A Novel UPLC-MS Metabolomic Analysis-Based Strategy to Monitor the Course and Extent of iPSC Differentiation to Hepatocytes

Moreno-Torres, Marta; Kumar, Manoj; Garcia-Llorens, Guillem; Quintás, Guillermo; Tricot, Tine; Boon, Ruben; Tolosa, Laia; Toprakhisar, Burak; Chesnais, François; Verfaillie, Cathérine; Castell, José V.

doi:10.1021/acs.jproteome.1c00779

Cited by 4 publications

(3 citation statements)

References 23 publications

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“…An analysis of the different altered pathways is a powerful tool to draw conclusions on the metabolic changes caused in the cell under different conditions (Chen et al 2015 ; Moreno-Torres et al 2022 ). Cholestasis biomarkers in vitro could not be properly identified in this exercise, most likely because of the inability of the HepG2 model cell system to synthesise bile acids and to uptake and transport bile acid conjugates.…”

Section: Discussionmentioning

confidence: 99%

Metabolomics-based strategy to assess drug hepatotoxicity and uncover the mechanisms of hepatotoxicity involved

et al. 2023

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Toxicity studies, among them hepatotoxicity, are key throughout preclinical stages of drug development to minimise undesired toxic effects that might eventually appear in the course of the clinical use of the new drug. Understanding the mechanism of injury of hepatotoxins is essential to efficiently anticipate their potential risk of toxicity in humans. The use of in vitro models and particularly cultured hepatocytes represents an easy and robust alternative to animal drug hepatotoxicity testing for predicting human risk. Here, we envisage an innovative strategy to identify potential hepatotoxic drugs, quantify the magnitude of the alterations caused, and uncover the mechanisms of toxicity. This strategy is based on the comparative analysis of metabolome changes induced by hepatotoxic and non-hepatotoxic compounds on HepG2 cells, assessed by untargeted mass spectrometry. As a training set, we used 25 hepatotoxic and 4 non-hepatotoxic compounds and incubated HepG2 cells for 24 h at a low and a high concentration (IC10 and IC50) to identify mechanism-related and cytotoxicity related metabolomic biomarkers and to elaborate prediction models accounting for global hepatotoxicity and mechanisms-related toxicity. Thereafter, a second set of 69 chemicals with known predominant mechanisms of toxicity and 18 non-hepatotoxic compounds were analysed at 1, 10, 100 and 1000 µM concentrations from which and based on the magnitude of the alterations caused as compared with non-toxic compounds, we defined a “toxicity index” for each compound. In addition, we extracted from the metabolome data the characteristic signatures for each mechanism of hepatotoxicity. The integration of all this information allowed us to identify specific metabolic patterns and, based on the occurrence of that specific metabolome changes, the models predicted the likeliness of a compound to behave as hepatotoxic and to act through a given toxicity mechanism (i.e., oxidative stress, mitochondrial disruption, apoptosis and steatosis) for each compound and concentration.

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Section: Discussionmentioning

confidence: 99%

Metabolomics-based strategy to assess drug hepatotoxicity and uncover the mechanisms of hepatotoxicity involved

et al. 2023

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“…This approach has already been applied to the examination of reproducibility in in vitro metabolomics studies (Moreno-Torres et al, 2021), for the analysis of the generalization of the outcomes from metabolomic studies, for the comparison of metabolic phenotypes, and for the evaluation of the degree of differentiation of hepatocytelike cells (Moreno-Torres et al, 2022b), which demonstrates its applicability and power as an additional source of information. Together, these applications demonstrate the algorithm's suitability for interpreting data and conducting meta-analyses, thereby promoting its use in metabolomic research.…”

Section: Figurementioning

confidence: 99%

The assessment of the potential hepatotoxicity of new drugs by in vitro metabolomics

2023

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Drug hepatotoxicity assessment is a relevant issue both in the course of drug development as well as in the post marketing phase. The use of human relevant in vitro models in combination with powerful analytical methods (metabolomic analysis) is a promising approach to anticipate, as well as to understand and investigate the effects and mechanisms of drug hepatotoxicity in man. The metabolic profile analysis of biological liver models treated with hepatotoxins, as compared to that of those treated with non-hepatotoxic compounds, provides useful information for identifying disturbed cellular metabolic reactions, pathways, and networks. This can later be used to anticipate, as well to assess, the potential hepatotoxicity of new compounds. However, the applicability of the metabolomic analysis to assess the hepatotoxicity of drugs is complex and requires careful and systematic work, precise controls, wise data preprocessing and appropriate biological interpretation to make meaningful interpretations and/or predictions of drug hepatotoxicity. This review provides an updated look at recent in vitro studies which used principally mass spectrometry-based metabolomics to evaluate the hepatotoxicity of drugs. It also analyzes the principal drawbacks that still limit its general applicability in safety assessment screenings. We discuss the analytical workflow, essential factors that need to be considered and suggestions to overcome these drawbacks, as well as recent advancements made in this rapidly growing field of research.

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“…As PLS-DA "y" predicted values used for sample classification are unbound, "y" predicted values higher than 1 or lower than 0 were replaced by 1 or 0, respectively, and the position within the ternary plot was defined by the relative constrained "y" values. By doing this, the ternary plot was an equilateral triangle with edges to graphically depict the constrained "y"-predicted values for DILI (PLS-DA model: recovered vs. Its applicability and relevance as a source of information have already been validated in several studies including the analysis of reproducibility in in vitro metabolomics studies and the identification of inconsistencies between metabolomic studies outcomes [54], comparison of different phenotypes, and analysis of the degree of differentiation of hepatocytelike cells [109], as well as in the evaluation of the toxicity mechanisms of action of certain drugs [110]. Altogether, these applications demonstrate that the algorithm is very attractive for data interpretation and meta-analysis, encouraging its use on a routine basis in clinical metabolomics studies.…”

Section: Metabolites Identified As Putative Biomarkers Of Dili In Humansmentioning

confidence: 99%

The Potential Role of Metabolomics in Drug-Induced Liver Injury (DILI) Assessment

2022

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Drug-induced liver injury (DILI) is one of the most frequent adverse clinical reactions and a relevant cause of morbidity and mortality. Hepatotoxicity is among the major reasons for drug withdrawal during post-market and late development stages, representing a major concern to the pharmaceutical industry. The current biochemical parameters for the detection of DILI are based on enzymes (alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transpeptidase (GGT), alkaline phosphatase (ALP)) and bilirubin serum levels that are not specific of DILI and therefore there is an increasing interest on novel, specific, DILI biomarkers discovery. Metabolomics has emerged as a tool with a great potential for biomarker discovery, especially in disease diagnosis, and assessment of drug toxicity or efficacy. This review summarizes the multistep approaches in DILI biomarker research and discovery based on metabolomics and the principal outcomes from the research performed in this field. For that purpose, we have reviewed the recent scientific literature from PubMed, Web of Science, EMBASE, and PubTator using the terms “metabolomics”, “DILI”, and “humans”. Despite the undoubted contribution of metabolomics to our understanding of the underlying mechanisms of DILI and the identification of promising novel metabolite biomarkers, there are still some inconsistencies and limitations that hinder the translation of these research findings into general clinical practice, probably due to the variability of the methods used as well to the different mechanisms elicited by the DILI causing agent.

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A Novel UPLC-MS Metabolomic Analysis-Based Strategy to Monitor the Course and Extent of iPSC Differentiation to Hepatocytes

Cited by 4 publications

References 23 publications

Metabolomics-based strategy to assess drug hepatotoxicity and uncover the mechanisms of hepatotoxicity involved

Metabolomics-based strategy to assess drug hepatotoxicity and uncover the mechanisms of hepatotoxicity involved

The assessment of the potential hepatotoxicity of new drugs by in vitro metabolomics

The Potential Role of Metabolomics in Drug-Induced Liver Injury (DILI) Assessment

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