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Renner N, Schöb F, Pape R, Suciu I, Spreng AS, Ückert AK, Cöllen E, Bovio F, Chilian B, Bauer J, Röpcke S, Bergemann J, Leist M, Schildknecht S. Modeling ferroptosis in human dopaminergic neurons: Pitfalls and opportunities for neurodegeneration research. Redox Biol 2024; 73:103165. [PMID: 38688061 PMCID: PMC11070765 DOI: 10.1016/j.redox.2024.103165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/17/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
The activation of ferroptosis is being pursued in cancer research as a strategy to target apoptosis-resistant cells. By contrast, in various diseases that affect the cardiovascular system, kidneys, liver, and central and peripheral nervous systems, attention is directed toward interventions that prevent ferroptotic cell death. Mechanistic insights into both research areas stem largely from studies using cellular in vitro models. However, intervention strategies that show promise in cellular test systems often fail in clinical trials, which raises concerns regarding the predictive validity of the utilized in vitro models. In this study, the human LUHMES cell line, which serves as a model for human dopaminergic neurons, was used to characterize factors influencing the activation of ferroptosis. Erastin and RSL-3 induced cell death that was distinct from apoptosis. Parameters such as the differentiation state of LUHMES cells, cell density, and the number and timing of medium changes were identified as determinants of sensitivity to ferroptosis activation. In differentiated LUHMES cells, interventions at mechanistically divergent sites (iron chelation, coenzyme Q10, peroxidase mimics, or inhibition of 12/15-lipoxygenase) provide almost complete protection from ferroptosis. LUHMES cells allowed the experimental modulation of intracellular iron concentrations and demonstrated a correlation between intracellular iron levels, the rate of lipid peroxidation, as well as the sensitivity of the cells to ferroptotic cell death. These findings underscore the importance of understanding the various factors that influence ferroptosis activation and highlight the need for well-characterized in vitro models to enhance the reliability and predictive value of observations in ferroptosis research, particularly when translating findings into in vivo contexts.
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Affiliation(s)
- Nadine Renner
- Albstadt-Sigmaringen University, Faculty of Life Sciences, 72488, Sigmaringen, Germany
| | - Franziska Schöb
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Regina Pape
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anna-Sophie Spreng
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Anna-Katharina Ückert
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Eike Cöllen
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Federica Bovio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Bruno Chilian
- TRI Thinking Research Instruments GmbH, Große Freiheit 77, 22767, Hamburg, Germany
| | - Johannes Bauer
- TRI Thinking Research Instruments GmbH, Große Freiheit 77, 22767, Hamburg, Germany
| | - Stefan Röpcke
- Stemick GmbH, Byk-Gulden Str. 2, 78467, Konstanz, Germany
| | - Jörg Bergemann
- Albstadt-Sigmaringen University, Faculty of Life Sciences, 72488, Sigmaringen, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Stefan Schildknecht
- Albstadt-Sigmaringen University, Faculty of Life Sciences, 72488, Sigmaringen, Germany.
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Eberhard P, Kern M, Aichem M, Borlinghaus H, Klein K, Delp J, Suciu I, Moser B, Dietrich D, Leist M, Schreiber F. PathwayNexus: a tool for interactive metabolic data analysis. Bioinformatics 2024; 40:btae310. [PMID: 38724240 PMCID: PMC11153943 DOI: 10.1093/bioinformatics/btae310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/28/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
MOTIVATION High-throughput omics methods increasingly result in large datasets including metabolomics data, which are often difficult to analyse. RESULTS To help researchers to handle and analyse those datasets by mapping and investigating metabolomics data of multiple sampling conditions (e.g. different time points or treatments) in the context of pathways, PathwayNexus has been developed, which presents the mapping results in a matrix format, allowing users to easily observe the relations between the compounds and the pathways. It also offers functionalities like ranking, sorting, clustering, pathway views, and further analytical tools. Its primary objective is to condense large sets of pathways into smaller, more relevant subsets that align with the specific interests of the user. AVAILABILITY AND IMPLEMENTATION The methodology presented here is implemented in PathwayNexus, an open-source add-on for Vanted available at www.cls.uni-konstanz.de/software/pathway-nexus. CONTACT falk.schreiber@unikonstanz.de. SUPPLEMENTARY INFORMATION Website: www.cls.uni-konstanz.de/software/pathway-nexus.
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Affiliation(s)
- Philipp Eberhard
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Martin Kern
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Hanna Borlinghaus
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Karsten Klein
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Johannes Delp
- Department of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany
| | - Ilinca Suciu
- Department of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany
| | - Benjamin Moser
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
| | - Daniel Dietrich
- Department of Human and Environmental Toxicology, University of Konstanz, Konstanz 78464, Germany
| | - Marcel Leist
- Department of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany
- Faculty of Information Technology, Monash University, Clayton, 3800, Australia
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Suciu I, Delp J, Gutbier S, Suess J, Henschke L, Celardo I, Mayer TU, Amelio I, Leist M. Definition of the Neurotoxicity-Associated Metabolic Signature Triggered by Berberine and Other Respiratory Chain Inhibitors. Antioxidants (Basel) 2023; 13:49. [PMID: 38247474 PMCID: PMC10812665 DOI: 10.3390/antiox13010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
To characterize the hits from a phenotypic neurotoxicity screen, we obtained transcriptomics data for valinomycin, diethylstilbestrol, colchicine, rotenone, 1-methyl-4-phenylpyridinium (MPP), carbaryl and berberine (Ber). For all compounds, the concentration triggering neurite degeneration correlated with the onset of gene expression changes. The mechanistically diverse toxicants caused similar patterns of gene regulation: the responses were dominated by cell de-differentiation and a triggering of canonical stress response pathways driven by ATF4 and NRF2. To obtain more detailed and specific information on the modes-of-action, the effects on energy metabolism (respiration and glycolysis) were measured. Ber, rotenone and MPP inhibited the mitochondrial respiratory chain and they shared complex I as the target. This group of toxicants was further evaluated by metabolomics under experimental conditions that did not deplete ATP. Ber (204 changed metabolites) showed similar effects as MPP and rotenone. The overall metabolic situation was characterized by oxidative stress, an over-abundance of NADH (>1000% increase) and a re-routing of metabolism in order to dispose of the nitrogen resulting from increased amino acid turnover. This unique overall pattern led to the accumulation of metabolites known as biomarkers of neurodegeneration (saccharopine, aminoadipate and branched-chain ketoacids). These findings suggest that neurotoxicity of mitochondrial inhibitors may result from an ensemble of metabolic changes rather than from a simple ATP depletion. The combi-omics approach used here provided richer and more specific MoA data than the more common transcriptomics analysis alone. As Ber, a human drug and food supplement, mimicked closely the mode-of-action of known neurotoxicants, its potential hazard requires further investigation.
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Affiliation(s)
- Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
- Graduate School of Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Johannes Delp
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Simon Gutbier
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Julian Suess
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Lars Henschke
- Graduate School of Chemical Biology, University of Konstanz, 78464 Konstanz, Germany
- Department of Molecular Genetics, University of Konstanz, 78464 Konstanz, Germany
| | - Ivana Celardo
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
| | - Thomas U. Mayer
- Department of Molecular Genetics, University of Konstanz, 78464 Konstanz, Germany
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78464 Konstanz, Germany
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Sinclair P, Hakeem J, Kumar SG, Loser D, Dixit K, Leist M, Kraushaar U, Kabbani N. Proteomic responses in the human dopaminergic LUHMES cell line to imidacloprid and its metabolites imidacloprid-olefin and desnitro-imidacloprid. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 194:105473. [PMID: 37532312 DOI: 10.1016/j.pestbp.2023.105473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 08/04/2023]
Abstract
Neonicotinoids (neonics) are amongst the most commonly used class of pesticides globally. In the United States, imidacloprid (IMI) is extensively used for agriculture and in other common applications such as house-hold pest control. Regular exposure to IMI, and several of its known metabolites including IMI-olefin and desnitro-imidacloprid (DN-IMI), has been shown to be harmful to many organisms including mammals, birds, and fish. Studies show that neonics bind human nicotinicacetylcholine receptors (nAChRs) and cause cellular toxicity. In the dopaminergic Lund human mesencephalic (LUHMES) cell line, IMI and other neonics (10-100 μM) have been recently shown to activate intracellular calcium signaling through nAChRs. Thus, we examined proteomic responses of LUHMES cells to a 48-h treatment with 50 μM IMI, IMI-olefin, or DN-IMI. Our findings show differential effects of these neonics on cellular protein expression. Bioinformatic analysis of significantly altered proteins indicates an effect of IMI, IMI-olefin, and DN-IMI on protein synthesis and ribosomal function. These findings suggest a role for protein synthesis and transcriptional regulation in neonic-mediated dopaminergic neurotoxicity.
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Affiliation(s)
| | - Julia Hakeem
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Sreehari G Kumar
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Dominik Loser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Kushan Dixit
- Interdisciplinary Program in Neuroscience, George Mason University
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457 Constance, Germany
| | - Udo Kraushaar
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Nadine Kabbani
- Interdisciplinary Program in Neuroscience, George Mason University; School of Systems Biology, George Mason University.
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Suciu I, Pamies D, Peruzzo R, Wirtz PH, Smirnova L, Pallocca G, Hauck C, Cronin MTD, Hengstler JG, Brunner T, Hartung T, Amelio I, Leist M. G × E interactions as a basis for toxicological uncertainty. Arch Toxicol 2023; 97:2035-2049. [PMID: 37258688 PMCID: PMC10256652 DOI: 10.1007/s00204-023-03500-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/02/2023]
Abstract
To transfer toxicological findings from model systems, e.g. animals, to humans, standardized safety factors are applied to account for intra-species and inter-species variabilities. An alternative approach would be to measure and model the actual compound-specific uncertainties. This biological concept assumes that all observed toxicities depend not only on the exposure situation (environment = E), but also on the genetic (G) background of the model (G × E). As a quantitative discipline, toxicology needs to move beyond merely qualitative G × E concepts. Research programs are required that determine the major biological variabilities affecting toxicity and categorize their relative weights and contributions. In a complementary approach, detailed case studies need to explore the role of genetic backgrounds in the adverse effects of defined chemicals. In addition, current understanding of the selection and propagation of adverse outcome pathways (AOP) in different biological environments is very limited. To improve understanding, a particular focus is required on modulatory and counter-regulatory steps. For quantitative approaches to address uncertainties, the concept of "genetic" influence needs a more precise definition. What is usually meant by this term in the context of G × E are the protein functions encoded by the genes. Besides the gene sequence, the regulation of the gene expression and function should also be accounted for. The widened concept of past and present "gene expression" influences is summarized here as Ge. Also, the concept of "environment" needs some re-consideration in situations where exposure timing (Et) is pivotal: prolonged or repeated exposure to the insult (chemical, physical, life style) affects Ge. This implies that it changes the model system. The interaction of Ge with Et might be denoted as Ge × Et. We provide here general explanations and specific examples for this concept and show how it could be applied in the context of New Approach Methodologies (NAM).
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Affiliation(s)
- Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - David Pamies
- Department of Biological Sciences, University of Lausanne, 1005, Lausanne, Switzerland
| | - Roberta Peruzzo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Petra H Wirtz
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457, Constance, Germany
- Biological Work and Health Psychology, Department of Psychology, University of Konstanz, 78457, Constance, Germany
| | - Lena Smirnova
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | - Christof Hauck
- Department of Cell Biology, University of Konstanz, 78457, Constance, Germany
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, 44139, Dortmund, Germany
| | - Thomas Brunner
- Biochemical Pharmacology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- CAAT Europe, University of Konstanz, 78457, Constance, Germany
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany.
- CAAT Europe, University of Konstanz, 78457, Constance, Germany.
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