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Nichol D, Robertson-Tessi M, Anderson ARA, Jeavons P. Model genotype-phenotype mappings and the algorithmic structure of evolution. J R Soc Interface 2019; 16:20190332. [PMID: 31690233 PMCID: PMC6893500 DOI: 10.1098/rsif.2019.0332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cancers are complex dynamic systems that undergo evolution and selection. Personalized medicine approaches in the clinic increasingly rely on predictions of tumour response to one or more therapies; these predictions are complicated by the inevitable evolution of the tumour. Despite enormous amounts of data on the mutational status of cancers and numerous therapies developed in recent decades to target these mutations, many of these treatments fail after a time due to the development of resistance in the tumour. The emergence of these resistant phenotypes is not easily predicted from genomic data, since the relationship between genotypes and phenotypes, termed the genotype-phenotype (GP) mapping, is neither injective nor functional. We present a review of models of this mapping within a generalized evolutionary framework that takes into account the relation between genotype, phenotype, environment and fitness. Different modelling approaches are described and compared, and many evolutionary results are shown to be conserved across studies despite using different underlying model systems. In addition, several areas for future work that remain understudied are identified, including plasticity and bet-hedging. The GP-mapping provides a pathway for understanding the potential routes of evolution taken by cancers, which will be necessary knowledge for improving personalized therapies.
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Affiliation(s)
- Daniel Nichol
- Department of Computer Science, University of Oxford, Oxford, UK
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alexander R. A. Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Peter Jeavons
- Department of Computer Science, University of Oxford, Oxford, UK
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2
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Abstract
Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine.
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Affiliation(s)
- Kalliopi Trachana
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Rhishikesh Bargaje
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Gustavo Glusman
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Nathan D Price
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Sui Huang
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.).,Department of Biological Sciences, University of Calgary, Alberta, Canada (S.H.)
| | - Leroy E Hood
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
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3
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A tutorial on model informed approaches to cardiovascular safety with focus on cardiac repolarisation. J Pharmacokinet Pharmacodyn 2018; 45:365-381. [PMID: 29736890 DOI: 10.1007/s10928-018-9589-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/16/2018] [Indexed: 12/19/2022]
Abstract
Drugs can affect the cardiovascular (CV) system either as an intended treatment or as an unwanted side effect. In both cases, drug-induced cardiotoxicities such as arrhythmia and unfavourable hemodynamic effects can occur, and be described using mathematical models; such a model informed approach can provide valuable information during drug development and can aid decision-making. However, in order to develop informative models, it is vital to understand CV physiology. The aims of this tutorial are to present (1) key background biological and medical aspects of the CV system, (2) CV electrophysiology, (3) CV safety concepts, (4) practical aspects of development of CV models and (5) regulatory expectations with a focus on using model informed and quantitative approaches to support nonclinical and clinical drug development. In addition, we share several case studies to provide practical information on project strategy (planning, key questions, assumptions setting, and experimental design) and mathematical models development that support decision-making during drug discovery and development.
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4
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Romero L, Cano J, Gomis-Tena J, Trenor B, Sanz F, Pastor M, Saiz J. In Silico QT and APD Prolongation Assay for Early Screening of Drug-Induced Proarrhythmic Risk. J Chem Inf Model 2018; 58:867-878. [PMID: 29547274 DOI: 10.1021/acs.jcim.7b00440] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue. Multiple channel-drug interactions and state-of-the-art human ventricular action potential models ( O'Hara , T. , PLos Comput. Biol. 2011 , 7 , e1002061 ) were used in our simulations. Specifically, 206.766 cellular and 7072 tissue simulations were performed by blocking the slow and the fast components of the delayed rectifier current ( IKs and IKr, respectively) and the L-type calcium current ( ICaL) at different levels. The performance of our system was validated by classifying the proarrhythmic risk of 84 compounds, 40 of which present torsadogenic properties. On the basis of these results, we propose the use of a new index (Tx) for discriminating torsadogenic compounds, defined as the ratio of the drug concentrations producing 10% prolongation of the cellular endocardial, midmyocardial, and epicardial APDs and the QT interval, over the maximum effective free therapeutic plasma concentration (EFTPC). Our results show that the Tx index outperforms standard methods for early identification of torsadogenic compounds. Indeed, for the analyzed compounds, the Tx tests accuracy was in the range of 87-88% compared with a 73% accuracy of the hERG IC50 based test.
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Affiliation(s)
- Lucia Romero
- Centro de Investigación e Innovación en Bioingeniería (CI2B) , Universitat Politècnica de València , camino de Vera, s/n , 46022 Valencia , Spain
| | - Jordi Cano
- Centro de Investigación e Innovación en Bioingeniería (CI2B) , Universitat Politècnica de València , camino de Vera, s/n , 46022 Valencia , Spain
| | - Julio Gomis-Tena
- Centro de Investigación e Innovación en Bioingeniería (CI2B) , Universitat Politècnica de València , camino de Vera, s/n , 46022 Valencia , Spain
| | - Beatriz Trenor
- Centro de Investigación e Innovación en Bioingeniería (CI2B) , Universitat Politècnica de València , camino de Vera, s/n , 46022 Valencia , Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Carrer del Dr. Aiguader 88 , 08002 Barcelona , Spain
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Carrer del Dr. Aiguader 88 , 08002 Barcelona , Spain
| | - Javier Saiz
- Centro de Investigación e Innovación en Bioingeniería (CI2B) , Universitat Politècnica de València , camino de Vera, s/n , 46022 Valencia , Spain
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5
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Musuamba FT, Manolis E, Holford N, Cheung S, Friberg LE, Ogungbenro K, Posch M, Yates J, Berry S, Thomas N, Corriol-Rohou S, Bornkamp B, Bretz F, Hooker AC, Van der Graaf PH, Standing JF, Hay J, Cole S, Gigante V, Karlsson K, Dumortier T, Benda N, Serone F, Das S, Brochot A, Ehmann F, Hemmings R, Rusten IS. Advanced Methods for Dose and Regimen Finding During Drug Development: Summary of the EMA/EFPIA Workshop on Dose Finding (London 4-5 December 2014). CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 6:418-429. [PMID: 28722322 PMCID: PMC5529745 DOI: 10.1002/psp4.12196] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 02/05/2023]
Abstract
Inadequate dose selection for confirmatory trials is currently still one of the most challenging issues in drug development, as illustrated by high rates of late‐stage attritions in clinical development and postmarketing commitments required by regulatory institutions. In an effort to shift the current paradigm in dose and regimen selection and highlight the availability and usefulness of well‐established and regulatory‐acceptable methods, the European Medicines Agency (EMA) in collaboration with the European Federation of Pharmaceutical Industries Association (EFPIA) hosted a multistakeholder workshop on dose finding (London 4–5 December 2014). Some methodologies that could constitute a toolkit for drug developers and regulators were presented. These methods are described in the present report: they include five advanced methods for data analysis (empirical regression models, pharmacometrics models, quantitative systems pharmacology models, MCP‐Mod, and model averaging) and three methods for study design optimization (Fisher information matrix (FIM)‐based methods, clinical trial simulations, and adaptive studies). Pairwise comparisons were also discussed during the workshop; however, mostly for historical reasons. This paper discusses the added value and limitations of these methods as well as challenges for their implementation. Some applications in different therapeutic areas are also summarized, in line with the discussions at the workshop. There was agreement at the workshop on the fact that selection of dose for phase III is an estimation problem and should not be addressed via hypothesis testing. Dose selection for phase III trials should be informed by well‐designed dose‐finding studies; however, the specific choice of method(s) will depend on several aspects and it is not possible to recommend a generalized decision tree. There are many valuable methods available, the methods are not mutually exclusive, and they should be used in conjunction to ensure a scientifically rigorous understanding of the dosing rationale.
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Affiliation(s)
- F T Musuamba
- EMA Modelling and Simulation Working Group, London, UK.,Federal Agency for Medicines and Health Products, Brussels, Belgium.,UMR850 INSERM, Université de Limoges, Limoges, France
| | - E Manolis
- EMA Modelling and Simulation Working Group, London, UK.,European Medicines Agency, London, UK
| | - N Holford
- Department of Pharmacology & Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | | | | | | | - M Posch
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - S Berry
- Berry consultants, Austin, Texas, USA
| | | | | | | | - F Bretz
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria.,Novartis, London, UK
| | | | - P H Van der Graaf
- Leiden Academic Centre for Drug Research, Leiden, The Netherlands.,Certara QSP, Canterbury, UK
| | - J F Standing
- EMA Modelling and Simulation Working Group, London, UK.,University College London, London, UK
| | - J Hay
- EMA Modelling and Simulation Working Group, London, UK.,Medicines and Healthcare Products Regulatory Agency, London, UK
| | - S Cole
- EMA Modelling and Simulation Working Group, London, UK.,Medicines and Healthcare Products Regulatory Agency, London, UK
| | - V Gigante
- EMA Modelling and Simulation Working Group, London, UK.,Agenzia Italiana del Farmaco, Roma, Italy
| | - K Karlsson
- EMA Modelling and Simulation Working Group, London, UK.,Medical Products Agency, Uppsala, Sweden
| | | | - N Benda
- EMA Modelling and Simulation Working Group, London, UK.,Bundesinstitut für Arzneimittel und Medizinprodukte, Bonn, Germany
| | - F Serone
- EMA Modelling and Simulation Working Group, London, UK.,Agenzia Italiana del Farmaco, Roma, Italy
| | - S Das
- AstraZeneca UK Limited, London, UK
| | | | - F Ehmann
- European Medicines Agency, London, UK
| | - R Hemmings
- Medicines and Healthcare Products Regulatory Agency, London, UK
| | - I Skottheim Rusten
- EMA Modelling and Simulation Working Group, London, UK.,Norvegian Medicines Agency, Oslo, Norway
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6
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Luo C, Wang K, Zhang H. In silico assessment of the effects of quinidine, disopyramide and E-4031 on short QT syndrome variant 1 in the human ventricles. PLoS One 2017. [PMID: 28632743 PMCID: PMC5478111 DOI: 10.1371/journal.pone.0179515] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Aims Short QT syndrome (SQTS) is an inherited disorder associated with abnormally abbreviated QT intervals and an increased incidence of atrial and ventricular arrhythmias. SQT1 variant (linked to the rapid delayed rectifier potassium channel current, IKr) of SQTS, results from an inactivation-attenuated, gain-of-function mutation (N588K) in the KCNH2-encoded potassium channels. Pro-arrhythmogenic effects of SQT1 have been well characterized, but less is known about the possible pharmacological antiarrhythmic treatment of SQT1. Therefore, this study aimed to assess the potential effects of E-4031, disopyramide and quinidine on SQT1 using a mathematical model of human ventricular electrophysiology. Methods The ten Tusscher et al. biophysically detailed model of the human ventricular action potential (AP) was modified to incorporate IKr Markov chain (MC) formulations based on experimental data of the kinetics of the N588K mutation of the KCNH2-encoded subunit of the IKr channels. The modified ventricular cell model was then integrated into one-dimensional (1D) strand, 2D regular and realistic tissues with transmural heterogeneities. The channel-blocking effect of the drugs on ion currents in healthy and SQT1 cells was modeled using half-maximal inhibitory concentration (IC50) and Hill coefficient (nH) values from literatures. Effects of drugs on cell AP duration (APD), effective refractory period (ERP) and pseudo-ECG traces were calculated. Effects of drugs on the ventricular temporal and spatial vulnerability to re-entrant excitation waves were measured. Re-entry was simulated in both 2D regular and realistic ventricular tissue. Results At the single cell level, the drugs E-4031 and disopyramide had hardly noticeable effects on the ventricular cell APD at 90% repolarization (APD90), whereas quinidine caused a significant prolongation of APD90. Quinidine prolonged and decreased the maximal transmural AP heterogeneity (δV); this led to the decreased transmural heterogeneity of APD across the 1D strand. Quinidine caused QT prolongation and a decrease in the T-wave amplitude, and increased ERP and decreased temporal susceptibility of the tissue to the initiation of re-entry and increased the minimum substrate size necessary to prevent re-entry in the 2D regular model, and further terminated re-entrant waves in the 2D realistic model. Quinidine exhibited significantly better therapeutic effects on SQT1 than E-4031 and disopyramide. Conclusions The simulated pharmacological actions of quinidine exhibited antiarrhythmic effects on SQT1. This study substantiates a causal link between quinidine and QT interval prolongation in SQT1 and suggests that quinidine may be a potential pharmacological agent for treating SQT1 patients.
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Affiliation(s)
- Cunjin Luo
- School of Computer Science and Technology, Harbin Institute of Technology (HIT), Harbin, China
| | - Kuanquan Wang
- School of Computer Science and Technology, Harbin Institute of Technology (HIT), Harbin, China
- * E-mail: (KW); (HZ)
| | - Henggui Zhang
- School of Computer Science and Technology, Harbin Institute of Technology (HIT), Harbin, China
- School of Physics and Astronomy, The University of Manchester, Manchester, United Kingdom
- Space Institute of Southern China, Shenzhen, China
- * E-mail: (KW); (HZ)
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7
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Gouveia PJ, Rosa S, Ricotti L, Abecasis B, Almeida HV, Monteiro L, Nunes J, Carvalho FS, Serra M, Luchkin S, Kholkin AL, Alves PM, Oliveira PJ, Carvalho R, Menciassi A, das Neves RP, Ferreira LS. Flexible nanofilms coated with aligned piezoelectric microfibers preserve the contractility of cardiomyocytes. Biomaterials 2017. [PMID: 28622605 DOI: 10.1016/j.biomaterials.2017.05.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The use of engineered cardiac tissue for high-throughput drug screening/toxicology assessment remains largely unexplored. Here we propose a scaffold that mimics aspects of cardiac extracellular matrix while preserving the contractility of cardiomyocytes. The scaffold is based on a poly(caprolactone) (PCL) nanofilm with magnetic properties (MNF, standing for magnetic nanofilm) coated with a layer of piezoelectric (PIEZO) microfibers of poly(vinylidene fluoride-trifluoroethylene) (MNF+PIEZO). The nanofilm creates a flexible support for cell contraction and the aligned PIEZO microfibers deposited on top of the nanofilm creates conditions for cell alignment and electrical stimulation of the seeded cells. Our results indicate that MNF+PIEZO scaffold promotes rat and human cardiac cell attachment and alignment, maintains the ratio of cell populations overtime, promotes cell-cell communication and metabolic maturation, and preserves cardiomyocyte (CM) contractility for at least 12 days. The engineered cardiac construct showed high toxicity against doxorubicin, a cardiotoxic molecule, and responded to compounds that modulate CM contraction such as epinephrine, propranolol and heptanol.
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Affiliation(s)
- P José Gouveia
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Instituto de Investigação Interdisciplinar, University of Coimbra, Casa Costa Alemão - Pólo II, Rua Dom Francisco de Lemos, 3030-789 Coimbra, Portugal
| | - S Rosa
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - L Ricotti
- The BioRobotics Institute, Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | - B Abecasis
- Instituto de Tecnologia Química e Biologica António Xavier, New University of Lisbon, Av. da Republica, 2780-157 Oeiras, Portugal
| | - H V Almeida
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - L Monteiro
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - J Nunes
- Center for Mechanical Engineering, University of Coimbra, 3030-788 Coimbra, Portugal
| | - F Sofia Carvalho
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Instituto de Investigação Interdisciplinar, University of Coimbra, Casa Costa Alemão - Pólo II, Rua Dom Francisco de Lemos, 3030-789 Coimbra, Portugal
| | - M Serra
- Instituto de Tecnologia Química e Biologica António Xavier, New University of Lisbon, Av. da Republica, 2780-157 Oeiras, Portugal
| | - S Luchkin
- CICECO - Materials Institute of Aveiro & Physics Department, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - A Leonidovitch Kholkin
- CICECO - Materials Institute of Aveiro & Physics Department, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; School of Natural Sciences and Mathematics, Ural Federal University, 620000 Ekaterinburg, Russia
| | - P Marques Alves
- Instituto de Tecnologia Química e Biologica António Xavier, New University of Lisbon, Av. da Republica, 2780-157 Oeiras, Portugal
| | - P Jorge Oliveira
- Instituto de Investigação Interdisciplinar, University of Coimbra, Casa Costa Alemão - Pólo II, Rua Dom Francisco de Lemos, 3030-789 Coimbra, Portugal
| | - R Carvalho
- Instituto de Investigação Interdisciplinar, University of Coimbra, Casa Costa Alemão - Pólo II, Rua Dom Francisco de Lemos, 3030-789 Coimbra, Portugal; Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - A Menciassi
- The BioRobotics Institute, Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | - R Pires das Neves
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Instituto de Investigação Interdisciplinar, University of Coimbra, Casa Costa Alemão - Pólo II, Rua Dom Francisco de Lemos, 3030-789 Coimbra, Portugal
| | - L Silva Ferreira
- CNC-Center of Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
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8
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Trame MN, Biliouris K, Lesko LJ, Mettetal JT. Systems pharmacology to predict drug safety in drug development. Eur J Pharm Sci 2016; 94:93-95. [PMID: 27251780 DOI: 10.1016/j.ejps.2016.05.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/05/2016] [Accepted: 05/28/2016] [Indexed: 12/20/2022]
Abstract
Ensuring that drugs are safe and effective is a very high priority for drug development and the US Food and Drug Administration review process. This is especially true today because of faster approval times and smaller clinical trials, especially in oncology and rare diseases. In light of these trends, systems pharmacology is seen as an essential strategy to understand and predict adverse drug events during drug development by analyzing interactions between drugs and multiple targets rather than the traditional "one-drug-one-target" approach. This commentary offers an overview of the current trends and challenges of using systems pharmacology to reduce the risks of unintended adverse events.
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Affiliation(s)
- Mirjam N Trame
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, University of Florida, Lake Nona, Orlando, FL, USA.
| | - Konstantinos Biliouris
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, University of Florida, Lake Nona, Orlando, FL, USA
| | - Lawrence J Lesko
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, University of Florida, Lake Nona, Orlando, FL, USA
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9
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Klimas A, Ambrosi CM, Yu J, Williams JC, Bien H, Entcheva E. OptoDyCE as an automated system for high-throughput all-optical dynamic cardiac electrophysiology. Nat Commun 2016; 7:11542. [PMID: 27161419 PMCID: PMC4866323 DOI: 10.1038/ncomms11542] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/05/2016] [Indexed: 01/11/2023] Open
Abstract
The improvement of preclinical cardiotoxicity testing, discovery of new ion-channel-targeted drugs, and phenotyping and use of stem cell-derived cardiomyocytes and other biologics all necessitate high-throughput (HT), cellular-level electrophysiological interrogation tools. Optical techniques for actuation and sensing provide instant parallelism, enabling contactless dynamic HT testing of cells and small-tissue constructs, not affordable by other means. Here we show, computationally and experimentally, the limits of all-optical electrophysiology when applied to drug testing, then implement and validate OptoDyCE, a fully automated system for all-optical cardiac electrophysiology. We validate optical actuation by virally introducing optogenetic drivers in rat and human cardiomyocytes or through the modular use of dedicated light-sensitive somatic ‘spark' cells. We show that this automated all-optical approach provides HT means of cellular interrogation, that is, allows for dynamic testing of >600 multicellular samples or compounds per hour, and yields high-content information about the action of a drug over time, space and doses. The efficiency of preclinical drug testing and characterization of cellular function can be improved through the use of optogenetic tools. Here Klimas et al. present and validate OptoDyCE, a fully automated system for all-optical high-throughput cardiac electrophysiology.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Christina M Ambrosi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Jinzhu Yu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - John C Williams
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Harold Bien
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
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10
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Paci M, Hyttinen J, Rodriguez B, Severi S. Human induced pluripotent stem cell-derived versus adult cardiomyocytes: an in silico electrophysiological study on effects of ionic current block. Br J Pharmacol 2015; 172:5147-60. [PMID: 26276951 PMCID: PMC4629192 DOI: 10.1111/bph.13282] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 12/28/2022] Open
Abstract
Background and Purpose Two new technologies are likely to revolutionize cardiac safety and drug development: in vitro experiments on human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs) and in silico human adult ventricular cardiomyocyte (hAdultV‐CM) models. Their combination was recently proposed as a potential replacement for the present hERG‐based QT study for pharmacological safety assessments. Here, we systematically compared in silico the effects of selective ionic current block on hiPSC‐CM and hAdultV‐CM action potentials (APs), to identify similarities/differences and to illustrate the potential of computational models as supportive tools for evaluating new in vitro technologies. Experimental Approach In silico AP models of ventricular‐like and atrial‐like hiPSC‐CMs and hAdultV‐CM were used to simulate the main effects of four degrees of block of the main cardiac transmembrane currents. Key Results Qualitatively, hiPSC‐CM and hAdultV‐CM APs showed similar responses to current block, consistent with results from experiments. However, quantitatively, hiPSC‐CMs were more sensitive to block of (i) L‐type Ca2+ currents due to the overexpression of the Na+/Ca2+ exchanger (leading to shorter APs) and (ii) the inward rectifier K+ current due to reduced repolarization reserve (inducing diastolic potential depolarization and repolarization failure). Conclusions and Implications In silico hiPSC‐CMs and hAdultV‐CMs exhibit a similar response to selective current blocks. However, overall hiPSC‐CMs show greater sensitivity to block, which may facilitate in vitro identification of drug‐induced effects. Extrapolation of drug effects from hiPSC‐CM to hAdultV‐CM and pro‐arrhythmic risk assessment can be facilitated by in silico predictions using biophysically‐based computational models.
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Affiliation(s)
- M Paci
- Department of Electronics and Communications Engineering, Tampere University of Technology, BioMediTech, Tampere, Finland
| | - J Hyttinen
- Department of Electronics and Communications Engineering, Tampere University of Technology, BioMediTech, Tampere, Finland
| | - B Rodriguez
- Department of Computer Science, University of Oxford, Oxford, UK
| | - S Severi
- Department of Electrical, Electronic and Information Engineering 'Guglielmo Marconi', University of Bologna, Cesena (FC), Italy
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11
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Lee S. Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine. J Pharmacopuncture 2015; 18:11-8. [PMID: 26388998 PMCID: PMC4573803 DOI: 10.3831/kpi.2015.18.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/31/2015] [Indexed: 12/14/2022] Open
Abstract
Objectives: Systems biology is a novel subject in the field of life science that aims at a systems’ level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.
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Affiliation(s)
- Soojin Lee
- Department of Physiology, College of Korean Medicine, Sangji University, Wonju, Korea
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12
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Wiśniowska B, Mendyk A, Fijorek K, Polak S. Computer-based prediction of the drug proarrhythmic effect: problems, issues, known and suspected challenges. Europace 2015; 16:724-35. [PMID: 24798962 DOI: 10.1093/europace/euu009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
It is likely that computer modelling and simulations will become an element of comprehensive cardiac safety testing. Their role would be primarily the integration and the interpretation of previously gathered data. There are still unanswered questions and issues which we list and describe below. They include sources of data used for the development of the models as well as data utilized as input information, which can come from the in vitro studies and the quantitative structure-activity relationship models. The pharmacokinetics of the drugs in question play a crucial role as their active concentration should be considered, yet the question remains where is the right place to assess it. The pharmacodynamic angle includes complications coming from multiple drugs (i.e. active metabolites) acting in parallel as well as the type of interaction with (potentially) multiple affected channels. Once established, the model and the methodology of its use should be further validated, optimistically against individual data reported at the clinical level as the physiological, anatomical, and genetic parameters play a crucial role in the drug-triggered arrhythmia induction. All the abovementioned issues should be at least considered and-hopefully-resolved, to properly utilize the mathematical models for a cardiac safety assessment.
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Affiliation(s)
- Barbara Wiśniowska
- Unit of Pharmacoepidemiology and Pharmacoeconomics, Faculty of Pharmacy, Medical College, Jagiellonian University, Medyczna 9 Street, 30-688 Kraków, Poland
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13
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Visser SAG, de Alwis DP, Kerbusch T, Stone JA, Allerheiligen SRB. Implementation of quantitative and systems pharmacology in large pharma. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2014; 3:e142. [PMID: 25338195 PMCID: PMC4474169 DOI: 10.1038/psp.2014.40] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/30/2014] [Indexed: 02/04/2023]
Abstract
Quantitative and systems pharmacology concepts and tools are the foundation of the model-informed drug development paradigm at Merck for integrating knowledge, enabling decisions, and enhancing submissions. Rigorous prioritization of modeling and simulation activities has enabled key drug development decisions and led to a high return on investment through significant cost avoidance. Critical factors for the successful implementation, examples on impact on decision making with associated return of investment, and drivers for continued success are discussed.
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Affiliation(s)
- S A G Visser
- Quantitative Pharmacology and Pharmacometrics, Merck Research Labs, Merck & Co, Rahway, New Jersey, USA
| | - D P de Alwis
- Quantitative Pharmacology and Pharmacometrics, Merck Research Labs, Merck & Co, Rahway, New Jersey, USA
| | - T Kerbusch
- Quantitive Pharmacology and Pharmacometrics, MSD, Oss, The Netherlands
| | - J A Stone
- Quantitative Pharmacology and Pharmacometrics, Merck Research Labs, Merck & Co, Rahway, New Jersey, USA
| | - S R B Allerheiligen
- Quantitative Pharmacology and Pharmacometrics, Merck Research Labs, Merck & Co, Rahway, New Jersey, USA
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14
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Zemzemi N, Rodriguez B. Effects of L-type calcium channel and human ether-a-go-go related gene blockers on the electrical activity of the human heart: a simulation study. Europace 2014; 17:326-33. [PMID: 25228500 PMCID: PMC4309991 DOI: 10.1093/europace/euu122] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aims Class III and IV drugs affect cardiac human ether-a-go-go related gene (IKr) and L-type calcium (ICaL) channels, resulting in complex alterations in repolarization with both anti- and pro-arrhythmic consequences. Interpretation of their effects on cellular and electrocardiogram (ECG)-based biomarkers for risk stratification is challenging. As pharmaceutical compounds often exhibit multiple ion channel effects, our goal is to investigate the simultaneous effect of ICaL and IKr block on human ventricular electrophysiology from ionic to ECG level. Methods and results Simulations are conducted using a human body torso bidomain model, which includes realistic representation of human membrane kinetics, anatomy, and fibre orientation. A simple block pore model is incorporated to simulate drug-induced ICaL and IKr blocks, for drug dose = 0, IC50, 2× IC50, 10× IC50, and 30× IC50. Drug effects on human ventricular activity are quantified for different degrees and combinations of ICaL and IKr blocks from the ionic to the body surface ECG level. Electrocardiogram simulations show that ICaL block results in shortening of the QT interval, ST elevation, and reduced T-wave amplitude, caused by reduction in action potential duration and action potential amplitude during the plateau phase, and in repolarization times. In contrast, IKr block results in QT prolongation and reduced T-wave amplitude. When ICaL and IKr blocks are combined, the degree of ICaL block strongly determines QT interval whereas the effect of IKr block is more pronounced on the T-wave amplitude. Conclusion Our simulation study provides new insights into the combined effect of ICaL and IKr blocks on human ventricular activity using a multiscale computational human torso model.
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Affiliation(s)
- Nejib Zemzemi
- Carmen team, INRIA Bordeaux Sud-Ouest, 200 avenue de la vieille tour, Talence Cedex 33405, France
| | - Blanca Rodriguez
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK
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15
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Images as drivers of progress in cardiac computational modelling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:198-212. [PMID: 25117497 PMCID: PMC4210662 DOI: 10.1016/j.pbiomolbio.2014.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/02/2014] [Indexed: 11/28/2022]
Abstract
Computational models have become a fundamental tool in cardiac research. Models are evolving to cover multiple scales and physical mechanisms. They are moving towards mechanistic descriptions of personalised structure and function, including effects of natural variability. These developments are underpinned to a large extent by advances in imaging technologies. This article reviews how novel imaging technologies, or the innovative use and extension of established ones, integrate with computational models and drive novel insights into cardiac biophysics. In terms of structural characterization, we discuss how imaging is allowing a wide range of scales to be considered, from cellular levels to whole organs. We analyse how the evolution from structural to functional imaging is opening new avenues for computational models, and in this respect we review methods for measurement of electrical activity, mechanics and flow. Finally, we consider ways in which combined imaging and modelling research is likely to continue advancing cardiac research, and identify some of the main challenges that remain to be solved.
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16
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Glynn P, Unudurthi SD, Hund TJ. Mathematical modeling of physiological systems: an essential tool for discovery. Life Sci 2014; 111:1-5. [PMID: 25064823 DOI: 10.1016/j.lfs.2014.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
Mathematical models are invaluable tools for understanding the relationships between components of a complex system. In the biological context, mathematical models help us understand the complex web of interrelations between various components (DNA, proteins, enzymes, signaling molecules etc.) in a biological system, gain better understanding of the system as a whole, and in turn predict its behavior in an altered state (e.g. disease). Mathematical modeling has enhanced our understanding of multiple complex biological processes like enzyme kinetics, metabolic networks, signal transduction pathways, gene regulatory networks, and electrophysiology. With recent advances in high throughput data generation methods, computational techniques and mathematical modeling have become even more central to the study of biological systems. In this review, we provide a brief history and highlight some of the important applications of modeling in biological systems with an emphasis on the study of excitable cells. We conclude with a discussion about opportunities and challenges for mathematical modeling going forward. In a larger sense, the review is designed to help answer a simple but important question that theoreticians frequently face from interested but skeptical colleagues on the experimental side: "What is the value of a model?"
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Affiliation(s)
- Patric Glynn
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Sathya D Unudurthi
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas J Hund
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA; Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
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17
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Zaniboni M, Cacciani F. Instantaneous current-voltage relationships during the course of the human cardiac ventricular action potential: new computational insights into repolarization dynamics. Europace 2014; 16:774-84. [PMID: 24798968 DOI: 10.1093/europace/eut397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AIMS To adopt a novel three-dimensional (3D) representation of cardiac action potential (AP) to compactly visualize dynamical properties of human cellular ventricular repolarization. METHODS AND RESULTS We have recently established a novel 3D representation of cardiac AP, which is based on the iterative measurement of instantaneous ion current-voltage profiles during the course of an AP. Such an approach has been originally developed on real patch-clamped ventricular cells, and subsequently improved in silico on several cardiac ventricular AP models of different mammals, and on models of different AP types of the human heart. We apply it here on two different models of human ventricular AP, and show that it compactly provides further insights into repolarization dynamics. The 3D representation of the AP includes equilibrium points during repolarization, and can be screened in terms of what we have shown to be a region, during late repolarization, when membrane conductance becomes negative and repolarization therefore auto-regenerative. We have called this time window auto-regenerative-repolarization-phase (ARRP). CONCLUSION In addition to previous findings obtained through the same procedure, we show here that 3D current-voltage-time representations of human ventricular AP allow compact visualization of dynamical properties, which are relevant for the physiology and pathology of ventricular repolarization. In particular, we suggest that the volume under the current surface corresponding to the ARRP might be used as a predictor of safety of repolarization, in single cells and during AP conduction in cell pairs.
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Affiliation(s)
- Massimiliano Zaniboni
- Department of Life Sciences, University of Parma, Italy, Parco Area delle Scienze 11A, 43124 Parma, Italy
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18
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Chow SK, Smith C, MacCarthy T, Pohl MA, Bergman A, Casadevall A. Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe 2014; 13:417-28. [PMID: 23601104 DOI: 10.1016/j.chom.2013.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/14/2013] [Accepted: 02/13/2013] [Indexed: 12/25/2022]
Abstract
During infection, humoral immunity produces a polyclonal response with various immunoglobulins recognizing different epitopes within the microbe or toxin. Despite this diverse response, the biological activity of an antibody (Ab) is usually assessed by the action of a monoclonal population. We demonstrate that a combination of monoclonal antibodies (mAbs) that are individually disease enhancing or neutralizing to Bacillus anthracis protective antigen (PA), a component of anthrax toxin, results in significantly augmented protection against the toxin. This boosted protection is Fc gamma receptor (FcγR) dependent and involves the formation of stoichiometrically defined mAb-PA complexes that requires immunoglobulin bivalence and simultaneous interaction between PA and the two mAbs. The formation of these mAb-PA complexes inhibits PA oligomerization, resulting in protection. These data suggest that functional assessments of single Abs may inaccurately predict how the same Abs will operate in polyclonal preparations and imply that potentially therapeutic mAbs may be overlooked in single Ab screens.
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Affiliation(s)
- Siu-Kei Chow
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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19
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Shin DS, Park MJ, Lee HA, Lee JY, Chung HC, Yoo DS, Chae CH, Park SJ, Kim KS, Bae MA. A novel assessment of nefazodone-induced hERG inhibition by electrophysiological and stereochemical method. Toxicol Appl Pharmacol 2014; 274:361-71. [DOI: 10.1016/j.taap.2013.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/16/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
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20
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Geenen S, Yates JWT, Kenna JG, Bois FY, Wilson ID, Westerhoff HV. Multiscale modelling approach combining a kinetic model of glutathione metabolism with PBPK models of paracetamol and the potential glutathione-depletion biomarkers ophthalmic acid and 5-oxoproline in humans and rats. Integr Biol (Camb) 2014; 5:877-88. [PMID: 23632663 DOI: 10.1039/c3ib20245c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A key role of the antioxidant glutathione is detoxification of chemically reactive electrophilic drug metabolites within the liver. Therefore glutathione depletion can have severe toxic consequences. Ophthalmic acid and 5-oxoproline are metabolites involved in glutathione metabolism, which can be measured readily in the blood and urine and have been proposed as candidate biomarkers of hepatic glutathione content. However, currently it is unclear whether their concentrations in plasma exhibit a robust correlation with hepatic glutathione content. To explore this important question, we have developed a novel approach which combines a physiologically based pharmacokinetic (PBPK) model of metabolism and disposition of paracetamol (acetaminophen) with a previously developed mathematical systems model of hepatic glutathione homeostasis. Paracetamol is metabolised to reactive intermediates which deplete glutathione and cause toxicity when given at high doses. Our model correctly predicted that hepatic glutathione depletion following paracetamol administration resulted in elevated concentrations of 5-oxoproline and ophthalmic acid in blood and of 5-oxoproline in urine. However, we also found from the model that concentrations of both of the compounds were likely to be influenced by prolonged administration of paracetamol and by the concentrations of intracellular metabolites such as methionine. We conclude that care must be taken when extrapolating from concentrations of these biomarkers to hepatic glutathione status.
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Affiliation(s)
- Suzanne Geenen
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK
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21
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Kohl P, Gourdie RG. Fibroblast-myocyte electrotonic coupling: does it occur in native cardiac tissue? J Mol Cell Cardiol 2014; 70:37-46. [PMID: 24412581 PMCID: PMC4001130 DOI: 10.1016/j.yjmcc.2013.12.024] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/05/2022]
Abstract
Heterocellular electrotonic coupling between cardiac myocytes and non-excitable connective tissue cells has been a long-established and well-researched fact in vitro. Whether or not such coupling exists in vivo has been a matter of considerable debate. This paper reviews the development of experimental insight and conceptual views on this topic, describes evidence in favour of and against the presence of such coupling in native myocardium, and identifies directions for further study needed to resolve the riddle, perhaps less so in terms of principal presence which has been demonstrated, but undoubtedly in terms of extent, regulation, patho-physiological context, and actual relevance of cardiac myocyte–non-myocyte coupling in vivo. This article is part of a Special Issue entitled "Myocyte-Fibroblast Signalling in Myocardium." Electrical coupling of cardiomyocytes and fibroblasts is well-established in vitro Whether such hetero-cellular coupling exists in vivo has been a matter of debate We review the development of experimental and conceptual insight into the topic Conclusion 1: hetero-cellular coupling in heart tissue has been shown in principle Conclusion 2: extent, regulation, context, and relevance remain to be established
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Affiliation(s)
- Peter Kohl
- Imperial College, National Heart and Lung Institute, Harefield Hospital, UB6 9JH, UK.
| | - Robert G Gourdie
- Virginia Tech, Carilion Research Institute, 2 Riverside Circle, Roanoke, VA 24015, USA
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22
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DI Veroli GY, Davies MR, Zhang H, Abi-Gerges N, Boyett MR. hERG inhibitors with similar potency but different binding kinetics do not pose the same proarrhythmic risk: implications for drug safety assessment. J Cardiovasc Electrophysiol 2013; 25:197-207. [PMID: 24118558 DOI: 10.1111/jce.12289] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/22/2013] [Accepted: 08/29/2013] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Since the discovery of the link that exists between drug-induced hERG inhibition and Torsade de Pointes (TdP), extreme attention has been given to avoid new drugs inhibiting this channel. hERG inhibition is routinely screened for in new drugs and, typically, IC50 values are compared to projected plasma concentrations to define a safety margin. METHODS AND RESULTS We aimed to show that drugs with similar hERG potency are not uniformly pro-arrhythmic-this depends on the drug binding kinetics and mode of action (trapped or not) rather than the IC50 value only. We used a mathematical model of hERG and its related encoded current IKr to simulate drug binding in different configurations. Expression systems mimicking the screening process were first investigated. hERG model was then incorporated into a canine action potential (AP) and tissue model to study the impact of drug binding configurations on AP and pseudo-ECG (QT interval prolongation). Our data show that: (1) trapped and not trapped configurations and different binding kinetics could be identified during hERG screening; (2) slow binding, not trapped drugs, induced less AP prolongation and minimal QT interval prolongation (4.7%) at a concentration equal to the IC50 whereas maximal pro-arrhythmic risk was observed for trapped drugs at the same concentration (QT interval prolongation, 23.1%). CONCLUSION Our study demonstrates the need for screening for hERG binding configurations rather than potency alone. It also demonstrates the potential link between hERG, drug mode of action and TdP, and the need to question the current regulatory guidance.
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Affiliation(s)
- Giovanni Y DI Veroli
- Institute of Cardiovascular Sciences, University of Manchester, Manchester, UK; Translational Safety, Drug Safety & Metabolism, AstraZeneca, Manchester, UK
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23
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Trayanova NA, O'Hara T, Bayer JD, Boyle PM, McDowell KS, Constantino J, Arevalo HJ, Hu Y, Vadakkumpadan F. Computational cardiology: how computer simulations could be used to develop new therapies and advance existing ones. Europace 2013; 14 Suppl 5:v82-v89. [PMID: 23104919 DOI: 10.1093/europace/eus277] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This article reviews the latest developments in computational cardiology. It focuses on the contribution of cardiac modelling to the development of new therapies as well as the advancement of existing ones for cardiac arrhythmias and pump dysfunction. Reviewed are cardiac modelling efforts aimed at advancing and optimizing existent therapies for cardiac disease (defibrillation, ablation of ventricular tachycardia, and cardiac resynchronization therapy) and at suggesting novel treatments, including novel molecular targets, as well as efforts to use cardiac models in stratification of patients likely to benefit from a given therapy, and the use of models in diagnostic procedures.
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Affiliation(s)
- Natalia A Trayanova
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.
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24
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Quinn TA, Kohl P. Combining wet and dry research: experience with model development for cardiac mechano-electric structure-function studies. Cardiovasc Res 2013; 97:601-11. [PMID: 23334215 PMCID: PMC3583260 DOI: 10.1093/cvr/cvt003] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 11/17/2022] Open
Abstract
Since the development of the first mathematical cardiac cell model 50 years ago, computational modelling has become an increasingly powerful tool for the analysis of data and for the integration of information related to complex cardiac behaviour. Current models build on decades of iteration between experiment and theory, representing a collective understanding of cardiac function. All models, whether computational, experimental, or conceptual, are simplified representations of reality and, like tools in a toolbox, suitable for specific applications. Their range of applicability can be explored (and expanded) by iterative combination of 'wet' and 'dry' investigation, where experimental or clinical data are used to first build and then validate computational models (allowing integration of previous findings, quantitative assessment of conceptual models, and projection across relevant spatial and temporal scales), while computational simulations are utilized for plausibility assessment, hypotheses-generation, and prediction (thereby defining further experimental research targets). When implemented effectively, this combined wet/dry research approach can support the development of a more complete and cohesive understanding of integrated biological function. This review illustrates the utility of such an approach, based on recent examples of multi-scale studies of cardiac structure and mechano-electric function.
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Affiliation(s)
- T Alexander Quinn
- National Heart and Lung Institute, Imperial College London, Heart Science Centre, Harefield UB9 6JH, UK.
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25
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Kuepfer L, Lippert J, Eissing T. Multiscale mechanistic modeling in pharmaceutical research and development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 736:543-61. [PMID: 22161351 DOI: 10.1007/978-1-4419-7210-1_32] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Discontinuation of drug development projects due to lack of efficacy or adverse events is one of the main cost drivers in pharmaceutical research and development (R&D). Investments have to be written-off and contribute to the total costs of a successful drug candidate receiving marketing authorization and allowing return on invest. A vital risk for pharmaceutical innovator companies is late stage clinical failure since costs for individual clinical trials may exceed the one billion Euro threshold. To guide investment decisions and to safeguard maximum medical benefit and safety for patients recruited in clinical trials, it is therefore essential to understand the clinical consequences of all information and data generated. The complexity of the physiological and pathophysiological processes and the sheer amount of information available overcharge the mental capacity of any human being and prevent a prediction of the success in clinical development. A rigorous integration of knowledge, assumption, and experimental data into computational models promises a significant improvement of the rationalization of decision making in pharmaceutical industry. We here give an overview of the current status of modeling and simulation in pharmaceutical R&D and outline the perspectives of more recent developments in mechanistic modeling. Specific modeling approaches for different biological scales ranging from intracellular processes to whole organism physiology are introduced and an example for integrative multiscale modeling of therapeutic efficiency in clinical oncology trials is showcased.
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Affiliation(s)
- Lars Kuepfer
- Systems Biology and Computational Solutions, Bayer Technology Services GmbH, Building 9115, 51368 Leverkusen, Germany.
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26
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Abstract
Pharmacometrics and systems pharmacology are emerging as principal quantitative sciences within drug development and experimental therapeutics. In recognition of the importance of pharmacometrics and systems pharmacology to the discipline of clinical pharmacology, the American Society for Clinical Pharmacology and Therapeutics (ASCPT), in collaboration with Nature Publishing Group and Clinical Pharmacology & Therapeutics, has established CPT: Pharmacometrics & Systems Pharmacology to inform the field and shape the discipline.
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27
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Trayanova NA. Computational cardiology: the heart of the matter. ISRN CARDIOLOGY 2012; 2012:269680. [PMID: 23213566 PMCID: PMC3505657 DOI: 10.5402/2012/269680] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/06/2012] [Indexed: 12/19/2022]
Abstract
This paper reviews the newest developments in computational cardiology. It focuses on the contribution of cardiac modeling to the development of new therapies as well as the advancement of existing ones for cardiac arrhythmias and pump dysfunction. Reviewed are cardiac modeling efforts aimed at advancing and optimizing existent therapies for cardiac disease (defibrillation, ablation of ventricular tachycardia, and cardiac resynchronization therapy) and at suggesting novel treatments, including novel molecular targets, as well as efforts to use cardiac models in stratification of patients likely to benefit from a given therapy, and the use of models in diagnostic procedures.
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Affiliation(s)
- Natalia A Trayanova
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Hackerman Hall Room 216, Baltimore, MD 21218, USA
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28
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Niklas J, Diaz Ochoa JG, Bucher J, Mauch K. Quantitative Evaluation and Prediction of Drug Effects and Toxicological Risk Using Mechanistic Multiscale Models. Mol Inform 2012; 32:14-23. [DOI: 10.1002/minf.201200043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/21/2012] [Indexed: 01/06/2023]
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Abstract
A new generation of technologies commonly named omics permits assessment of the entirety of the components of biological systems and produces an explosion of data and a major shift in our concepts of disease. These technologies will likely shape the future of health care. One aspect of these advances is that the data generated document the uniqueness of each human being in regard to disease risk and treatment response. These developments have reemphasized the concept of personalized medicine. Here we review the impact of omics technologies on one key aspect of personalized medicine: the individual drug response. We describe how knowledge of different omics may affect treatment decisions, namely drug choice and drug dose, and how it can be used to improve clinical outcomes.
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Affiliation(s)
- Urs A Meyer
- Division of Pharmacology and Neurobiology, Biozentrum of the University of Basel, CH-4056 Basel, Switzerland.
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30
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Mirams GR, Davies MR, Cui Y, Kohl P, Noble D. Application of cardiac electrophysiology simulations to pro-arrhythmic safety testing. Br J Pharmacol 2012; 167:932-45. [PMID: 22568589 PMCID: PMC3492977 DOI: 10.1111/j.1476-5381.2012.02020.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 03/23/2012] [Accepted: 04/26/2012] [Indexed: 12/19/2022] Open
Abstract
Concerns over cardiac side effects are the largest single cause of compound attrition during pharmaceutical drug development. For a number of years, biophysically detailed mathematical models of cardiac electrical activity have been used to explore how a compound, interfering with specific ion-channel function, may explain effects at the cell-, tissue- and organ-scales. With the advent of high-throughput screening of multiple ion channels in the wet-lab, and improvements in computational modelling of their effects on cardiac cell activity, more reliable prediction of pro-arrhythmic risk is becoming possible at the earliest stages of drug development. In this paper, we review the current use of biophysically detailed mathematical models of cardiac myocyte electrical activity in drug safety testing, and suggest future directions to employ the full potential of this approach.
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Affiliation(s)
- Gary R Mirams
- Computational Biology, Department of Computer Science, University of OxfordOxford, UK
| | - Mark R Davies
- Computational Biology, Discovery SciencesAstraZeneca, Alderley Park, UK
| | - Yi Cui
- Safety Pharmacology, Safety Assessment, GlaxoSmithKline, R&D WareUK
| | - Peter Kohl
- Computational Biology, Department of Computer Science, University of OxfordOxford, UK
- National Heart and Lung Institute, Imperial College LondonLondon, UK
| | - Denis Noble
- Computational Biology, Department of Computer Science, University of OxfordOxford, UK
- Department of Physiology, Anatomy & Genetics, University of OxfordOxford, UK
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31
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Wilhelms M, Rombach C, Scholz EP, Dossel O, Seemann G. Impact of amiodarone and cisapride on simulated human ventricular electrophysiology and electrocardiograms. Europace 2012; 14 Suppl 5:v90-v96. [DOI: 10.1093/europace/eus281] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Geenen S, Taylor PN, Snoep JL, Wilson ID, Kenna JG, Westerhoff HV. Systems biology tools for toxicology. Arch Toxicol 2012; 86:1251-71. [PMID: 22569772 DOI: 10.1007/s00204-012-0857-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/12/2012] [Indexed: 12/18/2022]
Abstract
An important goal of toxicology is to understand and predict the adverse effects of drugs and other xenobiotics. For pharmaceuticals, such effects often emerge unexpectedly in man even when absent from trials in vitro and in animals. Although drugs and xenobiotics act on molecules, it is their perturbation of intracellular networks that matters. The tremendous complexity of these networks makes it difficult to understand the effects of xenobiotics on their ability to function. Because systems biology integrates data concerning molecules and their interactions into an understanding of network behaviour, it should be able to assist toxicology in this respect. This review identifies how in silico systems biology tools, such as kinetic modelling, and metabolic control, robustness and flux analyse, may indeed help understanding network-mediated toxicity. It also shows how these approaches function by implementing them vis-à-vis the glutathione network, which is important for the detoxification of reactive drug metabolites. The tools enable the appreciation of the steady state concept for the detoxification network and make it possible to simulate and then understand effects of perturbations of the macromolecules in the pathway that are counterintuitive. We review how a glutathione model has been used to explain the impact of perturbation of the pathway at various molecular sites, as would be the effect of single-nucleotide polymorphisms. We focus on how the mutations impact the levels of glutathione and of two candidate biomarkers of hepatic glutathione status. We conclude this review by sketching how the various systems biology tools may help in the various phases of drug development in the pharmaceutical industry.
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Affiliation(s)
- Suzanne Geenen
- Manchester Centre for Integrative Systems Biology, University of Manchester, UK
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33
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Dössel O, Krueger MW, Weber FM, Wilhelms M, Seemann G. Computational modeling of the human atrial anatomy and electrophysiology. Med Biol Eng Comput 2012; 50:773-99. [PMID: 22718317 DOI: 10.1007/s11517-012-0924-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 05/21/2012] [Indexed: 01/08/2023]
Abstract
This review article gives a comprehensive survey of the progress made in computational modeling of the human atria during the last 10 years. Modeling the anatomy has emerged from simple "peanut"-like structures to very detailed models including atrial wall and fiber direction. Electrophysiological models started with just two cellular models in 1998. Today, five models exist considering e.g. details of intracellular compartments and atrial heterogeneity. On the pathological side, modeling atrial remodeling and fibrotic tissue are the other important aspects. The bridge to data that are measured in the catheter laboratory and on the body surface (ECG) is under construction. Every measurement can be used either for model personalization or for validation. Potential clinical applications are briefly outlined and future research perspectives are suggested.
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Affiliation(s)
- Olaf Dössel
- Institute of Biomedical Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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34
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Carusi A, Burrage K, Rodríguez B. Bridging experiments, models and simulations: an integrative approach to validation in computational cardiac electrophysiology. Am J Physiol Heart Circ Physiol 2012; 303:H144-55. [PMID: 22582088 DOI: 10.1152/ajpheart.01151.2011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational models in physiology often integrate functional and structural information from a large range of spatiotemporal scales from the ionic to the whole organ level. Their sophistication raises both expectations and skepticism concerning how computational methods can improve our understanding of living organisms and also how they can reduce, replace, and refine animal experiments. A fundamental requirement to fulfill these expectations and achieve the full potential of computational physiology is a clear understanding of what models represent and how they can be validated. The present study aims at informing strategies for validation by elucidating the complex interrelations among experiments, models, and simulations in cardiac electrophysiology. We describe the processes, data, and knowledge involved in the construction of whole ventricular multiscale models of cardiac electrophysiology. Our analysis reveals that models, simulations, and experiments are intertwined, in an assemblage that is a system itself, namely the model-simulation-experiment (MSE) system. We argue that validation is part of the whole MSE system and is contingent upon 1) understanding and coping with sources of biovariability; 2) testing and developing robust techniques and tools as a prerequisite to conducting physiological investigations; 3) defining and adopting standards to facilitate the interoperability of experiments, models, and simulations; 4) and understanding physiological validation as an iterative process that contributes to defining the specific aspects of cardiac electrophysiology the MSE system targets, rather than being only an external test, and that this is driven by advances in experimental and computational methods and the combination of both.
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35
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Sarkar AX, Christini DJ, Sobie EA. Exploiting mathematical models to illuminate electrophysiological variability between individuals. J Physiol 2012; 590:2555-67. [PMID: 22495591 DOI: 10.1113/jphysiol.2011.223313] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Across individuals within a population, several levels of variability are observed, from the differential expression of ion channels at the molecular level, to the various action potential morphologies observed at the cellular level, to divergent responses to drugs at the organismal level. However, the limited ability of experiments to probe complex interactions between components has hitherto hindered our understanding of the factors that cause a range of behaviours within a population. Variability is a challenging issue that is encountered in all physiological disciplines, but recent work suggests that novel methods for analysing mathematical models can assist in illuminating its causes. In this review, we discuss mathematical modelling studies in cardiac electrophysiology and neuroscience that have enhanced our understanding of variability in a number of key areas. Specifically, we discuss parameter sensitivity analysis techniques that may be applied to generate quantitative predictions based on considering behaviours within a population of models, thereby providing novel insight into variability. Our discussion focuses on four issues that have benefited from the utilization of these methods: (1) the comparison of different electrophysiological models of cardiac myocytes, (2) the determination of the individual contributions of different molecular changes in complex disease phenotypes, (3) the identification of the factors responsible for the variable response to drugs, and (4) the constraining of free parameters in electrophysiological models of heart cells. Together, the studies that we discuss suggest that rigorous analyses of mathematical models can generate quantitative predictions regarding how molecular-level variations contribute to functional differences between experimental samples. These strategies may be applicable not just in cardiac electrophysiology, but in a wide range of disciplines.
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Affiliation(s)
- Amrita X Sarkar
- Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
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36
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Davies MR, Mistry HB, Hussein L, Pollard CE, Valentin JP, Swinton J, Abi-Gerges N. An in silico canine cardiac midmyocardial action potential duration model as a tool for early drug safety assessment. Am J Physiol Heart Circ Physiol 2012; 302:H1466-80. [DOI: 10.1152/ajpheart.00808.2011] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell lines expressing ion channels (IC) and the advent of plate-based electrophysiology device have enabled a molecular understanding of the action potential (AP) as a means of early QT assessment. We sought to develop an in silico AP (isAP) model that provides an assessment of the effect of a compound on the myocyte AP duration (APD) using concentration-effect curve data from a panel of five ICs (hNav1.5, hCav1.2, hKv4.3/hKChIP2.2, hKv7.1/hminK, hKv11.1). A test set of 53 compounds was selected to cover a range of selective and mixed IC modulators that were tested for their effects on optically measured APD. A threshold of >10% change in APD at 90% repolarization (APD90) was used to signify an effect at the top test concentration. To capture the variations observed in left ventricular midmyocardial myocyte APD data from 19 different dogs, the isAP model was calibrated to produce an ensemble of 19 model variants that could capture the shape and form of the APs and also quantitatively replicate dofetilide- and diltiazem-induced APD90 changes. Provided with IC panel data only, the isAP model was then used, blinded, to predict APD90 changes greater than 10%. At a simulated concentration of 30 μM and based on a criterion that six of the variants had to agree, isAP prediction was scored as showing greater than 80% predictivity of compound activity. Thus, early in drug discovery, the isAP model allows integrating separate IC data and is amenable to the throughput required for use as a virtual screen.
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Affiliation(s)
| | | | - L. Hussein
- Safety Pharmacology, Safety Assessment United Kingdom, AstraZeneca R&D, Macclesfield, United Kingdom
| | - C. E. Pollard
- Safety Pharmacology, Safety Assessment United Kingdom, AstraZeneca R&D, Macclesfield, United Kingdom
| | - J.-P. Valentin
- Safety Pharmacology, Safety Assessment United Kingdom, AstraZeneca R&D, Macclesfield, United Kingdom
| | - J. Swinton
- Computational Biology, Discovery Sciences and
| | - N. Abi-Gerges
- Safety Pharmacology, Safety Assessment United Kingdom, AstraZeneca R&D, Macclesfield, United Kingdom
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37
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Sánchez C, Corrias A, Bueno-Orovio A, Davies M, Swinton J, Jacobson I, Laguna P, Pueyo E, Rodríguez B. The Na+/K+ pump is an important modulator of refractoriness and rotor dynamics in human atrial tissue. Am J Physiol Heart Circ Physiol 2012; 302:H1146-59. [PMID: 22198174 PMCID: PMC3311461 DOI: 10.1152/ajpheart.00668.2011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 12/04/2011] [Indexed: 11/22/2022]
Abstract
Pharmacological treatment of atrial fibrillation (AF) exhibits limited efficacy. Further developments require a comprehensive characterization of ionic modulators of electrophysiology in human atria. Our aim is to systematically investigate the relative importance of ionic properties in modulating excitability, refractoriness, and rotor dynamics in human atria before and after AF-related electrical remodeling (AFER). Computer simulations of single cell and tissue atrial electrophysiology were conducted using two human atrial action potential (AP) models. Changes in AP, refractory period (RP), conduction velocity (CV), and rotor dynamics caused by alterations in key properties of all atrial ionic currents were characterized before and after AFER. Results show that the investigated human atrial electrophysiological properties are primarily modulated by maximal value of Na(+)/K(+) pump current (G(NaK)) as well as conductances of inward rectifier potassium current (G(K1)) and fast inward sodium current (G(Na)). G(NaK) plays a fundamental role through both electrogenic and homeostatic modulation of AP duration (APD), APD restitution, RP, and reentrant dominant frequency (DF). G(K1) controls DF through modulation of AP, APD restitution, RP, and CV. G(Na) is key in determining DF through alteration of CV and RP, particularly in AFER. Changes in ionic currents have qualitatively similar effects in control and AFER, but effects are smaller in AFER. The systematic analysis conducted in this study unravels the important role of the Na(+)/K(+) pump current in determining human atrial electrophysiology.
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Affiliation(s)
- Carlos Sánchez
- Communications Technology Group, I3A and IIS, University of Zaragoza, Zaragoza
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38
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Moreno JD, Zhu ZI, Yang PC, Bankston JR, Jeng MT, Kang C, Wang L, Bayer JD, Christini DJ, Trayanova NA, Ripplinger CM, Kass RS, Clancy CE. A computational model to predict the effects of class I anti-arrhythmic drugs on ventricular rhythms. Sci Transl Med 2012; 3:98ra83. [PMID: 21885405 DOI: 10.1126/scitranslmed.3002588] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A long-sought, and thus far elusive, goal has been to develop drugs to manage diseases of excitability. One such disease that affects millions each year is cardiac arrhythmia, which occurs when electrical impulses in the heart become disordered, sometimes causing sudden death. Pharmacological management of cardiac arrhythmia has failed because it is not possible to predict how drugs that target cardiac ion channels, and have intrinsically complex dynamic interactions with ion channels, will alter the emergent electrical behavior generated in the heart. Here, we applied a computational model, which was informed and validated by experimental data, that defined key measurable parameters necessary to simulate the interaction kinetics of the anti-arrhythmic drugs flecainide and lidocaine with cardiac sodium channels. We then used the model to predict the effects of these drugs on normal human ventricular cellular and tissue electrical activity in the setting of a common arrhythmia trigger, spontaneous ventricular ectopy. The model forecasts the clinically relevant concentrations at which flecainide and lidocaine exacerbate, rather than ameliorate, arrhythmia. Experiments in rabbit hearts and simulations in human ventricles based on magnetic resonance images validated the model predictions. This computational framework initiates the first steps toward development of a virtual drug-screening system that models drug-channel interactions and predicts the effects of drugs on emergent electrical activity in the heart.
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Affiliation(s)
- Jonathan D Moreno
- Tri-Institutional MD-PhD Program, Weill Cornell Medical College/The Rockefeller University/Sloan-Kettering Cancer Institute, New York, NY 10021, USA
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39
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Abstract
PURPOSE OF REVIEW Heart failure remains a leading cause of morbidity and mortality in developed nations. Our current understanding of molecular pathways involved in heart failure reveals little of the multiscale biological systems at work. Here we consider recent advances in understanding the integrative multiscale biology, or systems biology, of heart failure and present a framework for future work in the area. RECENT FINDINGS Multiplexed assays of gene expression and the complex dynamics of protein-protein interactions in heart failure have illuminated key pathways important to myocardial adaptation. Modeling of complex systems has advanced to incorporate these dynamic data sources into networks that capture fundamental interactions on different biological scales. The complex syndrome of heart failure, like other complex disease syndromes, can be viewed as an emergent property of these multiscale systems. SUMMARY A comprehensive understanding of adaptive mechanisms in heart failure requires integration of multiple data sources on several biological scales. A combination of holistic systems biology approaches and traditional reductionist experimentation will be required for a nuanced understanding of this multifaceted disease process.
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40
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Romero L, Carbonell B, Trenor B, Rodríguez B, Saiz J, Ferrero JM. Systematic characterization of the ionic basis of rabbit cellular electrophysiology using two ventricular models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 107:60-73. [PMID: 21749896 DOI: 10.1016/j.pbiomolbio.2011.06.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 06/27/2011] [Indexed: 01/08/2023]
Abstract
Several mathematical models of rabbit ventricular action potential (AP) have been proposed to investigate mechanisms of arrhythmias and excitation-contraction coupling. Our study aims at systematically characterizing how ionic current properties modulate the main cellular biomarkers of arrhythmic risk using two widely-used rabbit ventricular models, and comparing simulation results using the two models with experimental data available for rabbit. A sensitivity analysis of AP properties, Ca²⁺ and Na⁺ dynamics, and their rate dependence to variations (±15% and ±30%) in the main transmembrane current conductances and kinetics was performed using the Shannon et al. (2004) and the Mahajan et al. (2008a,b) AP rabbit models. The effects of severe transmembrane current blocks (up to 100%) on steady-state AP and calcium transients, and AP duration (APD) restitution curves were also simulated using both models. Our simulations show that, in both virtual rabbit cardiomyocytes, APD is significantly modified by most repolarization currents, AP triangulation is regulated mostly by the inward rectifier K⁺ current (I(K1)) whereas APD rate adaptation as well as [Na⁺](i) rate dependence is influenced by the Na⁺/K⁺ pump current (I(NaK)). In addition, steady-state [Ca²⁺](i) levels, APD restitution properties and [Ca²⁺](i) rate dependence are strongly dependent on I(NaK), the L-Type Ca²⁺ current (I(CaL)) and the Na⁺/Ca²⁺ exchanger current (I(NaCa)), although the relative role of these currents is markedly model dependent. Furthermore, our results show that simulations using both models agree with many experimentally-reported electrophysiological characteristics. However, our study shows that the Shannon et al. model mimics rabbit electrophysiology more accurately at normal pacing rates, whereas Mahajan et al. model behaves more appropriately at faster rates. Our results reinforce the usefulness of sensitivity analysis for further understanding of cellular electrophysiology and validation of cardiac AP models.
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Affiliation(s)
- Lucía Romero
- Instituto de Investigación Interuniversitario en Bioingeniería y Tecnología Orientada al Ser Humano (I3BH), Universitat Politècnica de València (UPV), Camino de Vera s/n, 46022 Valencia, Spain.
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41
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Sharma S, Raju R, Sui S, Hu WS. Stem cell culture engineering - process scale up and beyond. Biotechnol J 2011; 6:1317-29. [PMID: 21721127 DOI: 10.1002/biot.201000435] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 04/28/2011] [Accepted: 05/11/2011] [Indexed: 12/23/2022]
Abstract
Advances in stem cell research and recent work on clinical trials employing stem cells have heightened the prospect of stem cell applications in regenerative medicine. The eventual clinical application of stem cells will require transforming cell production from laboratory practices to robust processes. Most stem cell applications will require extensive ex vivo handling of cells, from isolation, cultivation, and directed differentiation to product cell separation, cell derivation, and final formulation. Some applications require large quantities of cells in each defined batch for clinical use in multiple patients; others may be for autologous use and require only small-scale operations. All share a common requirement: the production must be robust and generate cell products of consistent quality. Unlike the established manufacturing process of recombinant protein biologics, stem cell applications will likely see greater variability in their cell source and more fluctuations in product quality. Nevertheless, in devising stem cell-based bioprocesses, much insight could be gained from the manufacturing of biological materials, including recombinant proteins and anti-viral vaccines. The key to process robustness is thus not only the control of traditional process chemical and physical variables, but also the sustenance of cells in the desired potency or differentiation state through controlling non-traditional variables, such as signaling pathway modulators.
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Affiliation(s)
- Shikha Sharma
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, USA
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42
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Noble D. Successes and failures in modeling heart cell electrophysiology. Heart Rhythm 2011; 8:1798-803. [PMID: 21699872 DOI: 10.1016/j.hrthm.2011.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/09/2011] [Indexed: 11/15/2022]
Abstract
Mathematical models of the electrical activity of the heart using equations for protein ion channels and other transporters began with the Noble 1962 model. These models then developed over a period of about 50 years. Cell types in all regions have been modeled and now are available for download from the CellML website (www.cellml.org). Simulation is a necessary tool of analysis in attempting to understand biological complexity. We often learn as much from the failures as from the successes of mathematical models. It is the iterative interaction between experiment and simulation that is important.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, UK.
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43
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Fletcher K, Shah RR, Thomas A, Tobin F, Rodriguez B, Mirams GR, Saiz J, Noble D. Novel approaches to assessing cardiac safety--proceedings of a workshop: regulators, industry and academia discuss the future of in silico cardiac modelling to predict the proarrhythmic safety of drugs. Drug Saf 2011; 34:439-43. [PMID: 21513366 PMCID: PMC3586146 DOI: 10.2165/11591950-000000000-00000] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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