bleeds, and the development of inhibiting antibodies against administered clotting factors. Emicizumab is a bispecific antibody, launched in India in April 2019, for managing patients with HA. To investigate the role of emicizumab in Indian patients with HA, opinions were sought from 13 eminent hematologists and experts from India on the effectiveness of emicizumab in preventing all bleeds, spontaneous bleeds, perioperative bleeds, and intracranial hemorrhage; resolving target joints; and reducing the rate of hospitalizations and fatality associated with HA in children and adults, with or without inhibitors. The benefits of emicizumab over traditional FVIII concentrates include the subcutaneous route of delivery, less frequent dosing, and a lack of inhibitor development, in addition to providing sustained hemostasis without in-depth monitoring. It is a safe and effective management option for all HA patients, especially for patients with certain archetypes, such as those with inhibitors, those with high annualized bleed rates, those living far away from hemophilia care centers, pediatric patients and infants with intravenous access challenges, and those with a history of life-threatening bleeding events.
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Affiliation(s)
- Naresh Gupta
- Medicine and Surgery, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
- Haematology & Haemophilia, Maulana Azad Medical College, Lok Nayak Hospital, New Delhi, IND
| | - Anupam Dutta
- General Medicine, Assam Medical College and Hospital, Dibrugarh, IND
| | - Bilal Ahmed
- Pathology, Transfusion Medicine & Hemophilia, Government Medical College, Srinagar, IND
| | - Cecil R Ross
- Hematology, St. John's Medical College and Hospital, Bangalore, IND
| | - Chandrakala S
- Clinical Haematology, King Edward Memorial Hospital, Mumbai, IND
| | - Gerard Dolan
- Haematology, St. Thomas' Haemophilia Comprehensive Care Centre, Bournemouth, GBR
| | - M J John
- Clinical Hematology, Hemato-Oncology & Bone Marrow Transplant, Christian Medical College & Hospital, Ludhiana, IND
| | - Nita Radhakrishnan
- Hematology and Oncology, Super Speciality Paediatric Hospital and Post Graduate Teaching Institute, Noida, IND
| | | | - Tulika Seth
- Hematology, All India Institute of Medical Sciences, New Delhi, New Delhi, IND
| | - Varun Kaul
- Pediatrics, Guru Gobind Singh Medical College & Hospital, Faridkot, IND
| | - Vijay Shah
- Pediatrics, Nirmal Hospital Pvt. Ltd., Surat, IND
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15
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Coyle CW, Knight KA, Brown HC, George SN, Denning G, Branella GM, Childers KC, Spiegel PC, Spencer HT, Doering CB. Humanization and functional characterization of enhanced coagulation factor IX variants identified through ancestral sequence reconstruction. J Thromb Haemost 2024; 22:633-644. [PMID: 38016519 PMCID: PMC10922771 DOI: 10.1016/j.jtha.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Laboratory resurrection of ancient coagulation factor (F) IX variants generated through ancestral sequence reconstruction led to the discovery of a FIX variant, designated An96, which possesses enhanced specific activity independent of and additive to that provided by human p.Arg384Lys, referred to as FIX-Padua. OBJECTIVES The goal of the current study was to identify the amino acid substitution(s) responsible for the enhanced activity of An96 and create a humanized An96 FIX transgene for gene therapy application. METHODS Reductionist screening approaches, including domain swapping and scanning residue substitution, were used and guided by one-stage FIX activity assays. In vitro characterization of top candidates included recombinant high-purity preparation, specific activity determination, and enzyme kinetic analysis. Final candidates were packaged into adeno-associated viral (AAV) vectors and delivered to hemophilia B mice. RESULTS Five of 42 total amino acid substitutions in An96 appear sufficient to retain the enhanced activity of An96 in an otherwise human FIX variant. Additional substitution of the Padua variant further increased the specific activity 5-fold. This candidate, designated ET9, demonstrated 51-fold greater specific activity than hFIX. AAV2/8-ET9 treated hemophilia B mice produced plasma FIX activities equivalent to those observed previously for AAV2/8-An96-Padua, which were 10-fold higher than AAV2/8-hFIX-Padua. CONCLUSION Starting from computationally inferred ancient FIX sequences, novel amino acid substitutions conferring activity enhancement were identified and translated into an AAV-FIX gene therapy cassette demonstrating high potency. This ancestral sequence reconstruction discovery and sequence mapping refinement approach represents a promising platform for broader protein drug and gene therapy candidate optimization.
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Affiliation(s)
- Christopher W Coyle
- Molecular and Systems Pharmacology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kristopher A Knight
- Molecular and Systems Pharmacology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | - Gianna M Branella
- Cancer Biology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kenneth C Childers
- Chemistry Department, Western Washington University, Bellingham, Washington, USA
| | - P Clint Spiegel
- Chemistry Department, Western Washington University, Bellingham, Washington, USA
| | - H Trent Spencer
- Cell and Gene Therapy Program, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - Christopher B Doering
- Cell and Gene Therapy Program, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA.
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16
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Tse V, Chacaltana G, Gutierrez M, Forino N, Jimenez A, Tao H, Do P, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone M, Sanford J. An intronic RNA element modulates Factor VIII exon-16 splicing. Nucleic Acids Res 2024; 52:300-315. [PMID: 37962303 PMCID: PMC10783525 DOI: 10.1093/nar/gkad1034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Pathogenic variants in the human Factor VIII (F8) gene cause Hemophilia A (HA). Here, we investigated the impact of 97 HA-causing single-nucleotide variants on the splicing of 11 exons from F8. For the majority of F8 exons, splicing was insensitive to the presence of HA-causing variants. However, splicing of several exons, including exon-16, was impacted by variants predicted to alter exonic splicing regulatory sequences. Using exon-16 as a model, we investigated the structure-function relationship of HA-causing variants on splicing. Intriguingly, RNA chemical probing analyses revealed a three-way junction structure at the 3'-end of intron-15 (TWJ-3-15) capable of sequestering the polypyrimidine tract. We discovered antisense oligonucleotides (ASOs) targeting TWJ-3-15 partially rescue splicing-deficient exon-16 variants by increasing accessibility of the polypyrimidine tract. The apical stem loop region of TWJ-3-15 also contains two hnRNPA1-dependent intronic splicing silencers (ISSs). ASOs blocking these ISSs also partially rescued splicing. When used in combination, ASOs targeting both the ISSs and the region sequestering the polypyrimidine tract, fully rescue pre-mRNA splicing of multiple HA-linked variants of exon-16. Together, our data reveal a putative RNA structure that sensitizes F8 exon-16 to aberrant splicing.
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Affiliation(s)
- Victor Tse
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Guillermo Chacaltana
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Martin Gutierrez
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Nicholas M Forino
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Arcelia G Jimenez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hanzhang Tao
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Phong H Do
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Catherine Oh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Priyanka Chary
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Isabel Quesada
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Antonia Hamrick
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sophie Lee
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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17
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Shu M, Malcolmson C, Bouskill V, Stain AM, Wakefield C, Blanchette VS, Carcao MD. Unravelling the effect of blood group on FVIII:C levels and response to DDAVP in 20 males with a single genotype (Twillingate Variant) causing Haemophilia A. Haemophilia 2024; 30:116-122. [PMID: 38037243 DOI: 10.1111/hae.14896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
INTRODUCTION The genetic variant responsible for haemophilia A (HA) significantly impacts endogenous coagulant factor VIII (FVIII:C) level, thus impacting DDAVP responsiveness. Blood group (BG) also impacts FVIII:C levels, but this is difficult to evaluate in a genetically heterogeneous population. Canada has a large cohort of mild-moderate HA due to a single point variant: c.6104T>C, p.Val2035Ala-the Twillingate variant. AIM To evaluate the impact of BG on endogenous FVIII:C levels and DDAVP responsiveness in a single genotype of mild-moderate HA. METHODS This was a retrospective, single-centre study. BG and FVIII:C levels were obtained for males with the Twillingate variant. One-hour absolute and fold increases in FVIII:C post-DDAVP were calculated. T-tests and Mann-Whitney U tests were used to compare FVIII:C levels and DDAVP challenge variables between individuals according to BGs (O vs. non-O). RESULTS Twenty males were included. There were significant differences between BGs (O vs. non-O) in their lowest FVIII:C level at age <12 years (medians: 0.05 vs. 0.08 IU/mL; P = .05). Fifteen subjects underwent DDAVP challenges. Mean 1-h FVIII:C were 0.29 (O BG) versus 0.41 IU/mL (non-O BG); P = .04. There were no significant differences between BGs (O vs. non-O) in mean absolute FVIII:C increase (0.20 vs. 0.27 IU/mL; P = .10) and FVIII:C fold increase (3.3-fold vs. 3.8-fold; P = .51). CONCLUSION In HA subjects with an identical genotype, BG significantly impacts baseline FVIII:C levels and FVIII:C levels post-DDAVP, but does not impact absolute and fold increases in FVIII:C with DDAVP.
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Affiliation(s)
- Michael Shu
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Caroline Malcolmson
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vanessa Bouskill
- Department of Nursing, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ann Marie Stain
- Department of Nursing, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cindy Wakefield
- Department of Nursing, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Victor S Blanchette
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Manuel D Carcao
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
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18
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Saleh S, Dabbous O, Sullivan SD, Ankleshwaria D, Trombini D, Toumi M, Diaa M, Patel A, Kazazoglu Taylor B, Tunis S. A practical approach for adoption of a hub and spoke model for cell and gene therapies in low- and middle-income countries: framework and case studies. Gene Ther 2024; 31:1-11. [PMID: 37903929 PMCID: PMC10788266 DOI: 10.1038/s41434-023-00425-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 11/01/2023]
Abstract
In the rapidly evolving landscape of biotechnologies, cell and gene therapies are being developed and adopted at an unprecedented pace. However, their access and adoption remain limited, particularly in low- and middle-income countries (LMICs). This study aims to address this critical gap by exploring the potential of applying a hub and spoke model for cell and gene therapy delivery in LMICs. We establish the identity and roles of relevant stakeholders, propose a hub and spoke model for cell and gene therapy delivery, and simulate its application in Brazil and the Middle East and North Africa. The development and simulation of this model were informed by a comprehensive review of academic articles, grey literature, relevant websites, and publicly available data sets. The proposed hub and spoke model is expected to expand availability of and access to cell and gene therapy in LMICs and presents a comprehensive framework for the roles of core stakeholders, laying the groundwork for more equitable access to these lifesaving therapies. More research is needed to explore the practical adoption and implications of this model.
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Affiliation(s)
- Shadi Saleh
- American University of Beirut, Beirut, Lebanon.
| | - Omar Dabbous
- Novartis Gene Therapies, Inc., Bannockburn, IL, USA
| | - Sean D Sullivan
- CHOICE Institute, School of Pharmacy, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Anish Patel
- Novartis Gene Therapies, Inc., Bannockburn, IL, USA
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19
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Li F, He L, Chen G, Lu Y, Li R, Zhang Y, Jing X, Ling R, Li D, Liao C. Variant spectrum of F8 and F9 in hemophilia patients from southern China and 26 novel variants. Front Genet 2023; 14:1254265. [PMID: 38196513 PMCID: PMC10775173 DOI: 10.3389/fgene.2023.1254265] [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: 07/06/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Hemophilia, an X-linked recessive disorder, is characterized by spontaneous or trauma-induced prolonged bleeding. It is classified as hemophilia A when caused by variants in the F8 gene, and hemophilia B when caused by F9 variants. Few studies have described hemophilia variants in the Chinese population. This study aimed to investigate the clinical and genetic profiles of 193 hemophilia patients from southern China. Utilizing Sanger sequencing, multiplex ligation-dependent probe amplification, gap detection, long-range PCR, and multiplex PCR, we identified both F8 and F9 gene variants. Pregnant women with a history of hemophilia A offspring underwent amniocentesis or villus sampling for the variant detection. Variants in F8 and F9 were pinpointed in 183 patients, with 26 being novel discoveries. Notably, genetic testing was absent in the initial evaluation of 133 out of 161 patients, leading to a protracted average definitive diagnosis timeline of 2 years. Remarkably, two hemophilia A cases with anticipated severe phenotypes due to protein-truncating variants presented with only moderate or mild clinical manifestations. Among the 40 fetuses tested, 34 were males, with 17 exhibiting hemizygous variants in the F8 gene. Our results contribute to the broader understanding of F8 and F9 variant spectrum and highlight the underuse of genetic analyses in southern China.
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Affiliation(s)
- Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liya He
- Hematology Department, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Guilan Chen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Lu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Rujuan Ling
- Department of Internal Medicine, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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20
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Stefanucci L, Collins J, Sims MC, Barrio-Hernandez I, Sun L, Burren OS, Perfetto L, Bender I, Callahan TJ, Fleming K, Guerrero JA, Hermjakob H, Martin MJ, Stephenson J, NIHR BioResource, Paneerselvam K, Petrovski S, Porras P, Robinson PN, Wang Q, Watkins X, Frontini M, Laskowski RA, Beltrao P, Di Angelantonio E, Gomez K, Laffan M, Ouwehand WH, Mumford AD, Freson K, Carss K, Downes K, Gleadall N, Megy K, Bruford E, Vuckovic D. The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants. Blood 2023; 142:2055-2068. [PMID: 37647632 PMCID: PMC10733830 DOI: 10.1182/blood.2023020118] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023] Open
Abstract
Rare genetic diseases affect millions, and identifying causal DNA variants is essential for patient care. Therefore, it is imperative to estimate the effect of each independent variant and improve their pathogenicity classification. Our study of 140 214 unrelated UK Biobank (UKB) participants found that each of them carries a median of 7 variants previously reported as pathogenic or likely pathogenic. We focused on 967 diagnostic-grade gene (DGG) variants for rare bleeding, thrombotic, and platelet disorders (BTPDs) observed in 12 367 UKB participants. By association analysis, for a subset of these variants, we estimated effect sizes for platelet count and volume, and odds ratios for bleeding and thrombosis. Variants causal of some autosomal recessive platelet disorders revealed phenotypic consequences in carriers. Loss-of-function variants in MPL, which cause chronic amegakaryocytic thrombocytopenia if biallelic, were unexpectedly associated with increased platelet counts in carriers. We also demonstrated that common variants identified by genome-wide association studies (GWAS) for platelet count or thrombosis risk may influence the penetrance of rare variants in BTPD DGGs on their associated hemostasis disorders. Network-propagation analysis applied to an interactome of 18 410 nodes and 571 917 edges showed that GWAS variants with large effect sizes are enriched in DGGs and their first-order interactors. Finally, we illustrate the modifying effect of polygenic scores for platelet count and thrombosis risk on disease severity in participants carrying rare variants in TUBB1 or PROC and PROS1, respectively. Our findings demonstrate the power of association analyses using large population datasets in improving pathogenicity classifications of rare variants.
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Affiliation(s)
- Luca Stefanucci
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Janine Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Matthew C. Sims
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luanluan Sun
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Oliver S. Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Livia Perfetto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biology and Biotechnology “C.Darwin,” Sapienza University of Rome, Rome, Italy
| | - Isobel Bender
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Tiffany J. Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
| | - Kathryn Fleming
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Jose A. Guerrero
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Maria J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - James Stephenson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - NIHR BioResource
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
- Department of Biology and Biotechnology “C.Darwin,” Sapienza University of Rome, Rome, Italy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Cambridge, United Kingdom
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, Australia
- Genomic Medicine, The Jackson Laboratory, Farmington, CT
- Institute for Systems Genomics, University of Connecticut, Farmington, CT
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences RILD Building, University of Exeter Medical School, Exeter, United Kingdom
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Heart and Lung Research Institute, University of Cambridge, Cambridge, United Kingdom
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Health Data Science Centre, Human Technopole, Milan, Italy
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, United Kingdom
- Department of Haematology, Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Trust, London, United Kingdom
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KULeuven, Leuven, Belgium
- Cambridge Genomics Laboratory, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Kalpana Paneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Cambridge, United Kingdom
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, Australia
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Peter N. Robinson
- Genomic Medicine, The Jackson Laboratory, Farmington, CT
- Institute for Systems Genomics, University of Connecticut, Farmington, CT
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Xavier Watkins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences RILD Building, University of Exeter Medical School, Exeter, United Kingdom
| | - Roman A. Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Emanuele Di Angelantonio
- British Heart Foundation, BHF Centre of Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Public Health and Primary Care, BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
- Heart and Lung Research Institute, University of Cambridge, Cambridge, United Kingdom
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Health Data Science Centre, Human Technopole, Milan, Italy
| | - Keith Gomez
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Mike Laffan
- Department of Haematology, Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, University College London Hospitals NHS Trust, London, United Kingdom
| | - Andrew D. Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KULeuven, Leuven, Belgium
| | - Keren Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Genomics Laboratory, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nick Gleadall
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Elspeth Bruford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Dragana Vuckovic
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
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21
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Strijbis VJF, Vatandoost J, Bos MHA. Crippling down factor IX for therapeutic gain. J Thromb Haemost 2023; 21:3287-3291. [PMID: 37678545 DOI: 10.1016/j.jtha.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Affiliation(s)
- Viola J F Strijbis
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands. https://twitter.com/ViolaStrijbis
| | - Jafar Vatandoost
- Department of Biology, Hakim Sabzevari University, Sabzevar, Iran
| | - Mettine H A Bos
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands.
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22
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Liu Y, Li D, Yu D, Liang Q, Chen G, Li F, Gao L, Li Z, Xie T, Wu L, Mao A, Wu L, Liang D. Comprehensive Analysis of Hemophilia A (CAHEA): Towards Full Characterization of the F8 Gene Variants by Long-Read Sequencing. Thromb Haemost 2023; 123:1151-1164. [PMID: 37285902 PMCID: PMC10686748 DOI: 10.1055/a-2107-0702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hemophilia A (HA) is the most frequently occurring X-linked bleeding disorder caused by heterogeneous variants in the F8 gene, one of the largest genes known. Conventional molecular analysis of F8 requires a combination of assays, usually including long-range polymerase chain reaction (LR-PCR) or inverse-PCR for inversions, Sanger sequencing or next-generation sequencing for single-nucleotide variants (SNVs) and indels, and multiplex ligation-dependent probe amplification for large deletions or duplications. MATERIALS AND METHODS This study aimed to develop a LR-PCR and long-read sequencing-based assay termed comprehensive analysis of hemophilia A (CAHEA) for full characterization of F8 variants. The performance of CAHEA was evaluated in 272 samples from 131 HA pedigrees with a wide spectrum of F8 variants by comparing to conventional molecular assays. RESULTS CAHEA identified F8 variants in all the 131 pedigrees, including 35 intron 22-related gene rearrangements, 3 intron 1 inversion (Inv1), 85 SNVs and indels, 1 large insertion, and 7 large deletions. The accuracy of CAHEA was also confirmed in another set of 14 HA pedigrees. Compared with the conventional methods combined altogether, CAHEA assay demonstrated 100% sensitivity and specificity for identifying various types of F8 variants and had the advantages of directly determining the break regions/points of large inversions, insertions, and deletions, which enabled analyzing the mechanisms of recombination at the junction sites and pathogenicity of the variants. CONCLUSION CAHEA represents a comprehensive assay toward full characterization of F8 variants including intron 22 and intron 1 inversions, SNVs/indels, and large insertions and deletions, greatly improving the genetic screening and diagnosis for HA.
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Affiliation(s)
- Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Guilan Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lu Gao
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Zhuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Le Wu
- Berry Genomics Corporation, Beijing, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Lingqian Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Desheng Liang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
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23
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Nguyen MT, Nguyen TT, Nguyen DB, Nguyen TM, Nguyen KN, Ngo VNM, Nguyen VD, Tran NA, Lian M, Tan ASC, Chong SS, Dang TT. Robust preimplantation genetic testing of the common F8 Inv22 pathogenic variant of severe hemophilia A using a highly polymorphic multi-marker panel encompassing the paracentric inversion. Thromb J 2023; 21:108. [PMID: 37864173 PMCID: PMC10588207 DOI: 10.1186/s12959-023-00552-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Hemophilia A (HEMA) is an X-linked bleeding disorder caused by reduced/absent coagulation factor VIII expression, as a result of pathogenic variants in the F8 gene. Preimplantation prevention of HEMA should ideally include direct pathogenic F8 variant detection, complemented by linkage analysis of flanking markers to identify the high-risk F8 allele. Linkage analysis is particularly indispensable when the pathogenic variant cannot be detected directly or identified. This study evaluated the suitability of a panel of F8 intragenic and extragenic short tandem repeat markers for standalone linkage-based preimplantation genetic testing for monogenic disorder (PGT-M) of the Inv22 pathogenic variant, an almost 600 kb paracentric inversion responsible for almost half of all severe HEMA globally, for which direct detection is challenging. METHODS Thirteen markers spanning 1 Mb and encompassing both F8 and the Inv22 inversion interval were genotyped in 153 unrelated females of Viet Kinh ethnicity. RESULTS All individuals were heterozygous for ≥ 1 marker, ~ 90% were heterozygous for ≥ 1 of the five F8 intragenic markers, and almost 98% were heterozygous for ≥ 1 upstream (telomeric) and ≥ 1 downstream (centromeric) markers. A prospective PGT-M couple at risk of transmitting F8 Inv22 were fully informative at four marker loci (2 intra-inversion, 1 centromeric, 1 telomeric) and partially informative at another five (2 intra-inversion, 3 centromeric), allowing robust phasing of low- and high-risk haplotypes. In vitro fertilization produced three embryos, all of which clearly inherited the low-risk maternal allele, enabling reliable unaffected diagnoses. A single embryo transfer produced a clinical pregnancy, which was confirmed as unaffected by amniocentesis and long-range PCR, and a healthy baby girl was delivered at term. CONCLUSION Robust and reliable PGT-M of HEMA, including the common F8 Inv22 pathogenic variant, can be achieved with sufficient informative intragenic and flanking markers.
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Affiliation(s)
- Minh Tam Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thanh Tung Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Duy Bac Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thi Mai Nguyen
- National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam
| | - Kim Ngan Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Van Nhat Minh Ngo
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Van Dieu Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Ngoc Anh Tran
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Centre, National University Centre for Women and Children, National University Hospital, Singapore, Singapore
| | - Arnold S C Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Samuel S Chong
- Preimplantation Genetic Diagnosis Centre, National University Centre for Women and Children, National University Hospital, Singapore, Singapore.
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
| | - Tien Truong Dang
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam.
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24
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Brinza M, Grigore A, Dragomir M, Jardan D, Jardan C, Balanescu P, Tarniceriu CC, Badulescu OV, Blag C, Tomuleasa C, Traila A, Serban M, Coriu D. Large Intron Inversions in Romanian Patients with Hemophilia A-First Report. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1821. [PMID: 37893540 PMCID: PMC10608589 DOI: 10.3390/medicina59101821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Despite the vast heterogeneity in the genetic defects causing hemophilia A (HA), large intron inversions represent a major cause of disease, accounting for almost half of the cases of severe HA worldwide. We investigated the intron 22 and intron 1 inversion status in a cohort of Romanian unrelated patients with severe HA. Moreover, we evaluated the role of these inversions as relative risk factors in inhibitor occurrence. Materials and Methods: Inverse shifting-a polymerase chain reaction method was used to detect the presence of intron 22 and intron 1 inversions in 156 Romanian patients with HA. Results: Intron inversion 22 was found in 41.7% of the patients, while intron 1 inversion was detected in 3.2% of the patients. Overall, large intron inversions represented the molecular defect in 44.9% of the studied patients. Our findings are in accord with previously published reports from Eastern Europe countries and with other international studies. The risk of inhibitor development was higher in patients with inversion 1 compared to the patients with HA without any inversion detected. Conclusions: The current study demonstrates the major causative role of large intron inversions in severe HA in Romanian patients. Moreover, our study confirms the contribution of intron 1 inversion in inhibitor development.
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Affiliation(s)
- Melen Brinza
- Department of Hematology and Bone Marrow Transplant, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andra Grigore
- Department of Hematology and Bone Marrow Transplant, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Department of Hematology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Mihaela Dragomir
- Department of Hematology and Bone Marrow Transplant, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Dumitru Jardan
- Molecular Biology Laboratory, Medlife, 010093 Bucharest, Romania
| | - Cerasela Jardan
- Department of Hematology and Bone Marrow Transplant, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Department of Hematology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Paul Balanescu
- Internal Medicine Chair, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Claudia Cristina Tarniceriu
- Department of Anatomy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Department of Hematology, “St Spiridon” County Clinical Emergency Hospital, 700111 Iasi, Romania
| | - Oana Viola Badulescu
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Cristina Blag
- Pediatric Discipline, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400177 Cluj Napoca, Romania
- Pediatric Clinic, Emergency Clinical Hospital for Children, 400177 Cluj Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Hematology, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj Napoca, Romania
- Department of Hematology, “Ion Chiricuta” Clinical Cancer Center, 400124 Cluj Napoca, Romania
| | - Adina Traila
- “Cristian Serban” Medical Center for Evaluation Therapy, Medical Education and Rehabilitation of Children and Young Adults, European Hemophilia Treatment Centre, 305100 Buzias, Romania
| | - Margit Serban
- Department of Onco-Hematology, “Louis Turcanu” Emergency Hospital for Children, 300011 Timisoara, Romania
- Department of Hematology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Daniel Coriu
- Department of Hematology and Bone Marrow Transplant, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Department of Hematology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
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25
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Zhang X, Chen K, Bian S, Wang G, Qin X, Zhang R, Yang L. Molecular Diagnosis of Hemophilia A and Pathogenesis of Novel F8 Variants in Shanxi, China. Glob Med Genet 2023; 10:247-262. [PMID: 37711502 PMCID: PMC10499503 DOI: 10.1055/s-0043-1774322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023] Open
Abstract
The aim of this study was to perform a molecular diagnosis of hemophilia A (HA) among patients in the Shanxi Province of China. Fifty-two HA patients were tested, including IVS22 (31 samples), IVS1 (3 samples), missense (11 samples), nonsense (3 samples), and 4 cases of frameshift (2 cases of deletion, 1 case of insertion, 1 case of single-base duplication). With the exception of the single-base G duplication variant (p.Ile1213Asnfs*28), this was the hotspot variant reported by research groups at an early stage. The remaining variants were found, for the first time, in the region. The missense variants p.Cys172Ser, p.Tyr404Ser, p.Asp1903Gly, and p.Ser2284Asn, the deletion variant p.Leu2249fs*9, and the insertion variant p.Pro2319fs*97 were novel variants. The application of next-generation sequencing (NGS) molecular diagnosis enriched the variant spectrum of HA, which is greatly significant for individualized genetic counseling, clinical diagnosis, and treatment. NGS and a variety of bioinformatics prediction methods can further analyze the impact of genetic variation on protein structure or function and lay the foundation to reveal the molecular pathogenic mechanism of novel variants.
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Affiliation(s)
- Xialin Zhang
- Department of Hematology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sicheng Bian
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Gang Wang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiuyu Qin
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruijuan Zhang
- Department of Hematology, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linhua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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Ferreira MV, Nogueira T, Rios RA, Lopes TJS. A graph-based machine learning framework identifies critical properties of FVIII that lead to hemophilia A. FRONTIERS IN BIOINFORMATICS 2023; 3:1152039. [PMID: 37235045 PMCID: PMC10206133 DOI: 10.3389/fbinf.2023.1152039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction: Blood coagulation is an essential process to cease bleeding in humans and other species. This mechanism is characterized by a molecular cascade of more than a dozen components activated after an injury to a blood vessel. In this process, the coagulation factor VIII (FVIII) is a master regulator, enhancing the activity of other components by thousands of times. In this sense, it is unsurprising that even single amino acid substitutions result in hemophilia A (HA)-a disease marked by uncontrolled bleeding and that leaves patients at permanent risk of hemorrhagic complications. Methods: Despite recent advances in the diagnosis and treatment of HA, the precise role of each residue of the FVIII protein remains unclear. In this study, we developed a graph-based machine learning framework that explores in detail the network formed by the residues of the FVIII protein, where each residue is a node, and two nodes are connected if they are in close proximity on the FVIII 3D structure. Results: Using this system, we identified the properties that lead to severe and mild forms of the disease. Finally, in an effort to advance the development of novel recombinant therapeutic FVIII proteins, we adapted our framework to predict the activity and expression of more than 300 in vitro alanine mutations, once more observing a close agreement between the in silico and the in vitro results. Discussion: Together, the results derived from this study demonstrate how graph-based classifiers can leverage the diagnostic and treatment of a rare disease.
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Affiliation(s)
| | - Tatiane Nogueira
- Institute of Computing, Federal University of Bahia, Salvador, Brazil
| | - Ricardo A. Rios
- Institute of Computing, Federal University of Bahia, Salvador, Brazil
| | - Tiago J. S. Lopes
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
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Tse V, Chacaltana G, Gutierrez M, Forino NM, Jimenez AG, Tao H, Do PH, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone MD, Sanford JR. Rescue of blood coagulation Factor VIII exon-16 mis-splicing by antisense oligonucleotides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535160. [PMID: 37034721 PMCID: PMC10081312 DOI: 10.1101/2023.03.31.535160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The human Factor VIII ( F8 ) protein is essential for the blood coagulation cascade and specific F8 mutations cause the rare bleeding disorder Hemophilia A (HA). Here, we investigated the impact of HA-causing single-nucleotide mutations on F8 pre-mRNA splicing. We found that 14/97 (∼14.4%) coding sequence mutations tested in our study induced exon skipping. Splicing patterns of 4/11 (∼36.4%) F8 exons tested were especially sensitive to the presence of common disease-causing mutations. RNA-chemical probing analyses revealed a three-way junction structure at the 3' end of intron 15 (TWJ-3-15). TWJ-3-15 sequesters the polypyrimidine tract, a key determinant of 3' splice site strength. Using exon-16 of the F8 gene as a model, we designed specific antisense oligonucleotides (ASOs) that target TWJ-3-15 and identified three that promote the splicing of F8 exon-16. Interaction of TWJ-3-15 with ASOs increases accessibility of the polypyrimidine tract and inhibits the binding of hnRNPA1-dependent splicing silencing factors. Moreover, ASOs targeting TWJ-3-15 rescue diverse splicing-sensitive HA-causing mutations, most of which are distal to the 3' splice site being impacted. The TWJ-3-15 structure and its effect on mRNA splicing provide a model for HA etiology in patients harboring specific F8 mutations and provide a framework for precision RNA-based HA therapies.
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Labarque V, Mancuso ME, Kartal-Kaess M, Ljung R, Mikkelsen TS, Andersson NG. F8/F9 variants in the population-based PedNet Registry cohort compared with locus-specific genetic databases of the European Association for Haemophilia and Allied Disorders and the Centers for Disease Control and Prevention Hemophilia A or Hemophilia B Mutation Project. Res Pract Thromb Haemost 2023; 7:100036. [PMID: 36798899 PMCID: PMC9926204 DOI: 10.1016/j.rpth.2023.100036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/11/2022] [Accepted: 12/17/2022] [Indexed: 01/11/2023] Open
Abstract
Background Hemophilia A and B are caused by variants in the factor (F) VIII or FIX gene. Selective reporting may influence the distribution of variants reported in genetic databases. Objectives To compare the spectrum of F8 and F9 variants in an international population-based pediatric cohort (PedNet Registry) with the spectrum found in the European Association for Haemophilia and Allied Disorders (EAHAD) and the Centers for Disease Control and Prevention Hemophilia A or Hemophilia B Mutation Project (CHAMP/CHBMP) databases. Methods All patients registered in the PedNet Registry on January 1, 2021 were included in this study. As comparators, data from patients with severe hemophilia included in the CHAMP/CHBMP registry (US center data) and EAHAD were used. Results Genetic information was available for 1941 patients. Intron 22 inversion was present in 52% of patients with severe hemophilia A; frameshift (36%), missense (28%), and nonsense (20%) were the most frequent variants in patients with severe hemophilia A who were inversion-negative. The most frequent variants in severe hemophilia B were missense (48%). In nonsevere disease, most variants were missense variants (moderate hemophilia A: 91%; mild hemophilia A: 95%, moderate and mild hemophilia B: 86% each). Comparison with the databases demonstrated a higher proportion of missense variants associated with severe hemophilia B in EAHAD (68%) than in PedNet (48%) and CHBMP (46%). Conclusion The PedNet population-based cohort provides an alternative to the established databases, which collect data by selective reporting, as it is a well-maintained database covering the full spectrum of pathogenic F8 and F9 variants, and indicates the number of patients affected by each particular variant.
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Affiliation(s)
- Veerle Labarque
- Department of Paediatrics, Paediatric Haematology and Oncology, University Hospitals Leuven, Leuven, Belgium,Correspondence Veerle Labarque, Department of Paediatrics, Paediatric Haematology and Oncology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Maria Elisa Mancuso
- Center for Thrombosis and Hemorrhagic Diseases, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy,Humanitas University, Rozzano, Milan, Italy
| | - Mutlu Kartal-Kaess
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Inselspital, University Hospital, University of Bern, Bern, Switzerland
| | - Rolf Ljung
- Department of Clinical Sciences and Paediatrics, Lund University, Lund, Sweden
| | - Torben S. Mikkelsen
- Department of Paediatric Oncology and Haematology, University Hospital, Aarhus, Denmark
| | - Nadine G. Andersson
- Department of Clinical Sciences and Paediatrics, Lund University, Lund, Sweden,Centre for Thrombosis and Haemostasis, Skåne University Hospital, Lund, Sweden
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Owaidah T, Bakr S, Al-Numair N, AbaAlkhail H, Alzahrani H, Saleh M, Khogeer H, Tarawah A, Akkad H, Al-Allaf F. Genotype Hemophilia Screening Program Identified 2 Novel Variants Including a Novel Variant (c.5816-2A > G) Causing a Pathogenic Variant of the Factor 8 Gene. Clin Appl Thromb Hemost 2023; 29:10760296231182410. [PMID: 37525882 PMCID: PMC10395182 DOI: 10.1177/10760296231182410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 08/02/2023] Open
Abstract
Establishing a national screening program for hemophilia patients is highly encouraged by the World Health Organization and the World Federation of Hemophilia. Hence, this study aimed to analyze the variant spectrum of F8 and F9 genes in Arab hemophilia patients. Molecular genetic and sequencing studies were performed on a cohort of 135 Saudi hemophilia patients. Out of all screened hemophilia patients (97 hemophilia A and 39 hemophilia B), 15 (11.1%) were positive for inversion 22 and 4 (3%) for inversion 1. Out of a total of 32 (23.7%) substitution/deletion mutations, 2 novel variants were identified: a novel splice acceptor site missense mutation (c.5816-2A > G) causing a pathogenic variant of the F8 gene and another splicing site point mutation in intron/exon 23 (g.164496G > A). The frequent F8 variants were (c.409A > C, p.T137P) in exon 4, (c.760A > G) in exon 6, and (c.1835G > C, p.R612P) in exon 12, while the frequent F9 variants were (c.580A > G) in exon 6 and (c.880C > T) in exon 8. These study data will enrich the spectrum of the genetic databases in the Arab population that could be applied in the future for national genetic counseling.
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Affiliation(s)
- Tarek Owaidah
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salwa Bakr
- Department of Clinical Pathology/Hematology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Nouf Al-Numair
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hala AbaAlkhail
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hazzaa Alzahrani
- Department of Adult Hematology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mahasen Saleh
- Department of Pediatric Hematology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haitham Khogeer
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Tarawah
- Madinah Hereditary Blood Disorders Center, Department of Pediatric Hematology, King Salman Medical City, Madinah, Saudi Arabia
| | - Hadeel Akkad
- Department of Hematology, National Blood Center, Riyadh, Saudi Arabia
| | - Faisal Al-Allaf
- Department of Medical Genetics, Umm Al-Qura University Faculty of Medicine, Makkah, Saudi Arabia
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De Mazancourt P, Harroche A, Pouymayou K, Sigaud M, Falaise C, Stieltjes N, Castet SM, Tardy B, Zawadzki C, Goudemand J, Dargaud Y. Reinvestigation of unidentified causative variants in FXI-deficient patients: Focus on gene segment deletions. Haemophilia 2023; 29:248-255. [PMID: 36195107 DOI: 10.1111/hae.14666] [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: 04/29/2022] [Revised: 07/06/2022] [Accepted: 09/08/2022] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Data on failure to identify the molecular mechanism underlying FXI deficiency by Sanger analysis and the contribution of gene segment deletions are almost inexistent. AIMS AND METHODS Prospective and retrospective analysis was conducted on FXI-deficient patients' DNA via Next Generation Sequencing (NGS), or Sanger sequencing and Multiplex Probe Ligation-dependent Assay (MLPA) to detect cryptic causative gene variants or gene segment deletions. RESULTS Sanger analysis or NGS enabled us to identify six severe and one partial (median activity 41 IU/dl) FXI deficient index cases with deletions encompassing exons 11-15, the whole gene, or both. After Sanger sequencing, retrospective evaluation using MLPA detected seven additional deletion cases in apparently homozygous cases in non-consanguineous families, or in previously unsolved FXI-deficiency cases. Among the 504 index cases with a complete genetic investigation (Sanger/MLPA, or NGS), 23 remained unsolved (no abnormality found [n = 14] or rare intronic variants currently under investigation, [n = 9]). In the 481 solved cases (95% efficiency), we identified F11 gene-deleted patients (14 cases; 2.9%). Among these, whole gene deletion accounted for four heterozygous cases, exons 11-15 deletion for five heterozygous and three homozygous ones, while compound heterozygous deletion and isolated exon 12 deletion accounted for one case each. CONCLUSION Given the high incidence of deletions in our population (2.9%), MLPA (or NGS with a reliable bioinformatic pipeline) should be systematically performed for unsolved FXI deficiencies or apparently homozygous cases in non-consanguineous families.
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Affiliation(s)
- Philippe De Mazancourt
- Laboratory of Molecular Biology, Ambroise Pare Hospital, GHU APHP Paris-Saclay, Boulogne-Billancourt, France.,UMR1179, Versailles St-Quentin University, Boulogne-Billancourt, France
| | - Annie Harroche
- Department of Hematology, Hospital Necker-Enfants Malades, GHU AP-HP, Centre - Université de Paris, Paris, France
| | - Katia Pouymayou
- Laboratory of Hematology, La Timone Hospital, APHM, Marseille, France
| | - Marianne Sigaud
- Ressources and Competence Center for Constitutional Bleeding Disorders - CRC-MHC, Nantes University Hospital, Nantes, France
| | - Céline Falaise
- Department of Pediatric Hematology, Immunology, and Oncology, La Timone Children's Hospital, APHM, Marseille, France
| | - Natalie Stieltjes
- Ressources and Competence Center for Constitutional Bleeding Disorders - CRC-MHC, Cochin Hospital, GHU AP-HP, Centre - Université de Paris, Paris, France
| | - Sabine-Marie Castet
- Department of Biological Hematology, CHU Bordeaux-GH Pellegrin, Bordeaux, France
| | - Brigitte Tardy
- Department of Hematology, CHU Nord, Saint Etienne, France
| | | | - Jenny Goudemand
- Department of Hematology, Biology-Pathology Center, CHU, Lille, France
| | - Yesim Dargaud
- Clinical Haemostasis Unit, Louis Pradel Heart Hospital, Lyon, France
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31
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Wang J, Gu J, Chen H, Wu Q, Xiong L, Qiao B, Zhang Y, Xiao H, Tong Y. A Novel Deletion Mutation of the F8 Gene for Hemophilia A. Diagnostics (Basel) 2022; 12:diagnostics12112876. [PMID: 36428936 PMCID: PMC9689134 DOI: 10.3390/diagnostics12112876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Hemophilia A (HA) is an X-linked recessive blood coagulation disorder caused by a variety of abnormalities in F8 gene, resulting in the absence of impaired molecule production of factor VIII (FVIII) in the plasma. The genetic testing of the F8 gene encoding FVIII is used for confirmation of HA diagnosis, which significantly reduced serious complications of this disease and, ultimately, increased life expectancy. Methods: Sanger sequencing was performed in F8 gene exons of the suspected patients with blood coagulation-related indicators. Results: A novel F8 indel variant c.6343delC, p.Leu2115SerfsTer28 in exon 22 of the F8 gene was identified in the suspected families. The infant with this novel variant appeared the symptom of minor bleeding and oral cavity bleeding, and decreased activity of FVIII, which is consistent with that of F8 deleterious variants. The 3'D protein structural analysis of the novel variant shows a change in FVIII protein stability, which may be responsible for the pathogenesis of HA. Conclusions: A novel deleterious variant was identified in our case, which expands the F8 variants spectrum. Our result is helpful for HA diagnosis and benefits carrier detection and prenatal diagnosis. Our study also reveals that mutation screening of the F8 gene should be necessary for HA suspected patients.
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Affiliation(s)
- Jingwei Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Clinical Molecular Diagnosis Institute, Wuhan University, Wuhan 430060, China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hongbing Chen
- Department of Pulmonary and Critical Care Medicine of Renmin Hospital, Wuhan University, Wuhan 430060, China
| | - Qian Wu
- Clinical Molecular Diagnosis Institute, Wuhan University, Wuhan 430060, China
| | - Liang Xiong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Bin Qiao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Hongjun Xiao
- Medical Vocational and Technical School, Wuhan University, Wuhan 430060, China
- Correspondence: (H.X.); (Y.T.); Tel.: +86-27-88041911 (H.X.); +86-27-88041911 (Y.T.)
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Clinical Molecular Diagnosis Institute, Wuhan University, Wuhan 430060, China
- Correspondence: (H.X.); (Y.T.); Tel.: +86-27-88041911 (H.X.); +86-27-88041911 (Y.T.)
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Johnsen JM, Fletcher SN, Dove A, McCracken H, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska SE, Valentino LA, Pierce GF, Watson C, Cheng D, Recht M, Konkle BA. Results of genetic analysis of 11 341 participants enrolled in the My Life, Our Future hemophilia genotyping initiative in the United States. J Thromb Haemost 2022; 20:2022-2034. [PMID: 35770352 DOI: 10.1111/jth.15805] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Hemophilia A (HA) and hemophilia B (HB) are rare inherited bleeding disorders. Although causative genetic variants are clinically relevant, in 2012 only 20% of US patients had been genotyped. OBJECTIVES My Life, Our Future (MLOF) was a multisector cross-sectional US initiative to improve our understanding of hemophilia through widespread genotyping. METHODS Subjects and potential genetic carriers were enrolled at US hemophilia treatment centers (HTCs). Bloodworks performed genotyping and returned results to providers. Clinical data were abstracted from the American Thrombosis and Hemostasis Network dataset. Community education was provided by the National Hemophilia Foundation. RESULTS From 2013 to 2017, 107 HTCs enrolled 11 341 subjects (68.8% male, 31.2% female) for testing for HA (n = 8976), HB (n = 2358), HA/HB (n = 3), and hemophilia not otherwise specified (n = 4). Variants were detected in most male patients (98.2%% HA, 98.1% HB). 1914 unique variants were found (1482 F8, 431 F9); 744 were novel (610 F8, 134 F9). Inhibitor data were available for 6986 subjects (5583 HA; 1403 HB). In severe HA, genotypes with the highest inhibitor rates were large deletions (77/80), complex intron 22 inversions (9/17), and no variant found (7/14). In severe HB, the highest rates were large deletions (24/42). Inhibitors were reported in 27.3% of Black versus 16.2% of White patients. CONCLUSIONS The findings of MLOF are reported, the largest hemophilia genotyping project performed to date. The results support the need for comprehensive genetic approaches in hemophilia. This effort has contributed significantly towards better understanding variation in the F8 and F9 genes in hemophilia and risks of inhibitor formation.
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Affiliation(s)
- Jill M Johnsen
- Research Institute, Bloodworks, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Angela Dove
- Research Institute, Bloodworks, Seattle, Washington, USA
| | | | - Beth K Martin
- Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Martin Kircher
- Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Neil C Josephson
- Research Institute, Bloodworks, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sarah E Ruuska
- Research Institute, Bloodworks, Seattle, Washington, USA
| | | | | | - Crystal Watson
- American Thrombosis and Hemostasis Network, Rochester, New York, USA
| | - Dunlei Cheng
- American Thrombosis and Hemostasis Network, Rochester, New York, USA
| | - Michael Recht
- American Thrombosis and Hemostasis Network, Rochester, New York, USA
| | - Barbara A Konkle
- Research Institute, Bloodworks, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
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Testa MF, Lombardi S, Bernardi F, Ferrarese M, Belvini D, Radossi P, Castaman G, Pinotti M, Branchini A. Translational readthrough at F8 nonsense variants in the factor VIII B domain contributes to residual expression and lowers inhibitor association. Haematologica 2022; 108:472-482. [PMID: 35924581 PMCID: PMC9890017 DOI: 10.3324/haematol.2022.281279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 02/03/2023] Open
Abstract
In hemophilia A, F8 nonsense variants, and particularly those affecting the large factor VIII (FVIII) B domain that is dispensable for coagulant activity, display lower association with replacement therapy-related anti-FVIII inhibitory antibodies as retrieved from multiple international databases. Since null genetic conditions favor inhibitor development, we hypothesized that translational readthrough over premature termination codons (PTC) may contribute to immune tolerance by producing full-length proteins through the insertion of amino acid subset(s). To quantitatively evaluate the readthrough output in vitro, we developed a very sensitive luciferase-based system to detect very low full-length FVIII synthesis from a wide panel (n=45; ~60% patients with PTC) of F8 nonsense variants. PTC not associated with inhibitors displayed higher readthrough-driven expression levels than inhibitor-associated PTC, a novel observation. Particularly, higher levels were detected for B-domain variants (n=20) than for variants in other domains (n=25). Studies on plasma from six hemophilia A patients with PTC, integrated by expression of the corresponding nonsense and readthrough-deriving missense variants, consistently revealed higher FVIII levels for B-domain variants. Only one B-domain PTC (Arg814*) was found among the highly represented PTC not sporadically associated with inhibitors, but with the lowest proportion of inhibitor cases (4 out of 57). These original insights into the molecular genetics of hemophilia A, and particularly into genotype-phenotype relationships related with disease treatment, demonstrate that B-domain features favor PTC readthrough output. This provides a potential molecular mechanism contributing to differential PTC-associated inhibitor occurrence, with translational implications for a novel, experimentally based classification of F8 nonsense variants.
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Affiliation(s)
- Maria Francesca Testa
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Silvia Lombardi
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara,°Current address: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Mattia Ferrarese
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Donata Belvini
- Transfusion Service, Hemophilia Center and Hematology, Castelfranco Veneto Hospital, Castelfranco Veneto
| | - Paolo Radossi
- Oncohematology-Oncologic Institute of Veneto, Castelfranco Veneto Hospital, Castelfranco Veneto
| | - Giancarlo Castaman
- Center for Bleeding Disorders and Coagulation, Careggi University Hospital, Florence, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara.
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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Nishiyama A, Ogiwara K, Mizumachi K, Hashimoto N, Takeyama M, Nogami K. Activated partial thromboplastin time-based clot waveform analysis enables measurement of very low levels of factor IX activity in patients with severe hemophilia B. Int J Hematol 2022; 116:778-786. [PMID: 35864291 DOI: 10.1007/s12185-022-03419-4] [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: 05/07/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
The precise measurement of very low levels of factor IX activity (FIX:C < 1 IU/dL) is essential for understanding clinical severity and risk of inhibitor development in patients with severe hemophilia B (Pw-SHB). However, such measurement sensitivity has not yet been achieved. We aimed to establish a measurement method using clot waveform analysis (CWA). Residual FIX:C by adding anti-FIX monoclonal antibody, FIX:C by adding recombinant (r)FIX to the commercial Pw-SHB plasmas, and FIX:C in our Pw-SHB were determined by CS-2000i™/CS-2400™, followed by analysis of CWA parameters. The presence of anti-FIX antibody in the commercial Pw-SHB plasmas significantly decreased coagulation potential compared to its absence. The addition of rFIX to these innate plasma samples produced significant changes in three parameters upon adding FIX:C at 0.1-1 IU/dL, supporting the presence of trace FIX:C in Pw-SHB. Therefore, appropriate FIX-depleted plasma containing minimum residual FIX:C was chosen from reference curves of FIX:C (0.01-1 IU/dL). Among patients with untreated Pw-SHB, two had FIX:C 0.6-0.7 IU/dL and two had lower than detectable levels using FIX-depleted plasma. One of the latter had detectable trough levels post-rFIX administration. In conclusion, CWA enabled measurement of very low levels of FIX:C using appropriate FIX-deficient plasma.
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Affiliation(s)
- Atsuko Nishiyama
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan
| | - Kenichi Ogiwara
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan.
| | - Kuniyoshi Mizumachi
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan
| | - Naoki Hashimoto
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan
| | - Masahiro Takeyama
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan
| | - Keiji Nogami
- Department of Pediatrics, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8522, Japan
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Christopherson PA, Haberichter SL, Flood VH, Perry CL, Sadler BE, Bellissimo DB, Di Paola J, Montgomery RR, the Zimmerman Program Investigators. Molecular pathogenesis and heterogeneity in type 3 VWD families in U.S. Zimmerman program. J Thromb Haemost 2022; 20:1576-1588. [PMID: 35343054 PMCID: PMC11892521 DOI: 10.1111/jth.15713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
| | - Sandra L. Haberichter
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children’s Research Institute, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Veronica H. Flood
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Division of Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children’s Research Institute, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Brooke E. 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, Pittsburgh, Pennsylvania, 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 Hematology/Oncology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children’s Research Institute, Children’s Hospital of Wisconsin, Milwaukee, Wisconsin, USA
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Bernardo Á, Caro A, Martínez-Carballeira D, Corte JR, Vázquez S, Palomo-Antequera C, Andreu A, Fernández-Pardo Á, Oto J, Gutiérrez L, Soto I, Medina P. Applicability of the Thrombin Generation Test to Evaluate the Hemostatic Status of Hemophilia A Patients in Daily Clinical Practice. J Clin Med 2022; 11:jcm11123345. [PMID: 35743412 PMCID: PMC9224793 DOI: 10.3390/jcm11123345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
Hemophilia A (HA) is a rare bleeding disorder caused by factor VIII (FVIII) deficiency due to various genetic mutations in the F8 gene. The disease severity inversely correlates with the plasma levels of functional FVIII. The treatment of HA patients is based on FVIII replacement therapy, either following a prophylactic or on-demand regime, depending on the severity of the disease at diagnosis and the patient’s clinical manifestations. The hemorrhagic manifestations are widely variable amongst HA patients, who may require monitoring and treatment re-adjustment to minimize bleeding symptoms. Notably, laboratory monitoring of the FVIII activity is difficult due to a lack of sensitivity to various FVIII-related molecules, including non-factor replacement therapies. Hence, patient management is determined mainly based on clinical manifestations and patient–clinician history. Our goal was to validate the ST Genesia® automated thrombin generation analyzer to quantify the relative hemostatic status in HA patients. We recruited a cohort of HA patients from the Principality of Asturias (Spain), following treatment and at a stable non-bleeding phase. The entire cohort (57 patients) had been comprehensively studied at diagnosis, including FVIII and VWF activity assays and F8 genetic screening, and then clinically monitored until the Thrombin Generation Test (TGT) was performed. All patients were recruited prior to treatment administration, at the maximum time-window following the previous dose. Interestingly, the severe/moderate patients had a similar TGT compared to the mild patients, reflecting the non-bleeding phase of our patient cohort, regardless of the initial diagnosis (i.e., the severity of the disease), treatment regime, and FVIII activity measured at the time of the TGT. Thus, TGT parameters, especially the peak height (Peak), may reflect the actual hemostatic status of a patient more accurately compared to FVIII activity assays, which may be compromised by non-factor replacement therapies. Furthermore, our data supports the utilization of combined TGT variables, together with the severity of patient symptoms, along with the F8 mutation type to augment the prognostic capacity of TGT. The results from this observational study suggest that TGT parameters measured with ST Genesia® may represent a suitable tool to monitor the hemostatic status of patients requiring a closer follow-up and a tailored therapeutic adjustment, including other hemophilia subtypes or bleeding disorders.
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Affiliation(s)
- Ángel Bernardo
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Correspondence:
| | - Alberto Caro
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Daniel Martínez-Carballeira
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - José Ramón Corte
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
| | - Sonia Vázquez
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
| | - Carmen Palomo-Antequera
- Department of Internal Medicine, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
- Bone Metabolism, Vascular Metabolism and Chronic Inflammatory Diseases Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Alfredo Andreu
- Department of Pharmacology, University of Navarra, 31008 Pamplona, Spain;
| | - Álvaro Fernández-Pardo
- Hemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), 46026 Valencia, Spain; (Á.F.-P.); (J.O.); (P.M.)
| | - Julia Oto
- Hemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), 46026 Valencia, Spain; (Á.F.-P.); (J.O.); (P.M.)
| | - Laura Gutiérrez
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
- Department of Medicine, University of Oviedo, 33006 Oviedo, Spain
| | - Inmaculada Soto
- Department of Hematology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain; (A.C.); (D.M.-C.); (J.R.C.); (S.V.); (I.S.)
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Pilar Medina
- Hemostasis, Thrombosis, Arteriosclerosis and Vascular Biology Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), 46026 Valencia, Spain; (Á.F.-P.); (J.O.); (P.M.)
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38
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Miyashita R, Shinozawa K, Inaba H, Amano K, Kinai E. Prolonged α-thrombin-related activation and delayed active protein C-associated degradation confer mild phenotype in a patient with severe hemophilia A with F8 p.H118R. Int J Hematol 2022; 116:489-499. [PMID: 35590009 DOI: 10.1007/s12185-022-03381-1] [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: 12/24/2021] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
In hemophilia A, bleeding mostly correlates with factor VIII activity (FVIII:C), although some patients show discrepancy in bleeding severity and FVIII:C. We report a novel procoagulant mechanism associated with F8 p.H118R (c.353A > G) in a young Japanese man with few bleeding episodes despite low levels of FVIII:C (< 1 IU/dL). Plasma FVIII:C was < 1 IU/dL measured by one-stage clotting assay (OSA) and chromogenic substrate assay (CSA), whereas FVIII antigen (FVIII:Ag) was 9.7%. The global coagulation assay showed higher max speed in clot waveform analysis (CWA), shorter clotting time in rotation thromboelastometry (ROTEM) (1605 vs. > 5000 s), shorter lag time (4.87 vs. 12.47 min) and larger ETP (207.9 vs. 53.3 nM*min) in thrombin generation assay, compared with FVIII-deficient control. Expressed recombinant H118R mutant in culture media showed low FVIII:C (1-5 IU/dL) by OSA, with non-hemophilia level of FVIII:Ag. Western blot analysis using recombinant H118R showed longer persistence of heavy-chain of H118R after incubation with α-thrombin, compared with wild-type. Incubation of H118R with activated protein C (APC) also showed longer persistence of A1-A2 domain. In conclusion, H118R showed prolonged activation by α-thrombin and delayed APC-related FVIII degradation. These properties may confer the procoagulant activity and few bleeding episodes despite low FVIII:C.
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Affiliation(s)
- Ryui Miyashita
- Department of Laboratory Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Keiko Shinozawa
- Department of Laboratory Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan.
| | - Hiroshi Inaba
- Department of Laboratory Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Kagehiro Amano
- Department of Laboratory Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
| | - Ei Kinai
- Department of Laboratory Medicine, Tokyo Medical University, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan
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39
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Gomez K. Advances in the diagnosis of heritable platelet disorders. Blood Rev 2022; 56:100972. [PMID: 35595614 DOI: 10.1016/j.blre.2022.100972] [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: 04/20/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
The last decade has seen large increases in the number of patients registered with heritable platelet disorders in national databases of bleeding disorders. Although individually rare, collectively they are a relatively common cause of heritable bleeding. This revolution has come about through the application of high-throughput sequencing strategies and efforts to standardize diagnostic testing. There is renewed interest in established parameters such as platelet volume and utilising simple tools such as blood smears. The diagnostic yield from peripheral blood smears can be improved with new microscopy techniques that could potentially assist in determining which patients need to be referred to tertiary centres for specialist testing. A better understanding of the other clinical features that can accompany abnormalities of platelet number or function, can lead to better clinical management and prevention of serious complications. There are challenges for clinicians who need to be aware of these developments, understand the limitations of new diagnostic techniques and keep abreast of strategies for incorporation into clinical practice. This review discusses some of these approaches, the limitations that clinicians need to be aware of and techniques that may enter clinical use in the future.
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Affiliation(s)
- Keith Gomez
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.
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40
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Kuder H, Dickeson SK, Brooks MB, Kehl A, Müller E, Gailani D, Giger U. A Common Missense Variant Causing Factor XI Deficiency and Increased Bleeding Tendency in Maine Coon Cats. Genes (Basel) 2022; 13:792. [PMID: 35627175 PMCID: PMC9140718 DOI: 10.3390/genes13050792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Hereditary factor XI (FXI) deficiency is characterized as an autosomal mild to moderate coagulopathy in humans and domestic animals. Coagulation testing revealed FXI deficiency in a core family of Maine Coon cats (MCCs) in the United States. Factor XI-deficient MCCs were homozygous for a guanine to adenine transition resulting in a methionine substitution for the highly conserved valine-516 in the FXI catalytic domain. Immunoblots detected FXI of normal size and quantity in plasmas of MCCs homozygous for V516M. Some FXI-deficient MCCs experienced excessive post-operative/traumatic bleeding. Screening of 263 MCCs in Europe revealed a mutant allele frequency of 0.232 (23.2%). However, V516M was not found among 100 cats of other breeds. Recombinant feline FXI-M516 (fFXI-M516) expressed ~4% of the activity of wild-type fFXI-V516 in plasma clotting assays. Furthermore, fFXIa-M516 cleaved the chromogenic substrate S-2366 with ~4.3-fold lower catalytic efficacy (kcat/Km) than fFXIa-V516, supporting a conformational alteration of the protease active site. The rate of FIX activation by fFXIa-M516 was reduced >3-fold compared with fFXIa-V516. The common missense variant FXI-V516M causes a cross-reactive material positive FXI deficiency in MCCs that is associated with mild-moderate bleeding tendencies. Given the prevalence of the variant in MCCs, genotyping is recommended prior to invasive procedures or breeding.
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Affiliation(s)
- Henrike Kuder
- Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 260, CH-8057 Zurich, Switzerland;
- Laboklin GmbH & Co. KG (Labogen), Steubenstrasse 4, D-97688 Bad Kissingen, Germany; (A.K.); (E.M.)
| | - S. Kent Dickeson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1301 Medical Center Dr, Nashville, TN 37232, USA; (S.K.D.); (D.G.)
| | - Marjory B. Brooks
- Comparative Coagulation Laboratory, Cornell University, 240 Farrier Road, Ithaca, NY 14853, USA;
| | - Alexandra Kehl
- Laboklin GmbH & Co. KG (Labogen), Steubenstrasse 4, D-97688 Bad Kissingen, Germany; (A.K.); (E.M.)
| | - Elisabeth Müller
- Laboklin GmbH & Co. KG (Labogen), Steubenstrasse 4, D-97688 Bad Kissingen, Germany; (A.K.); (E.M.)
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1301 Medical Center Dr, Nashville, TN 37232, USA; (S.K.D.); (D.G.)
| | - Urs Giger
- Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 260, CH-8057 Zurich, Switzerland;
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41
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Jesus SA, Schmidt A, Fickel J, Doherr MG, Boonprasert K, Thitaram C, Sariya L, Ratanakron P, Hildebrandt TB. Assessing Coagulation Parameters in Healthy Asian Elephants (Elephas maximus) from European and Thai Populations. Animals (Basel) 2022; 12:ani12030361. [PMID: 35158684 PMCID: PMC8833339 DOI: 10.3390/ani12030361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
The Asian elephant population is continuously declining due to several extrinsic reasons in their range countries, but also due to diseases in captive populations worldwide. One of these diseases, the elephant endotheliotropic herpesvirus (EEHV) hemorrhagic disease, is very impactful because it particularly affects Asian elephant calves. It is commonly fatal and presents as an acute and generalized hemorrhagic syndrome. Therefore, having reference values of coagulation parameters, and obtaining such values for diseased animals in a very short time, is of great importance. We analyzed prothrombin time (PT), activated partial thromboplastin time (aPTT), and fibrinogen concentrations using a portable and fast point-of-care analyzer (VetScan Pro) in 127 Asian elephants from Thai camps and European captive herds. We found significantly different PT and aPTT coagulation times between elephants from the two regions, as well as clear differences in fibrinogen concentration. Nevertheless, these alterations were not expected to have biological or clinical implications. We have also sequenced the coagulation factor VII gene of 141 animals to assess the presence of a previously reported hereditary coagulation disorder in Asian elephants and to investigate the presence of other mutations. We did not find the previously reported mutation in our study population. Instead, we discovered the presence of several new single nucleotide polymorphisms, two of them being considered as deleterious by effect prediction software.
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Affiliation(s)
- Sónia A. Jesus
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
- Correspondence:
| | - Anke Schmidt
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; (A.S.); (J.F.)
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; (A.S.); (J.F.)
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Marcus G. Doherr
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität, 14163 Berlin, Germany;
| | - Khajohnpat Boonprasert
- Center of Elephant and Wildlife Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (K.B.); (C.T.)
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (K.B.); (C.T.)
| | - Ladawan Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Parntep Ratanakron
- Faculty of Veterinary Science and Applied Zoology, Chulabhorn Royal Academy, Bangkok 10210, Thailand;
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
- Faculty of Veterinary Medicine, Freie Universität, 14163 Berlin, Germany
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42
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Letelier A, Ljung R, Olsson A, Andersson NG. Silent variant in F8:c.222G>T (p.Thr74Thr) causes a partial exon skipping in a patient with mild hemophilia A. Mol Genet Genomic Med 2021; 10:e1856. [PMID: 34962362 PMCID: PMC8801133 DOI: 10.1002/mgg3.1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
One of the challenges of genetic testing in patients with hemophilia A is the interpretation of sequence variants. Here we report a silent variant found in exon 2 in the F8 gene in a 47‐year‐old patient with a previous von Willebrand disease (VWD) type 1 diagnosis. Clinically he had mild bleeding symptoms restricted to prolonged bleeding from minor wounds. Sanger sequencing of F8 gene using genomic DNA showed a hemizygous silent variant in exon 2: c.222G>T, p.Thr74Thr. When applying ACMG criteria, the variant was predicted to be “likely benign” in the analyzing software or VUS after curating. Sanger sequencing of the patient's cDNA after nested polymerase chain reaction showed that the patient had both a normal transcript containing exons 1–4 and a defect transcript lacking exon 2. These findings explain the patient's low FVIII:C level and led to the diagnosis of mild hemophilia A instead of VWD type 1. This case illustrates that mRNA work‐up may be needed to clarify a patient's phenotype–genotype.
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Affiliation(s)
- Anna Letelier
- Department of Clinical Sciences Lund (IKVL)-Pediatrics, Lund University, Lund, Sweden.,Department for Molecular Diagnostics, Clinical Genetics Hemophilia Laboratory, Region Skåne, Skåne University Hospital, Lund, Sweden
| | - Rolf Ljung
- Department of Clinical Sciences Lund (IKVL)-Pediatrics, Lund University, Lund, Sweden
| | - Anna Olsson
- Department of Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nadine G Andersson
- Department of Clinical Sciences Lund (IKVL)-Pediatrics, Lund University, Lund, Sweden.,Department of Pediatric Hematology and Oncology, Region Skåne, Skåne University Hospital, Lund, Sweden
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Nguyen BST, Le XTT, Huynh N, Nguyen HH, Truong Nguyen CM, Nguyen BH. Determining common variants in patients with haemophilia A in South Vietnam and screening female carriers in their family members. J Clin Pathol 2021; 76:339-344. [PMID: 34844950 PMCID: PMC10176336 DOI: 10.1136/jclinpath-2021-207703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/01/2021] [Indexed: 11/04/2022]
Abstract
AIMS The aim of this study was to determine common variants in F8, including intron 22 inversion (Inv22), intron 1 inversion (Inv1) and point mutations, the transmission of these variants between patients with haemophilia A (HA) and their family members. METHODS Genetic analysis was conducted in 71 patients who were clinically diagnosed with HA and 152 related female members in South Vietnam by a combination of inversion PCR (I-PCR), multiplex PCR and direct sequencing. RESULTS Variants in F8, including Inv22, point mutations (with 37 genotypes) and two novel variants, occupied 60 patients with HA. Among severe patients, the rate of Inv22 was 44%. Missense was the common point mutation of over 50% in patients with moderate HA and mild HA. Inv1 was absent in all patients. F8 variants were also found in 119 female carriers (FCs) (78.3%) from families related to patients with HA. There were 56 mothers (93.3%) carrying F8 variants and passing the same variants to their sons. CONCLUSIONS These findings were the first to provide important information about the presence of Inv22 and point mutation in Vietnamese patients with HA, the mothers and their female family members. It demonstrated that genetic diagnosis and counselling for HA carriers were essential factors for future improvements in comprehensive and equitable healthcare polices for patients with HA and FCs in Vietnam.
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Affiliation(s)
- Bang Suong Thi Nguyen
- Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam.,Laboratory Department, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City University Medical Center, Ho Chi Minh City, Vietnam
| | - Xuan Thao Thi Le
- Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam.,Laboratory Department, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City University Medical Center, Ho Chi Minh City, Vietnam
| | - Nghia Huynh
- Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Huy Huu Nguyen
- Laboratory Department, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City University Medical Center, Ho Chi Minh City, Vietnam
| | - Cong-Minh Truong Nguyen
- Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam.,Laboratory Department, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City University Medical Center, Ho Chi Minh City, Vietnam
| | - Bac Hoang Nguyen
- Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam .,Laboratory Department, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh City University Medical Center, Ho Chi Minh City, Vietnam
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44
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Lago J, Groot H, Navas D, Lago P, Gamboa M, Calderón D, Polanía-Villanueva DC. Genetic and Bioinformatic Strategies to Improve Diagnosis in Three Inherited Bleeding Disorders in Bogotá, Colombia. Genes (Basel) 2021; 12:genes12111807. [PMID: 34828413 PMCID: PMC8625804 DOI: 10.3390/genes12111807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/03/2022] Open
Abstract
Inherited bleeding disorders (IBDs) are the most frequent congenital diseases in the Colombian population; three of them are hemophilia A (HA), hemophilia B (HB), and von Willebrand Disease (VWD). Currently, diagnosis relies on multiple clinical laboratory assays to assign a phenotype. Due to the lack of accessibility to these tests, patients can receive an incomplete diagnosis. In these cases, genetic studies reinforce the clinical diagnosis. The present study characterized the molecular genetic basis of 11 HA, three HB, and five VWD patients by sequencing the F8, F9, or the VWF gene. Twelve variations were found in HA patients, four in HB patients, and 19 in WVD patients. From these variations a total of 25 novel variations were found. Disease-causing variations were used as positive controls for validation of the high-resolution melting (HRM) variant-scanning technique. This approach is a low-cost genetic diagnostic method proposed to be incorporated in developing countries. For the data analysis, we developed an accessible open-source code in Python that improves HRM data analysis with better sensitivity of 95% and without bias when using different HRM equipment and software. Analysis of amplicons with a length greater than 300 bp can be performed by implementing an analysis by denaturation domains.
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Affiliation(s)
- Juliana Lago
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Helena Groot
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Diego Navas
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
| | - Paula Lago
- Department of Basic Sciences, Kyushu Institute of Technology, Kitakyushu 804-8550, Japan;
| | - María Gamboa
- Laboratorio de Referencia en Hemostasia, Bogotá 110231, Colombia;
| | - Dayana Calderón
- Corporación Corpogen, Universidad Central, Bogotá 110311, Colombia;
| | - Diana C. Polanía-Villanueva
- Laboratorio de Genética Humana, Universidad de Los Andes, Bogotá 111711, Colombia; (J.L.); (H.G.); (D.N.)
- Correspondence:
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45
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Hermans C. Haemophilia diagnostics with modern genomics. Haemophilia 2021; 27:e754-e755. [PMID: 34748251 DOI: 10.1111/hae.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cedric Hermans
- Division of Hematology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), Brussels, Belgium
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46
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Kuder H, Sandzhieva-Vuzzo L, Kehl A, Rappaport JM, Müller E, Giger U. A Single Base Insertion in F9 Causing Hemophilia B in a Family of Newfoundland-Parti Standard Poodle Hybrid Dogs. Genes (Basel) 2021; 12:genes12101491. [PMID: 34680886 PMCID: PMC8535623 DOI: 10.3390/genes12101491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/26/2022] Open
Abstract
Hemophilia B is an x-linked recessive hereditary coagulopathy that has been reported in various species. We describe a male Newfoundland–Parti Standard Poodle hybrid puppy and its family with hemophilia B from clinical manifestations to the molecular genetic defect. The index case presented for dyspnea was found to have a mediastinal hematoma, while surgical removal and transfusion support brought some relief, progressive hematoma formations led to humane euthanasia. Sequencing the F9 exons revealed a single nucleotide insertion resulting in a frameshift in the last exon (NM_001003323.2:c.821_822insA), predicted to result in a premature stop codon (NP_001003323.1:p.Asn274LysfsTer23) with a loss of 178 of 459 amino acids. The unexpected high residual plasma factor IX activity (3% to 11% of control) was likely erroneous, but no further studies were performed. Both the purebred Newfoundland dam and her sister were heterozygous for the insertion. Five additional male offspring developed severe hemorrhage and were hemizygous for the F9 variant and/or had a prolonged aPTT. In contrast, other male littermates had normal aPTTs and no evidence of bleeding. While they are related to a common Newfoundland granddam, the prevalence of the pathogenic variant in the Newfoundland breed is currently unknown. These clinical to molecular genetic studies illustrate that precision medicine is achievable in clinical companion animal practice.
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Affiliation(s)
- Henrike Kuder
- Laboklin GmbH & Co. KG (Labogen), Steubenstraße 4, D-97688 Bad Kissingen, Germany; (H.K.); (A.K.); (E.M.)
- Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
| | - Liubov Sandzhieva-Vuzzo
- Advanced Veterinary Care Center, 8920 W. State Road 84, Davie, FL 33324, USA; (L.S.-V.); (J.M.R.)
| | - Alexandra Kehl
- Laboklin GmbH & Co. KG (Labogen), Steubenstraße 4, D-97688 Bad Kissingen, Germany; (H.K.); (A.K.); (E.M.)
| | - Jonathan M. Rappaport
- Advanced Veterinary Care Center, 8920 W. State Road 84, Davie, FL 33324, USA; (L.S.-V.); (J.M.R.)
| | - Elisabeth Müller
- Laboklin GmbH & Co. KG (Labogen), Steubenstraße 4, D-97688 Bad Kissingen, Germany; (H.K.); (A.K.); (E.M.)
| | - Urs Giger
- Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 260, CH-8057 Zürich, Switzerland
- Section of Medical Genetics (PennGen), School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104, USA
- Correspondence:
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47
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Hotea I, Brinza M, Blag C, Zimta AA, Dirzu N, Burzo C, Rus I, Apostu D, Benea H, Marian M, Mester A, Pasca S, Iluta S, Teodorescu P, Jitaru C, Zdrenghea M, Bojan A, Torok-Vistai T, Niculescu R, Tarniceriu C, Dima D, Truica C, Serban M, Tomuleasa C, Coriu D. Current therapeutic approaches in the management of hemophilia-a consensus view by the Romanian Society of Hematology. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1091. [PMID: 34423003 PMCID: PMC8339806 DOI: 10.21037/atm-21-747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022]
Abstract
Hemophilia A (HA) and hemophilia B (HB) are rare disorders, being caused by the total lack or under-expression of two factors from the coagulation cascade coded by genes of the X chromosome. Thus, in hemophilic patients, the blood does not clot properly. This results in spontaneous bleeding episodes after an injury or surgical intervention. A patient-centered regimen is considered optimal. Age, pharmacokinetics, bleeding phenotype, joint status, adherence, physical activity, personal goals are all factors that should be considered when individualizing therapy. In the past 10 years, many innovations in the diagnostic and treatment options were presented as being either approved or in development, thus helping clinicians to improve the standard-of-care for patients with hemophilia. Recombinant factors still remain the standard of care in hemophilia, however they pose a challenge to treatment adherence because they have short half-life, which where the extended half-life (EHL) factors come with the solution, increasing the half-life to 96 hours. Gene therapies have a promising future with proven beneficial effects in clinical trials. We present and critically analyze in the current manuscript the pros and cons of all the major discoveries in the diagnosis and treatment of HA and HB, as well as identify key areas of hemophilia research where improvements are needed.
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Affiliation(s)
- Ionut Hotea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.,Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Melen Brinza
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Cristina Blag
- Department of Pediatrics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Emergency Clinical Children's Hospital, Cluj Napoca, Romania
| | - Alina-Andreea Zimta
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Noemi Dirzu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Corina Burzo
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Ioana Rus
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Dragos Apostu
- Department of Orthopedics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Orthopedics, Emergency Clinical County Hospital, Cluj Napoca, Romania
| | - Horea Benea
- Department of Orthopedics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Orthopedics, Emergency Clinical County Hospital, Cluj Napoca, Romania
| | - Mirela Marian
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Alexandru Mester
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Ciprian Jitaru
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Anca Bojan
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Tunde Torok-Vistai
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Radu Niculescu
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania
| | - Cristina Tarniceriu
- Department of Anatomy, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania.,Department of Hematology, St. Spiridon County Clinical Emergency Hospital, Iasi, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Cristina Truica
- Department of Hematology, Constantin Opris Emergency Hospital, Baia Mare, Romania
| | - Margit Serban
- Department of Hematology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania.,European Haemophilia Treatment Center, Timisoara, Romania
| | - Ciprian Tomuleasa
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.,Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Daniel Coriu
- Department of Hematology, Fundeni Clinical Institute, Bucharest, Romania.,Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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48
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Zaninetti C, Wolff M, Greinacher A. Diagnosing Inherited Platelet Disorders: Modalities and Consequences. Hamostaseologie 2021; 41:475-488. [PMID: 34391210 DOI: 10.1055/a-1515-0813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Inherited platelet disorders (IPDs) are a group of rare conditions featured by reduced circulating platelets and/or impaired platelet function causing variable bleeding tendency. Additional hematological or non hematological features, which can be congenital or acquired, distinctively mark the clinical picture of a subgroup of patients. Recognizing an IPD is challenging, and diagnostic delay or mistakes are frequent. Despite the increasing availability of next-generation sequencing, a careful phenotyping of suspected patients-concerning the general clinical features, platelet morphology, and function-is still demanded. The cornerstones of IPD diagnosis are clinical evaluation, laboratory characterization, and genetic testing. Achieving a diagnosis of IPD is desirable for several reasons, including the possibility of tailored therapeutic strategies and individual follow-up programs. However, detailed investigations can also open complex scenarios raising ethical issues in case of IPDs predisposing to hematological malignancies. This review offers an overview of IPD diagnostic workup, from the interview with the proband to the molecular confirmation of the suspected disorder. The main implications of an IPD diagnosis are also discussed.
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Affiliation(s)
- Carlo Zaninetti
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany.,Department of Internal Medicine, University of Pavia, Pavia, Italy
| | - Martina Wolff
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
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49
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Lombardi S, Leo G, Merlin S, Follenzi A, McVey JH, Maestri I, Bernardi F, Pinotti M, Balestra D. Dissection of pleiotropic effects of variants in and adjacent to F8 exon 19 and rescue of mRNA splicing and protein function. Am J Hum Genet 2021; 108:1512-1525. [PMID: 34242570 DOI: 10.1016/j.ajhg.2021.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
The pathogenic significance of nucleotide variants commonly relies on nucleotide position within the gene, with exonic changes generally attributed to quantitative or qualitative alteration of protein biosynthesis, secretion, activity, or clearance. However, these changes may exert pleiotropic effects on both protein biology and mRNA splicing due to the overlapping of the amino acid and splicing codes, thus shaping the disease phenotypes. Here, we focused on hemophilia A, in which the definition of F8 variants' causative role and association to bleeding phenotypes is crucial for proper classification, genetic counseling, and management of affected individuals. We extensively characterized a large panel of hemophilia A-causing variants (n = 30) within F8 exon 19 by combining and comparing in silico and recombinant expression analyses. We identified exonic variants with pleiotropic effects and dissected the altered protein features of all missense changes. Importantly, results from multiple prediction algorithms provided qualitative results, while recombinant assays allowed us to correctly infer the likely phenotype severity for 90% of variants. Molecular characterization of pathogenic variants was also instrumental for the development of tailored correction approaches to rescue splicing affecting variants or missense changes impairing protein folding. A single engineered U1snRNA rescued mRNA splicing of nine different variants and the use of a chaperone-like drug resulted in improved factor VIII protein secretion for four missense variants. Overall, dissection of the molecular mechanisms of a large panel of HA variants allowed precise classification of HA-affected individuals and favored the development of personalized therapeutic approaches.
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Affiliation(s)
- Silvia Lombardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Gabriele Leo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Simone Merlin
- Department of Health Sciences, University of Piemonte Orientale, Novara 28100, Italy
| | - Antonia Follenzi
- Department of Health Sciences, University of Piemonte Orientale, Novara 28100, Italy
| | - John H McVey
- School of Bioscience and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Iva Maestri
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara 44123, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy.
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy.
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50
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Lopes TJS, Rios R, Nogueira T, Mello RF. Protein residue network analysis reveals fundamental properties of the human coagulation factor VIII. Sci Rep 2021; 11:12625. [PMID: 34135429 PMCID: PMC8209229 DOI: 10.1038/s41598-021-92201-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Hemophilia A is an X-linked inherited blood coagulation disorder caused by the production and circulation of defective coagulation factor VIII protein. People living with this condition receive either prophylaxis or on-demand treatment, and approximately 30% of patients develop inhibitor antibodies, a serious complication that limits treatment options. Although previous studies performed targeted mutations to identify important residues of FVIII, a detailed understanding of the role of each amino acid and their neighboring residues is still lacking. Here, we addressed this issue by creating a residue interaction network (RIN) where the nodes are the FVIII residues, and two nodes are connected if their corresponding residues are in close proximity in the FVIII protein structure. We studied the characteristics of all residues in this network and found important properties related to disease severity, interaction to other proteins and structural stability. Importantly, we found that the RIN-derived properties were in close agreement with in vitro and clinical reports, corroborating the observation that the patterns derived from this detailed map of the FVIII protein architecture accurately capture the biological properties of FVIII.
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Affiliation(s)
- Tiago J S Lopes
- Department of Reproductive Biology, Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Ricardo Rios
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Tatiane Nogueira
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Rodrigo F Mello
- Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil.,Itaú Unibanco, Av. Eng. Armando de Arruda Pereira, 707, Jabaquara, São Paulo, 04309-010, Brazil
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