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Cestari RN, de Oliveira RDR, de Souza FFL, Pippa LF, Nardotto GHB, Rocha A, Donadi EA, Lanchote VL. Systemic Lupus Erythematosus Activity Affects the Sinusoidal Uptake Transporter OATP1B1 Evaluated by the Pharmacokinetics of Atorvastatin. Clin Transl Sci 2020; 13:1227-1235. [PMID: 32463566 PMCID: PMC7719393 DOI: 10.1111/cts.12808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/10/2020] [Indexed: 12/30/2022] Open
Abstract
The present study assessed the effect of systemic lupus erythematosus (SLE) activity, a chronic and inflammatory autoimmune disease, on the sinusoidal uptake transporter OATP1B1 using atorvastatin (ATV) as a probe drug. Fifteen healthy subjects, 13 patients with controlled SLE (SLEDAI 0-4), and 12 patients with uncontrolled SLE (SLEDAI from 6 to 15), all women, were investigated. Apparent total clearance of midazolam (MDZ), a marker of CYP3A4 activity, did not vary among the three investigated groups. The controlled and uncontrolled SLE groups showed higher plasma concentrations of MCP-1 and TNF-α, while the uncontrolled SLE group also showed higher plasma concentrations of IL-10. The uncontrolled SLE group showed higher area under the curve (AUC) for ATV (60.47 (43.76-83.56) vs. 30.56 (22.69-41.15) ng⋅hour/mL) and its inactive metabolite ATV-lactone (98.74 (74.31-131.20) vs. 49.21 (34.89-69.42) ng⋅hour/mL), and lower apparent total clearance (330.7 (239.30-457.00) vs. 654.5 (486.00-881.4) L/hour) and apparent volume of distribution (2,609 (1,607-4,234) vs. 7,159 (4,904-10,450) L), when compared to the healthy subjects group (geometric mean and 95% confidence interval). The pharmacokinetics of ATV and its metabolites did not differ between the healthy subject group and the patients with controlled SLE group. In conclusion, uncontrolled SLE increased the systemic exposure to both ATV and ATV-lactone, inferring inhibition of OATP1B1 activity, once in vivo CYP3A4 activity assessed by oral clearance of MDZ was unaltered. The inflammatory state, not the disease itself, was responsible for the changes described in the uncontrolled SLE group as a consequence of inhibition of OATP1B1, because systemic exposure to ATV and its metabolites were not altered in patients with controlled SLE.
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Affiliation(s)
- Roberta Natália Cestari
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | - Flávio Falcão Lima de Souza
- Department of Internal Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Leandro Francisco Pippa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Glauco Henrique Balthazar Nardotto
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Adriana Rocha
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Eduardo Antônio Donadi
- Department of Internal Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Vera Lucia Lanchote
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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Buchweitz LF, Yurkovich JT, Blessing C, Kohler V, Schwarzkopf F, King ZA, Yang L, Jóhannsson F, Sigurjónsson ÓE, Rolfsson Ó, Heinrich J, Dräger A. Visualizing metabolic network dynamics through time-series metabolomic data. BMC Bioinformatics 2020; 21:130. [PMID: 32245365 PMCID: PMC7119163 DOI: 10.1186/s12859-020-3415-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 02/12/2020] [Indexed: 11/23/2022] Open
Abstract
Background New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of innovative computational visualization methodologies. Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps. We demonstrate the utility of the GEM-Vis method by examining previously published data for two cellular systems—the human platelet and erythrocyte under cold storage for use in transfusion medicine. Results The results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation that mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures. Conclusions The new visualization technique GEM-Vis introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal -omics data types. The supplement includes a comprehensive user’s guide and links to a series of tutorial videos that explain how to prepare model and data files, and how to use the software SBMLsimulator in combination with further tools to create similar animations as highlighted in the case studies.
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Affiliation(s)
- Lea F Buchweitz
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), Sand 14, Tübingen, 72076, Germany
| | - James T Yurkovich
- Institute for Systems Biology, 401 Terry Ave. N., Seattle, 98109, WA, United States
| | - Christoph Blessing
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), Sand 14, Tübingen, 72076, Germany.,Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Veronika Kohler
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), Sand 14, Tübingen, 72076, Germany.,Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | | | - Zachary A King
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Kgs.Lyngby, 2800, Denmark
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Freyr Jóhannsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavík, 101, Iceland
| | - Ólafur E Sigurjónsson
- The Blood Bank, Landspítali-University Hospital, Reykjavík, 101, Iceland.,School of Science and Engineering, Reykjavík University, Menntavegi 1, Reykjavík, 101, Iceland
| | - Óttar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavík, 101, Iceland
| | - Julian Heinrich
- Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), Sand 14, Tübingen, 72076, Germany. .,Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany. .,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, 72076, Germany.
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Al-Habsi AA, Massarsky A, Moon TW. Atorvastatin alters gene expression and cholesterol synthesis in primary rainbow trout (Oncorhynchus mykiss) hepatocytes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:262-269. [DOI: 10.1016/j.cbpb.2017.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/22/2017] [Accepted: 08/29/2017] [Indexed: 12/24/2022]
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Oguz C, Watson LT, Baumann WT, Tyson JJ. Predicting network modules of cell cycle regulators using relative protein abundance statistics. BMC SYSTEMS BIOLOGY 2017; 11:30. [PMID: 28241833 PMCID: PMC5329933 DOI: 10.1186/s12918-017-0409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/17/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studies have shown that one usually finds a set of "feasible" parameter vectors that fit the available experimental data equally well, and that these alternative vectors can make different predictions under novel experimental conditions. In this study, we characterize the feasible region of a complex model of the budding yeast cell cycle under a large set of discrete experimental constraints in order to test whether the statistical features of relative protein abundance predictions are influenced by the topology of the cell cycle regulatory network. RESULTS Using differential evolution, we generate an ensemble of feasible parameter vectors that reproduce the phenotypes (viable or inviable) of wild-type yeast cells and 110 mutant strains. We use this ensemble to predict the phenotypes of 129 mutant strains for which experimental data is not available. We identify 86 novel mutants that are predicted to be viable and then rank the cell cycle proteins in terms of their contributions to cumulative variability of relative protein abundance predictions. Proteins involved in "regulation of cell size" and "regulation of G1/S transition" contribute most to predictive variability, whereas proteins involved in "positive regulation of transcription involved in exit from mitosis," "mitotic spindle assembly checkpoint" and "negative regulation of cyclin-dependent protein kinase by cyclin degradation" contribute the least. These results suggest that the statistics of these predictions may be generating patterns specific to individual network modules (START, S/G2/M, and EXIT). To test this hypothesis, we develop random forest models for predicting the network modules of cell cycle regulators using relative abundance statistics as model inputs. Predictive performance is assessed by the areas under receiver operating characteristics curves (AUC). Our models generate an AUC range of 0.83-0.87 as opposed to randomized models with AUC values around 0.50. CONCLUSIONS By using differential evolution and random forest modeling, we show that the model prediction statistics generate distinct network module-specific patterns within the cell cycle network.
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Affiliation(s)
- Cihan Oguz
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA.
| | - Layne T Watson
- Department of Computer Science, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Mathematics, Virginia Tech, Blacksburg VA, 24061, USA.,Department of Aerospace and Ocean Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - William T Baumann
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg VA, 24061, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061, USA
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Parton A, McGilligan V, O’Kane M, Baldrick FR, Watterson S. Computational modelling of atherosclerosis. Brief Bioinform 2015; 17:562-75. [DOI: 10.1093/bib/bbv081] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 12/24/2022] Open
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Drasdo D, Bode J, Dahmen U, Dirsch O, Dooley S, Gebhardt R, Ghallab A, Godoy P, Häussinger D, Hammad S, Hoehme S, Holzhütter HG, Klingmüller U, Kuepfer L, Timmer J, Zerial M, Hengstler JG. The virtual liver: state of the art and future perspectives. Arch Toxicol 2015; 88:2071-5. [PMID: 25331938 DOI: 10.1007/s00204-014-1384-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Dirk Drasdo
- Institut National de Recherche en Informatique et en Automatique (INRIA), Domaine de Voluceau - Rocquencourt, Paris, France
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Smutny T, Duintjer Tebbens J, Pavek P. Bioinformatic analysis of miRNAs targeting the key nuclear receptors regulating CYP3A4 gene expression: The challenge of the CYP3A4 "missing heritability" enigma. J Appl Biomed 2015. [DOI: 10.1016/j.jab.2015.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Weiß F, Schnabel A, Planatscher H, van den Berg BHJ, Serschnitzki B, Nuessler AK, Thasler WE, Weiss TS, Reuss M, Stoll D, Templin MF, Joos TO, Marcus K, Poetz O. Indirect protein quantification of drug-transforming enzymes using peptide group-specific immunoaffinity enrichment and mass spectrometry. Sci Rep 2015; 5:8759. [PMID: 25737130 PMCID: PMC4348618 DOI: 10.1038/srep08759] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/03/2015] [Indexed: 02/07/2023] Open
Abstract
Immunoaffinity enrichment of proteotypic peptides, coupled with selected reaction monitoring, enables indirect protein quantification. However the lack of suitable antibodies limits its widespread application. We developed a method in which multi-specific antibodies are used to enrich groups of peptides, thus facilitating multiplexed quantitative protein assays. We tested this strategy in a pharmacokinetic experiment by targeting a group of homologous drug transforming proteins in human hepatocytes. Our results indicate the generic applicability of this method to any biological system.
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Affiliation(s)
- Frederik Weiß
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
| | - Anke Schnabel
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Hannes Planatscher
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
| | - Bart H J van den Berg
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
| | | | - Andreas K Nuessler
- Department of Traumatology, Eberhard Karls Universität Tübingen, Tuebingen, Germany
| | | | - Thomas S Weiss
- Department of Pediatrics and Juvenile Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Matthias Reuss
- Center Systems Biology, University of Stuttgart, Stuttgart, Germany
| | - Dieter Stoll
- University of Applied Sciences, Albstadt Sigmaringen, Germany
| | - Markus F Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, Reutlingen, Germany
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Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Abstract
The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.
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11
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Iwuchukwu OF, Feng Q, Wei WQ, Jiang L, Jiang M, Xu H, Denny JC, Wilke RA, Krauss RM, Roden DM, Stein CM. Genetic variation in the UGT1A locus is associated with simvastatin efficacy in a clinical practice setting. Pharmacogenomics 2014; 15:1739-1747. [PMID: 25493567 PMCID: PMC4292894 DOI: 10.2217/pgs.14.128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/26/2014] [Indexed: 01/11/2023] Open
Abstract
Aim: Simvastatin is a lactone prodrug that exists in equilibrium with its active hydroxyacid through a process mediated by UGT1A enzymes. The UGT1A locus has been associated with simvastatin response and disposition in humans. Therefore, we fine-mapped the UGT1A locus to identify genetic variations contributing to simvastatin disposition and response variability. Methods: Using de-identified electronic medical records linked to a DNA biobank, we extracted information about dose and low-density lipo-protein cholesterol (LDL-C) concentrations for patients who received more than two different doses of simvastatin. Pharmacodynamic measures of simvastatin potency and efficacy were calculated from dose-response curves (E0 = baseline LDL-C, ED50 = dose yielding 50% maximum response, and Emax = maximum decrease in LDL-C) in 1100 patients. We selected 153 polymorphisms in UGT1A1 and UGT1A3 for genotyping and conducted genotype-phenotype associations using a prespecified additive model. Results: Two variants in UGT1A1 (rs2003569 and rs12052787) were associated with Emax (p = 0.0059 and 0.031, respectively; for rs2003569 the mean Emax was 59.3 ± 23.0, 62.0 ± 22.4, and 69.7 ± 24.8 mg/dl, for patients with 0, 1 or 2 copies of the minor A allele, respectively). When stratified by race, the difference in response was greater in African-Americans than in European Americans. Rs2003569 was also negatively associated with total serum bilirubin levels (p = 7.85 × 10-5). Four rare SNPs were nominally associated with E0 and ED50. Conclusion: We identified a UGT1A1 promoter variant (rs2003569) associated with simvastatin efficacy. Original submitted 26 March 2014; Revision submitted 26 August 2014.
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Affiliation(s)
- Otito F Iwuchukwu
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Medical Bioinformatics, Vanderbilt University School of Medicine, TN, USA
| | - Lan Jiang
- Center for Human Genetics Research, Vanderbilt University School of Medicine, TN, USA
| | - Min Jiang
- Department of Biomedical Informatics, University of Texas, TX, USA
| | - Hua Xu
- Department of Biomedical Informatics, University of Texas, TX, USA
| | - Joshua C Denny
- Department of Medical Bioinformatics, Vanderbilt University School of Medicine, TN, USA
| | | | | | - Dan M Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of Medicine Nashville, TN, USA
| | - C Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of Medicine Nashville, TN, USA
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van de Pas NCA, Rullmann JAC, Woutersen RA, van Ommen B, Rietjens IMCM, de Graaf AA. Predicting individual responses to pravastatin using a physiologically based kinetic model for plasma cholesterol concentrations. J Pharmacokinet Pharmacodyn 2014; 41:351-62. [PMID: 25106950 DOI: 10.1007/s10928-014-9369-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 07/03/2014] [Indexed: 12/17/2022]
Abstract
We used a previously developed physiologically based kinetic (PBK) model to analyze the effect of individual variations in metabolism and transport of cholesterol on pravastatin response. The PBK model is based on kinetic expressions for 21 reactions that interconnect eight different body cholesterol pools including plasma HDL and non-HDL cholesterol. A pravastatin pharmacokinetic model was constructed and the simulated hepatic pravastatin concentration was used to modulate the reaction rate constant of hepatic free cholesterol synthesis in the PBK model. The integrated model was then used to predict plasma cholesterol concentrations as a function of pravastatin dose. Predicted versus observed values at 40 mg/d pravastatin were 15 versus 22 % reduction of total plasma cholesterol, and 10 versus 5.6 % increase of HDL cholesterol. A population of 7,609 virtual subjects was generated using a Monte Carlo approach, and the response to a 40 mg/d pravastatin dose was simulated for each subject. Linear regression analysis of the pravastatin response in this virtual population showed that hepatic and peripheral cholesterol synthesis had the largest regression coefficients for the non-HDL-C response. However, the modeling also showed that these processes alone did not suffice to predict non-HDL-C response to pravastatin, contradicting the hypothesis that people with high cholesterol synthesis rates are good statin responders. In conclusion, we have developed a PBK model that is able to accurately describe the effect of pravastatin treatment on plasma cholesterol concentrations and can be used to provide insight in the mechanisms behind individual variation in statin response.
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Affiliation(s)
- Niek C A van de Pas
- The Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, P.O. Box 360, 3700 AJ, Zeist, The Netherlands
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Poulin P, Haddad S. Hepatocyte Composition-Based Model as a Mechanistic Tool for Predicting the Cell Suspension: Aqueous Phase Partition Coefficient of Drugs in In Vitro Metabolic Studies. J Pharm Sci 2013; 102:2806-18. [DOI: 10.1002/jps.23602] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 12/21/2022]
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Diaz Ochoa JG, Bucher J, Péry ARR, Zaldivar Comenges JM, Niklas J, Mauch K. A multi-scale modeling framework for individualized, spatiotemporal prediction of drug effects and toxicological risk. Front Pharmacol 2013; 3:204. [PMID: 23346056 PMCID: PMC3551257 DOI: 10.3389/fphar.2012.00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/17/2012] [Indexed: 12/14/2022] Open
Abstract
In this study, we focus on a novel multi-scale modeling approach for spatiotemporal prediction of the distribution of substances and resulting hepatotoxicity by combining cellular models, a 2D liver model, and whole body model. As a case study, we focused on predicting human hepatotoxicity upon treatment with acetaminophen based on in vitro toxicity data and potential inter-individual variability in gene expression and enzyme activities. By aggregating mechanistic, genome-based in silico cells to a novel 2D liver model and eventually to a whole body model, we predicted pharmacokinetic properties, metabolism, and the onset of hepatotoxicity in an in silico patient. Depending on the concentration of acetaminophen in the liver and the accumulation of toxic metabolites, cell integrity in the liver as a function of space and time as well as changes in the elimination rate of substances were estimated. We show that the variations in elimination rates also influence the distribution of acetaminophen and its metabolites in the whole body. Our results are in agreement with experimental results. What is more, the integrated model also predicted variations in drug toxicity depending on alterations of metabolic enzyme activities. Variations in enzyme activity, in turn, reflect genetic characteristics or diseases of individuals. In conclusion, this framework presents an important basis for efficiently integrating inter-individual variability data into models, paving the way for personalized or stratified predictions of drug toxicity and efficacy.
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Chakrabarty A, Buzzard GT, Rundell AE. Model-based design of experiments for cellular processes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:181-203. [PMID: 23293047 DOI: 10.1002/wsbm.1204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ankush Chakrabarty
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
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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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Teeguarden JG, Housand CJ, Smith JN, Hinderliter PM, Gunawan R, Timchalk CA. A multi-route model of nicotine-cotinine pharmacokinetics, pharmacodynamics and brain nicotinic acetylcholine receptor binding in humans. Regul Toxicol Pharmacol 2012; 65:12-28. [PMID: 23099439 DOI: 10.1016/j.yrtph.2012.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 10/12/2012] [Accepted: 10/15/2012] [Indexed: 02/04/2023]
Abstract
The pharmacokinetics of nicotine, the pharmacologically active alkaloid in tobacco responsible for addiction, are well characterized in humans. We developed a physiologically based pharmacokinetic/pharmacodynamic model of nicotine pharmacokinetics, brain dosimetry and brain nicotinic acetylcholine receptor (nAChRs) occupancy. A Bayesian framework was applied to optimize model parameters against multiple human data sets. The resulting model was consistent with both calibration and test data sets, but in general underestimated variability. A pharmacodynamic model relating nicotine levels to increases in heart rate as a proxy for the pharmacological effects of nicotine accurately described the nicotine related changes in heart rate and the development and decay of tolerance to nicotine. The PBPK model was utilized to quantitatively capture the combined impact of variation in physiological and metabolic parameters, nicotine availability and smoking compensation on the change in number of cigarettes smoked and toxicant exposure in a population of 10,000 people presented with a reduced toxicant (50%), reduced nicotine (50%) cigarette Across the population, toxicant exposure is reduced in some but not all smokers. Reductions are not in proportion to reductions in toxicant yields, largely due to partial compensation in response to reduced nicotine yields. This framework can be used as a key element of a dosimetry-driven risk assessment strategy for cigarette smoke constituents.
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Affiliation(s)
- Justin G Teeguarden
- Battelle, Pacific Northwest Division, 902 Battelle Blvd., Richland, WA 99352, USA.
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