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Ma C, Zhou Z, Liu H, Koslicki D. KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description. Gigascience 2022; 12:giad057. [PMID: 37602759 PMCID: PMC10441000 DOI: 10.1093/gigascience/giad057] [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: 01/31/2023] [Revised: 05/05/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action (MOAs) between repurposed drugs and their target diseases remain largely unknown, which is still a main obstacle for computational drug repurposing methods to be widely adopted in clinical settings. RESULTS In this work, we propose KGML-xDTD: a Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases. It is a 2-module framework that not only predicts the treatment probabilities between drugs/compounds and diseases but also biologically explains them via knowledge graph (KG) path-based, testable MOAs. We leverage knowledge-and-publication-based information to extract biologically meaningful "demonstration paths" as the intermediate guidance in the Graph-based Reinforcement Learning (GRL) path-finding process. Comprehensive experiments and case study analyses show that the proposed framework can achieve state-of-the-art performance in both predictions of drug repurposing and recapitulation of human-curated drug MOA paths. CONCLUSIONS KGML-xDTD is the first model framework that can offer KG path explanations for drug repurposing predictions by leveraging the combination of prediction outcomes and existing biological knowledge and publications. We believe it can effectively reduce "black-box" concerns and increase prediction confidence for drug repurposing based on predicted path-based explanations and further accelerate the process of drug discovery for emerging diseases.
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Affiliation(s)
- Chunyu Ma
- Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Zhihan Zhou
- Department of Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - Han Liu
- Department of Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - David Koslicki
- Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
- Department of Computer Science and Engineering, Pennsylvania State University, State College, PA 16801, USA
- Department of Biology, Pennsylvania State University, State College, PA 16801, USA
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Kishimoto TK. Development of ImmTOR Tolerogenic Nanoparticles for the Mitigation of Anti-drug Antibodies. Front Immunol 2020; 11:969. [PMID: 32508839 PMCID: PMC7251066 DOI: 10.3389/fimmu.2020.00969] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
The development of anti-drug antibodies (ADAs) is a common cause for treatment failure and hypersensitivity reactions for many biologics. The focus of this review is the development of ImmTOR, a platform technology designed to prevent the formation of ADAs that can be applied broadly across a wide variety of biologics by inducing immunological tolerance with ImmTOR nanoparticles encapsulating rapamycin. The induction of tolerance is antigen-specific and dependent on the incorporation of rapamycin in nanoparticles and the presence of the antigen at the time of administration of ImmTOR. Evidence for the induction of specific immune tolerance vs. general immune suppression is supported by the findings that: (1) ImmTOR induces regulatory T cells specific to the co-administered antigen; (2) tolerance can be transferred by adoptive transfer of splenocytes from treated animals to naïve recipients; (3) the tolerance is durable to subsequent challenge with antigen alone; and (4) animals tolerized to a specific antigen are capable of responding to an unrelated antigen. ImmTOR nanoparticles can be added to new or existing biologics without the need to modify or reformulate the biologic drug. The ability of ImmTOR to mitigate the formation of ADAs has been demonstrated for coagulation factor VIII in a mouse model of hemophilia A, an anti-TNFα monoclonal antibody in a mouse model of inflammatory arthritis, pegylated uricase in hyperuricemic mice and in non-human primates, acid alpha-glucosidase in a mouse model of Pompe disease, recombinant immunotoxin in a mouse model of mesothelioma, and adeno-associated vectors in a model of repeat dosing of gene therapy vectors in mice and in non-human primates. Human proof-of concept for the mitigation of ADAs has been demonstrated with SEL-212, a combination product consisting of ImmTOR + pegadricase, a highly immunogenic enzyme therapy for the treatment of gout. ImmTOR represents a promising approach to preventing the formation of ADAs to a broad range of biologic drugs.
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Kafal AR, Vinh DC, Langelier MJ. Prefilled syringes for immunoglobulin G (IgG) replacement therapy: clinical experience from other disease settings. Expert Opin Drug Deliv 2018; 15:1199-1209. [DOI: 10.1080/17425247.2018.1546692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ayman R. Kafal
- Medical Affairs, CSL Behring LLC, King of Prussia, PA, USA
| | - Donald C. Vinh
- Infectious Disease Susceptibility Program, Research Institute – McGill University Health Centre, Montreal, Quebec, Canada
| | - Mélanie J. Langelier
- Infectious Disease Susceptibility Program, Research Institute – McGill University Health Centre, Montreal, Quebec, Canada
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Principles of treatment and update of recommendations for the management of haemophilia and congenital bleeding disorders in Italy. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2015; 12:575-98. [PMID: 25350962 DOI: 10.2450/2014.0223-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Patel N, Wyrko Z, Naqvi S, Croft AP. Acquired haemophilia A: the importance of early recognition in cases of spontaneous bleeding in the elderly. BMJ Case Rep 2014; 2014:bcr-2014-206911. [PMID: 25414221 DOI: 10.1136/bcr-2014-206911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We describe the case of a 79-year-old man who presented 'off legs' with acute right leg pain. He was initially treated for suspected cellulitis but subsequently found to have spontaneous soft tissue bleeding into the right thigh. He was eventually diagnosed with idiopathic acquired haemophilia A and treated with activated prothrombin complex concentrates to control acute bleeding followed by immunosuppressant therapy. Acquired haemophilia A is a potentially life-threatening and under-recognised bleeding disorder that results from the immune-mediated development of autoantibodies directed against coagulation factor VIII. The disease is more common in elderly individuals where early recognition and treatment is compounded by the presence of other comorbid conditions, including other potential causes of bleeding. These confounding factors and lack of awareness among non-specialists accounts for the delay in diagnosis that is common in this disease and contributes to the persistently high mortality in this age group.
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Affiliation(s)
- Neeral Patel
- Department of Geriatric Medicine, Queen Elizabeth Hospital, Birmimgham, UK
| | - Zoe Wyrko
- Department of Geriatric Medicine, Queen Elizabeth Hospital, Birmimgham, UK
| | - Syeda Naqvi
- Sandwell General Hospital, West Bromwich, UK
| | - Adam P Croft
- Department of Rheumatology, University of Birmingham, Birmingham, UK
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Arrieta-Blanco JJ, Oñate-Sánchez R, Martínez-López F, Oñate-Cabrerizo D, Cabrerizo-Merino MDC. Inherited, congenital and acquired disorders by hemostasis (vascular, platelet & plasmatic phases) with repercussions in the therapeutic oral sphere. Med Oral Patol Oral Cir Bucal 2014; 19:e280-8. [PMID: 24121923 PMCID: PMC4048118 DOI: 10.4317/medoral.19560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 09/08/2013] [Indexed: 11/05/2022] Open
Abstract
The hemostasis alterations, either congenital or hereditary origin, and acquired, are circumstances that hinder oral care to patients who suffer them and also generates in the professional who has to attend, high stress. Bleeding control once established and dental treatment planning, both in the aspect of preparation, as the realization of the odonto-stomatological therapeutic, has suffered updates that do need to remember certain aspects of the care of these patients. But we must not forget that the hematologist or internist who controls the patient's medical condition, is a cornerstone for the planning and implementation of treatment plans. We must also remember that, in certain circumstances, treatment should be performed in a hospital setting. In this review, we aim to provide the odonto-stomatologist guidance on how to address the problem and provide simple and updated guidelines to apply in the treatment of these people.
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Affiliation(s)
- Juan-José Arrieta-Blanco
- Unidad Docente de Pacientes Especiales, Clínica Odontológica Universitaria 2 Planta, Hospital Morales Meseguer, Avenida Marqués de los Velez s/n, 30.008 Murcia,
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Girolami A, Bertozzi I, de Marinis GB, Bonamigo E, Fabris F. Activated FVII levels in factor VII Padua (Arg304Gln) coagulation disorder and in true factor VII deficiency: a study in homozygotes and heterozygotes. Hematology 2013; 16:308-12. [DOI: 10.1179/102453311x13085644680069] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- A Girolami
- Department of Medical and Surgical SciencesUniversity of Padua Medical School, Italy
| | - I Bertozzi
- Department of Medical and Surgical SciencesUniversity of Padua Medical School, Italy
| | - G Berti de Marinis
- Department of Medical and Surgical SciencesUniversity of Padua Medical School, Italy
| | - E Bonamigo
- Department of Medical and Surgical SciencesUniversity of Padua Medical School, Italy
| | - F Fabris
- Department of Medical and Surgical SciencesUniversity of Padua Medical School, Italy
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Cortese L, Pedone C, Laudisio A, Danti M, Incalzi RA. Acquired Hemophilia A: From Diagnosis to Treatment: A Case Report of an 88-Year-Old Woman. J Am Geriatr Soc 2013; 61:659-61. [DOI: 10.1111/jgs.12189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livio Cortese
- Area di Geriatria; Università Campus Bio-Medico; Rome Italy
| | - Claudio Pedone
- Area di Geriatria; Università Campus Bio-Medico; Rome Italy
- Fondazione Alberto Sordi; Rome Italy
| | - Alice Laudisio
- Area di Geriatria; Università Campus Bio-Medico; Rome Italy
| | | | - Raffaele Antonelli Incalzi
- Area di Geriatria; Università Campus Bio-Medico; Rome Italy
- Fondazione San Raffaele; Cittadella della Carità; Taranto Italy
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Sborov DW, Rodgers GM. How I manage patients with acquired haemophilia A. Br J Haematol 2013; 161:157-65. [DOI: 10.1111/bjh.12228] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Douglas W. Sborov
- Division of Hematology and Oncology; Ohio State University Medical Center; The Arthur G. James Comprehensive Cancer Center; Columbus; OH; USA
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Effect of hemodilution on coagulation and recombinant factor VIIa efficacy in human blood in vitro. ACTA ACUST UNITED AC 2011; 71:1152-63. [PMID: 21610535 DOI: 10.1097/ta.0b013e318215178c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND This study evaluates the effect of hemodilution by various common resuscitation fluids, and the efficacy of activated recombinant factor VII (rFVIIa) on coagulation parameters in human blood in vitro. METHODS Samples from normal healthy volunteers (n = 9) were hemodiluted from 0% to 90% with normal saline, or 0%, 40%, 60%, and 80% with 5% albumin, Hespan, Hextend, normal saline, or lactated Ringer's, and incubated at 37°C ± 1°C for 30 minutes with and without rFVIIa (1.26 μg/mL). RESULTS There was a strong correlation between the dilution of hemoglobin (Hb), platelets, or fibrinogen and coagulation parameters. Hemodilution 0% to 90% changed coagulation parameters (prothrombin time [PT], activated partial thromboplastin time [aPTT], and thromboelastography) in an exponential fashion; the greatest changes occurred after hemodilution lowered Hb <6 mg/dL, platelet count < 100,000/mm(3), and fibrinogen concentration <200 mg/dL. PT and aPTT were significantly prolonged after 60% and 80% dilution for all fluids. Hemodilution of 60% and 80% significantly decreased clot strength (maximum amplitude) and the kinetics of clot development (α angle) and increased the clot formation time (K). Hemodilution with Hextend and Hespan decreased maximum amplitude and α angle >5% albumin, lactated Ringer's, or normal saline. rFVIIa significantly improved PT at 60% and 80% dilutions, and aPTT at 80% dilution. There was a significant effect of dilution, but not fluid type, on the efficacy of rFVIIa to change PT and aPTT, and the onset of clotting (R). CONCLUSIONS We have strong in vitro evidence that Hb <6 mg/dL, platelet count <100,000/mm(3), and fibrinogen concentration <200 mg/dL can be used as indexes of hemodilution-induced coagulopathy. This study also shows that Hextend and Hespan tend to decrease the clotting ability >5% albumin or the crystalloids. rFVIIa significantly decreased PT at all dilutions and aPTT at the highest dilution. The effectiveness of rFVIIa on PT and aPTT was significantly affected by the degree of dilution, but not by the type of fluid.
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Sørensen B, Dargaud Y, Kenet G, Lusher J, Mumford A, Pipe S, Tiede A. On-demand treatment of bleeds in haemophilia patients with inhibitors: strategies for securing and maintaining predictable efficacy with recombinant activated factor VII. Haemophilia 2011; 18:255-62. [PMID: 21771206 DOI: 10.1111/j.1365-2516.2011.02612.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- B Sørensen
- Haemostasis Research Unit, Centre for Haemostasis & Thrombosis, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London, UK.
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Tiede A, Friedrich U, Stenmo C, Allen G, Giangrande P, Goudemand J, Hay C, Holmström M, Klamroth R, Lethagen S, McKenzie S, Miesbach W, Negrier C, Yuste VJ, Berntorp E. Safety and pharmacokinetics of subcutaneously administered recombinant activated factor VII (rFVIIa). J Thromb Haemost 2011; 9:1191-9. [PMID: 21489128 DOI: 10.1111/j.1538-7836.2011.04293.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Recombinant activated factor VIIa (rFVIIa) is used to treat bleeds in hemophilia patients with inhibitors. A subcutaneous formulation could potentially improve its half-life and make it suitable for prophylactic treatment. OBJECTIVES A study was conducted to determine the safety of subcutaneously administered rFVIIa in patients with hemophilia and the pharmacokinetic profile (including bioavailability). PATIENTS/METHODS This was a multicenter, open-label, cross-over comparison of single doses of intravenous rFVIIa 90μgkg(-1) and a new formulation of rFVIIa for subcutaneous injection at dose levels of 45, 90, 180, 270 and 360μgkg(-1) . Sixty subjects (12 per dose cohort) with hemophilia A or B were enrolled. RESULTS Subcutaneously administered rFVIIa showed lower mean peak plasma concentrations and prolonged FVII activity (C(max) , 0.44-5.16IU mL(-1) [across doses]; t(1/2) , 12.4h; t(max) , 5.6h) compared with intravenously administered rFVIIa (C(max) , 51.7IUmL(-1) ; t(1/2) , 2.7h; t(max) , <10min). The absolute bioavailability of subcutaneous rFVIIa ranged from 21.1 to 30.1% across dose levels. Dose proportionality was observed within a 2-fold dose increase but not across the full dose range. No thromboembolic events, drug-related serious adverse events, severe injection-site reactions or neutralizing antibodies were reported (primary endpoint). Mild and moderate injection-site reactions were more frequent with subcutaneous than with intravenous injections. CONCLUSION This phase I clinical trial did not identify safety concerns of prolonged exposure to rFVIIa administered subcutaneously in single doses to hemophilia patients.
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Affiliation(s)
- A Tiede
- Hannover Medical School, Hannover, Germany
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KAVAKLI K, YESILIPEK A, ANTMEN B, AKSU S, BALKAN C, YILMAZ D, KUPESIZ A, SASMAZ I, LINDGREN P, MESTERTON J. The value of early treatment in patients with haemophilia and inhibitors. Haemophilia 2010; 16:487-94. [DOI: 10.1111/j.1365-2516.2009.02179.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Huth-Kühne A, Baudo F, Collins P, Ingerslev J, Kessler CM, Lévesque H, Castellano MEM, Shima M, St-Louis J. International recommendations on the diagnosis and treatment of patients with acquired hemophilia A. Haematologica 2009; 94:566-75. [PMID: 19336751 DOI: 10.3324/haematol.2008.001743] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Acquired hemophilia A (AHA) is a rare bleeding disorder characterized by autoantibodies directed against circulating coagulation factor (F) VIII. Typically, patients with no prior history of a bleeding disorder present with spontaneous bleeding and an isolated prolonged aPTT. AHA may, however, present without any bleeding symptoms, therefore an isolated prolonged aPTT should always be investigated further irrespective of the clinical findings. Control of acute bleeding is the first priority, and we recommend first-line therapy with bypassing agents such as recombinant activated FVII or activated prothrombin complex concentrate. Once the diagnosis has been achieved, immediate autoantibody eradication to reduce subsequent bleeding risk should be performed. We recommend initial treatment with corticosteroids or combination therapy with corticosteroids and cyclophosphamide and suggest second-line therapy with rituximab if first-line therapy fails or is contraindicated. In contrast to congenital hemophilia, no comparative studies exist to support treatment recommendations for patients with AHA, therefore treatment guidance must rely on the expertise and clinical experience of specialists in the field. The aim of this document is to provide a set of international practice guidelines based on our collective clinical experience in treating patients with AHA and contribute to improved care for this patient group.
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Affiliation(s)
- Angela Huth-Kühne
- SRH Kurpfalzkrankenhaus and Hemophilia Center Heidelberg gGmbH Bonhoefferstrasse 5, 69123 Heidelberg.
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Sfaihi Ben Mansour L, Thabet A, Aloulou H, Turki H, Chabchoub I, Mhiri F, Mnif Z, Ben Ali H, Kammoun T, Hachicha M. Déficit congénital en facteur VII de la coagulation, révélé par une hémorragie cérébrale. Arch Pediatr 2009; 16:1024-7. [DOI: 10.1016/j.arcped.2009.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 09/06/2008] [Accepted: 03/25/2009] [Indexed: 11/16/2022]
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