In vitro assessment of hepatotoxicity by metabolomics: a review

Abstract

Omics technologies, and in particular metabolomics, have received an increasing attention during the assessment of hepatotoxicity in vitro. However, at present, a consensus on good metabolomics practices has yet to be reached. Therefore, in this review, a range of experimental approaches, applied methodologies, and data processing workflows are compared and critically evaluated. Experimental designs among the studies are similar, reporting the use of primary hepatocytes or hepatic cell lines as the most frequently used cell sources. Experiments are usually conducted in short time-frames (< 48 h) at sub-toxic dosages. Applied sample preparations are protein precipitation or Bligh-and-Dyer extraction. Most analytical platforms rely on chromatographic separations with mass spectrometric detection using high-resolution instruments. Untargeted metabolomics was typically used to allow the simultaneous detection of several classes of the metabolome, including endogenous metabolites that are not initially linked to toxicity. This non-biased detection platform is a valuable tool for generating hypothesis-based mechanistic research. The most frequently reported metabolites that are altered under toxicological impulses are alanine, lactate, and proline, which are often correlated. Other unspecific biomarkers of hepatotoxicity in vitro are the down-regulation of choline, glutathione, and 3-phospho-glycerate. Disruptions on the Krebs cycle are associated with increased glutamate, tryptophan, and valine. Phospholipid alterations are described in steatosis, lipo-apoptosis, and oxidative stress. Although there is a growing trend towards quality control, data analysis procedures do often not follow good contemporary metabolomics practices, which include feature filtering, false-discovery rate correction, and reporting the confidence of metabolite annotation. The currently annotated biomarkers can be used to identify hepatotoxicity in general and provide, to a certain extent, a tool for mechanistic distinction.

Utility of Three-Dimensional Cultures of Primary Human Hepatocytes (Spheroids) as Pharmacokinetic Models

“…As regards PK, it is important to study the absorption, distribution, metabolism, and excretion of candidate drugs in the liver, small intestine, and kidney [ 4 ]. In this context, hepatocytes and liver-derived materials are widely used in studies such as metabolite analysis (i.e., metabolomics) [ 5 , 6 ], inhibition or induction of cytochrome P450 (CYP) enzymes (at the mRNA, protein, and activity levels) [ 7 , 8 , 9 ], non-CYP enzyme metabolism [ 10 , 11 ], and prodrug metabolism [ 12 , 13 ]. On the other hand, hepatotoxicity (i.e., drug-induced liver injury, DILI) is often evaluated as part of an exploratory safety screening in the evaluation of new drug candidates.…”

LC-MS-Based Metabolomic Study of Oleanolic Acid-Induced Hepatotoxicity in Mice

“…(Lu et al, 2018;Liu and Zhong, 2019). Moreover, metabolomics can provide valuable markers for predicting DILI (Cuykx et al, 2018). Using metabolomics, Pannala et al identified the markers of acetaminophen-induced toxicity in rats, and they found that nucleotide, lipid, and amino acid metabolism were the major pathways (Pannala et al, 2019).…”

“…( Lu et al., 2018 ; Liu and Zhong, 2019 ). Moreover, metabolomics can provide valuable markers for predicting DILI ( Cuykx et al., 2018 ). Using metabolomics, Pannala et al.…”

Involvement of Reactive Oxygen Species in the Hepatorenal Toxicity of Actinomycin V In Vitro and In Vivo

“…In an in vitro experiment, it can be difficult to observe drug toxicity to organs in the absence of the body’s overall regulation [ 12 , 13 ]. Mammalian models give integrated results, but the mechanism of toxicity cannot be tested [ 14 ].…”