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

Abstract

Interpretations of elevated blood levels of alanine aminotransferase (ALT) for drug-induced liver injury often assume that the biomarker is released passively from dying cells. However, the mechanisms driving that release have not been explored experimentally. The usefulness of ALT and related biomarkers will improve by developing mechanism-based explanations of elevated levels that can be expanded and elaborated incrementally. We provide the means to challenge the ability of closely related model mechanisms to generate patterns of simulated hepatic injury and ALT release that scale (or not) to be quantitatively similar to the wet-lab validation targets, which are elevated plasma ALT values following acetaminophen (APAP) exposure in mice. We build on a published model mechanism that helps explain the generation of characteristic spatiotemporal features of APAP hepatotoxicity within hepatic lobules. Discrete event and agent-oriented software methods are most prominent. We instantiate and leverage a small constellation of concrete model mechanisms. Their details during execution help bring into focus ways in which particular sources of uncertainty become entangled with cause-effect details within and across several levels. We scale ALT amounts in virtual mice directly to target plasma ALT values in individual mice. A virtual experiment comprises a set of Monte Carlo simulations. We challenge the sufficiency of four potentially explanatory theories for ALT release. The first of the tested model theories failed to achieve the initial validation target, but each of the three others succeeded. Results for one of the three model mechanisms matched all target ALT values quantitatively. It explains how ALT externalization is the combined consequence of lobular-location-dependent drug-induced cellular damage and hepatocyte death. Falsification of one (or more) of the model mechanisms provides new knowledge and incrementally shrinks the constellation of model mechanisms. The modularity and biomimicry of our explanatory models enable seamless transition from mice to humans.

Utilizing virtual experiments to increase understanding of discrepancies involving in vitro-in vivo predictions of hepatic clearance

“…1) is strongly analogous to the histological organization of hepatocytes within rat and human lobules (Teutsch et al, 1999;Teutsch, 2005;Smith et al, 2020). 2) vHPC components and vCompound removal mechanisms are concrete, biomimetic, and strongly analogous to counterparts in vivo and in vitro (Smith et al, 2018(Smith et al, , 2020Peterson et al, 2016;Hunt et al, 2011). 3) The structural organization of vHPCs within vCultures is sufficiently biomimetic to simulate the in vitro experiments used to derive measures of intrinsic clearance Smith et al, 2018).…”

“…This work is conditioned on four postulates: 1) The structural organization of vHPCs within the vLobules (Fig. 1) is strongly analogous to the histological organization of hepatocytes within rat and human lobules (Teutsch et al, 1999;Teutsch, 2005;Smith et al, 2020). 2) vHPC components and vCompound removal mechanisms are concrete, biomimetic, and strongly analogous to counterparts in vivo and in vitro (Smith et al, 2018(Smith et al, , 2020Peterson et al, 2016;Hunt et al, 2011).…”

“…3) The structural organization of vHPCs within vCultures is sufficiently biomimetic to simulate the in vitro experiments used to derive measures of intrinsic clearance Smith et al, 2018). 4) When averaged over many events and many Monte Carlo-sampled executions (hereafter, simply executions), measures of vCompound dynamics within and between spaces in vLobules (and vCultures) can scale quantitatively to match comparable measurements of actual chemical entities, within wet-lab measurement errors (Smith et al, 2020).…”

“…However, events occurring within a particular vHPC do map directly to corresponding events believed to occur within hepatocytes at a comparable location. vHPCs contain four types of physiomimetic modules to control material entry, removal, binding and transformations needed to simulate acetaminophen hepatotoxicity (Smith et al, 2020):…”

“…The duration of each execution is 21,600 TS. During previous virtual acetaminophen hepatotoxicity experiments, one TS mapped to one second (Smith et al, 2020). The mapping of TS to clock wet-lab time for a pharmacokinetic study in rats may be different (e.g., 1 TS = 4 seconds).…”