title: Virtual Experiments Enable Exploring and Challenging Explanatory Mechanisms of Immune-Mediated P450 Down-Regulation.
abstract: Hepatic cytochrome P450 levels are down-regulated during inflammatory disease states, which can cause changes in downstream drug metabolism and hepatotoxicity. Long-term, we seek sufficient new insight into P450-regulating mechanisms to correctly anticipate how an individual's P450 expressions will respond when health and/or therapeutic interventions change. To date, improving explanatory mechanistic insight relies on knowledge gleaned from in vitro, in vivo, and clinical experiments augmented by case reports. We are working to improve that reality by developing means to undertake scientifically useful virtual experiments. So doing requires translating an accepted theory of immune system influence on P450 regulation into a computational model, and then challenging the model via in silico experiments. We build upon two existing agent-based models-an in silico hepatocyte culture and an in silico liver-capable of exploring and challenging concrete mechanistic hypotheses. We instantiate an in silico version of this hypothesis: in response to lipopolysaccharide, Kupffer cells down-regulate hepatic P450 levels via inflammatory cytokines, thus leading to a reduction in metabolic capacity. We achieve multiple in vitro and in vivo validation targets gathered from five wet-lab experiments, including a lipopolysaccharide-cytokine dose-response curve, time-course P450 down-regulation, and changes in several different measures of drug clearance spanning three drugs: acetaminophen, antipyrine, and chlorzoxazone. Along the way to achieving validation targets, various aspects of each model are falsified and subsequently refined. This iterative process of falsification-refinement-validation leads to biomimetic yet parsimonious mechanisms, which can provide explanatory insight into how, where, and when various features are generated. We argue that as models such as these are incrementally improved through multiple rounds of mechanistic falsification and validation, we will generate virtual systems that embody deeper credible, actionable, explanatory insight into immune system-drug metabolism interactions within individuals.
authors.affiliation: UCSF/UCB Joint Graduate Group in Bioengineering, University of California, Berkeley, California, United States of America.
authors.forename: Brenden K
authors.initials: BK
authors.lastname: Petersen
authors.affiliation: Tempus Dictum, Inc., Portland, Oregon, United States of America.
authors.forename: Glen E P
authors.initials: GE
authors.lastname: Ropella
authors.affiliation: UCSF/UCB Joint Graduate Group in Bioengineering, University of California, Berkeley, California, United States of America.|Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Hunt
mesh_terms: D003198:Computer Simulation; D003577:Cytochrome P-450 Enzyme System / Q000187:drug effects / Q000378:metabolism*; D016207:Cytokines / Q000378:metabolism; D004347:Drug Interactions; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D007155:Immunologic Factors / Q000378:metabolism*; D008658:Inactivation, Metabolic / Q000276:immunology*; D008070:Lipopolysaccharides / Q000494:pharmacology; D008099:Liver / Q000276:immunology* / Q000378:metabolism*
chemical_list: D016207:Cytokines; D007155:Immunologic Factors; D008070:Lipopolysaccharides; D003577:Cytochrome P-450 Enzyme System