Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms

PLoS Computational Biology - Tập 16 Số 6 - Trang e1007622
Andrew Smith1, Glen E. P. Ropella2, Mitchell R. McGill3, Preethi Krishnan1, Lopamudra Dutta1, Ryan Kennedy1, Hartmut Jaeschke4, C. Anthony Hunt1
1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
2Tempus Dictum, Inc., Milwaukie, Oregon, United States of America
3Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
4Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, United States of America

Tóm tắt

Từ khóa


Tài liệu tham khảo

MR McGill, 2016, The past and present of serum aminotransferases and the future of liver injury biomarkers, EXCLI J, 15, 817

MR McGill, 2018, Biomarkers of drug-induced liver injury: progress and utility in research, medicine, and regulation, Expert Rev Mol Diagn, 18, 797, 10.1080/14737159.2018.1508998

A Karmen, 1995, Transaminase activity in human blood, J Clin Invest, 34, 126, 10.1172/JCI103055

PB Watkins, 2006, Aminotransferase elevations in healthy adults receiving 4 grams of acetaminophen daily: a randomized controlled trial, JAMA, 296, 87, 10.1001/jama.296.1.87

AH Harrill, 2009, Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans, Genome Res, 19, 1507, 10.1101/gr.090241.108

BA Howell, 2014, A mechanistic model of drug-induced liver injury AIDS the interpretation of elevated liver transaminase levels in a phase I clinical trial, CPT Pharmacomet Syst Pharmacol, 3, e98, 10.1038/psp.2013.74

MR McGill, 2013, Plasma and liver acetaminophen-protein adduct levels in mice after acetaminophen treatment: dose-response, mechanisms, and clinical implications, Toxicol Appl Pharmacol, 269, 240, 10.1016/j.taap.2013.03.026

AK Smith, 2016, Competing mechanistic hypotheses of acetaminophen-induced hepatotoxicity challenged by virtual experiments, PLoS Comput Biol, 12, e1005253, 10.1371/journal.pcbi.1005253

X Fu, 2018, Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models, PLoS one, 13, e0198060, 10.1371/journal.pone.0198060

CA Hunt, 2009, At the biological modeling and simulation frontier, Pharm Res, 26, 2369, 10.1007/s11095-009-9958-3

AK Smith, 2018, A model mechanism-based explanation of an in vitro-in vivo disconnect for improving extrapolation and translation, J Pharmacol Exp Ther, 365, 127, 10.1124/jpet.117.245019

DE Kirschner, 2014, Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models, Wiley Interdiscip Rev Syst Biol Med, 6, 289, 10.1002/wsbm.1270

BK Petersen, 2016, Developing a vision for executing scientifically useful virtual biomedical experiments, Proceedings of the Agent-Directed Simulation Symposium

Bartha P. Analogy and Analogical Reasoning. In: Zalta EN, editor. The Stanford Encyclopedia of Philosophy (Spring 2019 Edition). 2019. Available from: https://plato.stanford.edu/archives/spr2019/entries/reasoning-analogy/

BK Petersen, 2016, Virtual experiments enable exploring and challenging explanatory mechanisms of immune-mediated P450 down-regulation, PloS One, 11, e0155855, 10.1371/journal.pone.0155855

J Tang, 2010, Identifying the rules of engagement enabling leukocyte rolling, activation, and adhesion, PLoS Comput Biol, 6, e1000681, 10.1371/journal.pcbi.1000681

SHJ Kim, 2012, Individualized, discrete event, simulations provide insight into inter- and intra-subject variability of extended-release, drug products, Theor Biol Med Model, 9, 39, 10.1186/1742-4682-9-39

PM Illari, 2012, What is a mechanism? Thinking about mechanisms across the sciences, Eur J Philos Sci, 2, 119, 10.1007/s13194-011-0038-2

L. Darden, 2008, Thinking again about biological mechanisms, Philos Sci, 75, 958, 10.1086/594538

M Pogson, 2006, Formal agent-based modelling of intracellular chemical interactions, Biosystems, 85, 37, 10.1016/j.biosystems.2006.02.004

CA Hunt, 2011, Relational grounding facilitates development of scientifically useful multiscale models, Theor Biol Med Model, 8, 35, 10.1186/1742-4682-8-35

Frigg R, Hartmann S. Models in Science. In: Zalta EN, editor. The Stanford Encyclopedia of Philosophy (Summer 2018 Edition). 2018. Available from: https://plato.stanford.edu/archives/sum2018/entries/models-science/

L Yan, 2008, Modeling and simulation of hepatic drug disposition using a physiologically based, multi-agent in silico liver, Pharm Res, 25, 1023, 10.1007/s11095-007-9494-y

AK Smith, 2014, Mechanistic agent-based damage and repair models as hypotheses for patterns of necrosis caused by drug induced liver injury, SummerSim '14 Proceedings of the 2014 Summer Simulation Multiconference

L Yan, 2008, Predictions of hepatic disposition properties using a mechanistically realistic, physiologically based model, Drug Metab Dispos, 36, 759, 10.1124/dmd.107.019067

K Miyakawa, 2015, Cytochrome P450-independent mechanism of acetaminophen-induced injury in cultured mouse hepatocytes, J Pharmacol Exp Ther, 354, 230, 10.1124/jpet.115.223537

D Uzi, 2013, CHOP is a critical regulator of acetaminophen-induced hepatotoxicity, J Hepatol, 59, 495, 10.1016/j.jhep.2013.04.024

CA Hunt, 2018, The spectrum of mechanism-oriented models and methods for explanations of biological phenomena, Processes, 6, 56, 10.3390/pr6050056

CM Macal, 2010, Tutorial on agent-based modelling and simulation, J Simul, 4, 151, 10.1057/jos.2010.3

GEP Ropella, 2010, Cloud computing and validation of expandable in silico livers, BMC Syst Biol, 4, 168, 10.1186/1752-0509-4-168

W Gamal, 2017, Low-dose acetaminophen induces early disruption of cell-cell tight junctions in human hepatic cells and mouse liver, Sci Rep, 7, 37541, 10.1038/srep37541

HM Ni, 2013, Zonated induction of autophagy and mitochondrial spheroids limits acetaminophen-induced necrosis in the liver, Redox Biol, 1, 427, 10.1016/j.redox.2013.08.005

LP James, 2013, Acetaminophen protein adduct formation following low-dose acetaminophen exposure: comparison of immediate-release vs extended-release formulations, Eur J Clin Pharmacol, 69, 851, 10.1007/s00228-012-1410-7

RS Kutzman, 1990, 1989 Toxic Hazards Research Unit Annual Report., Annual Report For The Period 1 October 1988–30 September 1989, 1

JA Lawson, 1999, Inhibition of Fas receptor (CD95)-induced hepatic caspase activation and apoptosis by acetaminophen in mice, Toxicol Appl Pharmacol, 156, 179, 10.1006/taap.1999.8635

C Cover, 2005, Pathophysiological role of poly(ADP-ribose) polymerase (PARP) activation during acetaminophen-induced liver cell necrosis in mice, Toxicol Sci, 84, 201, 10.1093/toxsci/kfi065

MR McGill, 2012, Acetaminophen-induced liver injury in rats and mice: comparison of protein adducts, mitochondrial dysfunction, and oxidative stress in the mechanism of toxicity, Toxicol Appl Pharmacol, 264, 387, 10.1016/j.taap.2012.08.015

RC Kennedy, 2019, Propagation of pericentral necrosis during acetaminophen-induced liver injury: evidence for early interhepatocyte communication and information exchange, Toxicol Sci, 169, 151, 10.1093/toxsci/kfz029

MR McGill, 2017, Biomarkers in Liver Disease, 71, 10.1007/978-94-007-7675-3_5

M Gascon-Barré, 1989, Hepatic zonation of drug metabolizing enzymes. Studies on hepatocytes isolated from the periportal or perivenous region of the liver acinus, Can J Physiol Pharmacol, 67, 1015, 10.1139/y89-160

KB Halpern, 2017, Single-cell spatial reconstruction reveals global division of labour in the mammalian liver, Nature, 542, 352, 10.1038/nature21065