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Vlasveld M, Callegaro G, Fisher C, Eakins J, Walker P, Lok S, van Oost S, de Jong B, Pellegrino-Coppola D, Burger G, Wink S, van de Water B. The integrated stress response-related expression of CHOP due to mitochondrial toxicity is a warning sign for DILI liability. Liver Int 2024; 44:760-775. [PMID: 38217387 DOI: 10.1111/liv.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND AND AIMS Drug-induced liver injury (DILI) is one of the most frequent reasons for failure of drugs in clinical trials or market withdrawal. Early assessment of DILI risk remains a major challenge during drug development. Here, we present a mechanism-based weight-of-evidence approach able to identify certain candidate compounds with DILI liabilities due to mitochondrial toxicity. METHODS A total of 1587 FDA-approved drugs and 378 kinase inhibitors were screened for cellular stress response activation associated with DILI using an imaging-based HepG2 BAC-GFP reporter platform including the integrated stress response (CHOP), DNA damage response (P21) and oxidative stress response (SRXN1). RESULTS In total 389, 219 and 104 drugs were able to induce CHOP-GFP, P21-GFP and SRXN1-GFP expression at 50 μM respectively. Concentration response analysis identified 154 FDA-approved drugs as critical CHOP-GFP inducers. Based on predicted and observed (pre-)clinical DILI liabilities of these drugs, nine antimycotic drugs (e.g. butoconazole, miconazole, tioconazole) and 13 central nervous system (CNS) agents (e.g. duloxetine, fluoxetine) were selected for transcriptomic evaluation using whole-genome RNA-sequencing of primary human hepatocytes. Gene network analysis uncovered mitochondrial processes, NRF2 signalling and xenobiotic metabolism as most affected by the antimycotic drugs and CNS agents. Both the selected antimycotics and CNS agents caused impairment of mitochondrial oxygen consumption in both HepG2 and primary human hepatocytes. CONCLUSIONS Together, the results suggest that early pre-clinical screening for CHOP expression could indicate liability of mitochondrial toxicity in the context of DILI, and, therefore, could serve as an important warning signal to consider during decision-making in drug development.
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Affiliation(s)
- Matthijs Vlasveld
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Giulia Callegaro
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | - Samantha Lok
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Siddh van Oost
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Brechtje de Jong
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Damiano Pellegrino-Coppola
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gerhard Burger
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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2
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Niemeijer M, Więcek W, Fu S, Huppelschoten S, Bouwman P, Baze A, Parmentier C, Richert L, Paules RS, Bois FY, van de Water B. Mapping Interindividual Variability of Toxicodynamics Using High-Throughput Transcriptomics and Primary Human Hepatocytes from Fifty Donors. Environ Health Perspect 2024; 132:37005. [PMID: 38498338 PMCID: PMC10947137 DOI: 10.1289/ehp11891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Understanding the variability across the human population with respect to toxicodynamic responses after exposure to chemicals, such as environmental toxicants or drugs, is essential to define safety factors for risk assessment to protect the entire population. Activation of cellular stress response pathways are early adverse outcome pathway (AOP) key events of chemical-induced toxicity and would elucidate the estimation of population variability of toxicodynamic responses. OBJECTIVES We aimed to map the variability in cellular stress response activation in a large panel of primary human hepatocyte (PHH) donors to aid in the quantification of toxicodynamic interindividual variability to derive safety uncertainty factors. METHODS High-throughput transcriptomics of over 8,000 samples in total was performed covering a panel of 50 individual PHH donors upon 8 to 24 h exposure to broad concentration ranges of four different toxicological relevant stimuli: tunicamycin for the unfolded protein response (UPR), diethyl maleate for the oxidative stress response (OSR), cisplatin for the DNA damage response (DDR), and tumor necrosis factor alpha (TNF α ) for NF- κ B signaling. Using a population mixed-effect framework, the distribution of benchmark concentrations (BMCs) and maximum fold change were modeled to evaluate the influence of PHH donor panel size on the correct estimation of interindividual variability for the various stimuli. RESULTS Transcriptome mapping allowed the investigation of the interindividual variability in concentration-dependent stress response activation, where the average of BMCs had a maximum difference of 864-, 13-, 13-, and 259-fold between different PHHs for UPR, OSR, DDR, and NF- κ B signaling-related genes, respectively. Population modeling revealed that small PHH panel sizes systematically underestimated the variance and gave low probabilities in estimating the correct human population variance. Estimated toxicodynamic variability factors of stress response activation in PHHs based on this dataset ranged between 1.6 and 6.3. DISCUSSION Overall, by combining high-throughput transcriptomics and population modeling, improved understanding of interindividual variability in chemical-induced activation of toxicity relevant stress pathways across the human population using a large panel of plated cryopreserved PHHs was established, thereby contributing toward increasing the confidence of in vitro-based prediction of adverse responses, in particular hepatotoxicity. https://doi.org/10.1289/EHP11891.
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Affiliation(s)
- Marije Niemeijer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | | | - Shuai Fu
- Simcyp Division, CERTARA, Sheffield, UK
| | - Suzanna Huppelschoten
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | | | | | | | - Richard S. Paules
- Division of the National Toxicology Program, NIEHS, NIH, Research Triangle Park, North Carolina, USA
| | | | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
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3
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Wijaya LS, Gabor A, Pot IE, van de Have L, Saez-Rodriguez J, Stevens JL, Le Dévédec SE, Callegaro G, van de Water B. A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury. Toxicol Sci 2024; 198:14-30. [PMID: 38015832 PMCID: PMC10901150 DOI: 10.1093/toxsci/kfad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Drug-induced liver injury (DILI) remains the main reason for drug development attritions largely due to poor mechanistic understanding. Toxicogenomic to interrogate the mechanism of DILI has been broadly performed. Gene coregulation network-based transcriptome analysis is a bioinformatics approach that potentially contributes to improve mechanistic interpretation of toxicogenomic data. Here we performed an extensive concentration time course response-toxicogenomic study in the HepG2 cell line exposed to 20 DILI compounds, 7 reference compounds for stress response pathways, and 10 agonists for cytokines and growth factor receptors. We performed whole transcriptome targeted RNA sequencing to more than 500 conditions and applied weighted gene coregulated network analysis to the transcriptomics data followed by the identification of gene coregulated networks (modules) that were strongly modulated upon the exposure of DILI compounds. Preservation analysis on the module responses of HepG2 and PHH demonstrated highly preserved adaptive stress response gene coregulated networks. We correlated gene coregulated networks with cell death onset and causal relationships of 67 critical target genes of these modules with the onset of cell death was evaluated using RNA interference screening. We identified GTPBP2, HSPA1B, IRF1, SIRT1, and TSC22D3 as essential modulators of DILI compound-induced cell death. These genes were also induced by DILI compounds in PHH. Altogether, we demonstrate the application of large transcriptome datasets combined with network-based analysis and biological validation to uncover the candidate determinants of DILI.
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Affiliation(s)
- Lukas S Wijaya
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Attila Gabor
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg University Hospital, Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Iris E Pot
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Luca van de Have
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg University Hospital, Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - James L Stevens
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Giulia Callegaro
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Bob van de Water
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
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4
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Kunnen SJ, Arnesdotter E, Willenbockel CT, Vinken M, van de Water B. Qualitative and quantitative concentration-response modelling of gene co-expression networks to unlock hepatotoxic mechanisms for next generation chemical safety assessment. ALTEX 2024; 41:213-232. [PMID: 38376873 DOI: 10.14573/altex.2309201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
Next generation risk assessment of chemicals revolves around the use of mechanistic information without animal experimentation. In this regard, toxicogenomics has proven to be a useful tool to elucidate the underlying mechanisms of adverse effects of xenobiotics. In the present study, two widely used human in vitro hepatocyte culture systems, namely primary human hepatocytes (PHH) and human hepatoma HepaRG cells, were exposed to liver toxicants known to induce liver cholestasis, steatosis or necrosis. Benchmark concentration-response modelling was applied to transcriptomics gene co-expression networks (modules) to derive benchmark concentrations (BMCs) and to gain mechanistic insight into the hepatotoxic effects. BMCs derived by concentration-response modelling of gene co-expression modules recapitulated concentration-response modelling of individual genes. Although PHH and HepaRG cells showed overlap in deregulated genes and modules by the liver toxicants, PHH demonstrated a higher responsiveness, based on the lower BMCs of co-regulated gene modules. Such BMCs can be used as transcriptomics point of departure (tPOD) for assessing module-associated cellular (stress) pathways/processes. This approach identified clear tPODs of around maximum systemic concentration (Cmax) levels for the tested drugs, while for cosmetics ingredients the BMCs were 10-100-fold higher than the estimated plasma concentrations. This approach could serve next generation risk assessment practice to identify early responsive modules at low BMCs, that could be linked to key events in liver adverse outcome pathways. In turn, this can assist in delineating potential hazards of new test chemicals using in vitro systems and used in a risk assessment when BMCs are paired with chemical exposure assessment.
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Affiliation(s)
- Steven J Kunnen
- Leiden University, Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - Emma Arnesdotter
- Vrije Universiteit Brussel, Department of Pharmaceutical and Pharmacological Sciences, Brussels, Belgium
| | | | - Mathieu Vinken
- Vrije Universiteit Brussel, Department of Pharmaceutical and Pharmacological Sciences, Brussels, Belgium
| | - Bob van de Water
- Leiden University, Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
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5
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Bergonzini C, Gregori A, Hagens TMS, van der Noord VE, van de Water B, Zweemer AJM, Coban B, Capula M, Mantini G, Botto A, Finamore F, Garajova I, McDonnell LA, Schmidt T, Giovannetti E, Danen EHJ. ABCB1 overexpression through locus amplification represents an actionable target to combat paclitaxel resistance in pancreatic cancer cells. J Exp Clin Cancer Res 2024; 43:4. [PMID: 38163893 PMCID: PMC10759666 DOI: 10.1186/s13046-023-02879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest types of cancer and the chemotherapies such as gemcitabine/nab-paclitaxel are confronted with intrinsic or acquired resistance. The aim of this study was to investigate mechanisms underlying paclitaxel resistance in PDAC and explore strategies to overcome it. METHODS Three paclitaxel (PR) and gemcitabine resistant (GR) PDAC models were established. Transcriptomics and proteomics were used to identify conserved mechanisms of drug resistance. Genetic and pharmacological approaches were used to overcome paclitaxel resistance. RESULTS Upregulation of ABCB1 through locus amplification was identified as a conserved feature unique to PR cells. ABCB1 was not affected in any of the GR models and no cross resistance was observed. The ABCB1 inhibitor verapamil or siRNA-mediated ABCB1 depletion sensitized PR cells to paclitaxel and prevented efflux of ABCB1 substrates in all models. ABCB1 expression was associated with a trend towards shorter survival in patients who had received gemcitabine/nab-paclitaxel treatment. A pharmacological screen identified known and novel kinase inhibitors that attenuate efflux of ABCB1 substrates and sensitize PR PDAC cells to paclitaxel. CONCLUSION Upregulation of ABCB1 through locus amplification represents a novel, conserved mechanism of PDAC paclitaxel resistance. Kinase inhibitors identified in this study can be further (pre) clinically explored as therapeutic strategies to overcome paclitaxel resistance in PDAC.
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Affiliation(s)
- Cecilia Bergonzini
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Alessandro Gregori
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Tessa M S Hagens
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Vera E van der Noord
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Annelien J M Zweemer
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bircan Coban
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mjriam Capula
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam, The Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana Per La Scienza, San Giuliano, Pisa, Italy
| | - Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Asia Botto
- Proteomics and Metabolomics Lab, Fondazione Pisana Per La Scienza, San Giuliano, Pisa, Italy
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Francesco Finamore
- Proteomics and Metabolomics Lab, Fondazione Pisana Per La Scienza, San Giuliano, Pisa, Italy
| | - Ingrid Garajova
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Liam A McDonnell
- Proteomics and Metabolomics Lab, Fondazione Pisana Per La Scienza, San Giuliano, Pisa, Italy
| | - Thomas Schmidt
- Physics of Life Processes, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam, The Netherlands.
- Cancer Pharmacology Lab, Fondazione Pisana Per La Scienza, San Giuliano, Pisa, Italy.
| | - Erik H J Danen
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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6
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Zobl W, Bitsch A, Blum J, Boei JJWA, Capinha L, Carta G, Castell J, Davoli E, Drake C, Fisher CP, Heldring MM, Islam B, Jennings P, Leist M, Pellegrino-Coppola D, Schimming JP, Snijders KE, Tolosa L, van de Water B, van Vugt-Lussenburg BMA, Walker P, Wehr MM, Wijaya LS, Escher SE. Protectiveness of NAM-based hazard assessment - which testing scope is required? ALTEX 2023; 41:302-319. [PMID: 38048429 DOI: 10.14573/altex.2309081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/24/2023] [Indexed: 12/06/2023]
Abstract
Hazard assessment (HA) requires toxicity tests to allow deriving protective points of departure (PoDs) for risk assessment irrespective of a compound's mode of action (MoA). The scope of in vitro test batteries (ivTB) thereby necessitated for systemic toxicity is still unclear. We explored the protectiveness regarding systemic toxicity of an ivTB with a scope, which was guided by previous findings from rodent studies, where examining six main targets, including liver and kidney, was sufficient to predict the guideline scope-based PoD with high probability. The ivTB comprises human in vitro models representing liver, kidney, lung and the neuronal system covering transcriptome, mitochondrial dysfunction and neuronal outgrowth. Additionally, 32 CALUX®- and 10 HepG2 BAC-GFP reporters cover a broad range of disturbance mechanisms. Eight compounds were chosen for causing adverse effects such as immunotoxicity or anemia in vivo, i.e., effects not directly covered by assays in the ivTB. PoDs derived from the ivTB and from oral repeated dose studies in rodents were extrapolated to maximum unbound plasma concentrations for comparison. The ivTB-based PoDs were one to five orders of magnitude lower than in vivo PoDs for six of eight compounds, implying that they were protective. The extent of in vitro response varied across test compounds. Especially for hematotoxic substances, the ivTB showed either no response or only cytotoxicity. Assays better capturing this type of hazard would be needed to complement the ivTB. This study highlights the potentially broad applicability of ivTBs for deriving protective PoDs of compounds with unknown MoA.
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Affiliation(s)
- Walter Zobl
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Annette Bitsch
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | | | - Jan J W A Boei
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - Giada Carta
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jose Castell
- Instituto de Investigación Sanitaria La Fe, CIBEREHD, CIBERBBN, Valencia, Spain
| | - Enrico Davoli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Christina Drake
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | | | - Muriel M Heldring
- Leiden University, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Barira Islam
- Certara - Simcyp Division, Sheffield, United Kingdom
| | - Paul Jennings
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | | | - Johannes P Schimming
- Leiden University, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Kirsten E Snijders
- Leiden University, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Laia Tolosa
- Instituto de Investigación Sanitaria La Fe, CIBEREHD, CIBERBBN, Valencia, Spain
| | - Bob van de Water
- Leiden University, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | | | - Paul Walker
- Cyprotex Discovery Ltd UK, Macclesfield, United Kingdom
| | - Matthias M Wehr
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
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7
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Carta G, van der Stel W, Scuric EWJ, Capinha L, Delp J, Bennekou SH, Forsby A, Walker P, Leist M, van de Water B, Jennings P. Transcriptional landscape of mitochondrial electron transport chain inhibition in renal cells. Cell Biol Toxicol 2023; 39:3031-3059. [PMID: 37353587 PMCID: PMC10693540 DOI: 10.1007/s10565-023-09816-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/23/2023] [Indexed: 06/25/2023]
Abstract
Analysis of the transcriptomic alterations upon chemical challenge, provides in depth mechanistic information on the compound's toxic mode of action, by revealing specific pathway activation and other transcriptional modulations. Mapping changes in cellular behaviour to chemical insult, facilitates the characterisation of chemical hazard. In this study, we assessed the transcriptional landscape of mitochondrial impairment through the inhibition of the electron transport chain (ETC) in a human renal proximal tubular cell line (RPTEC/TERT1). We identified the unfolded protein response pathway (UPR), particularly the PERK/ATF4 branch as a common cellular response across ETC I, II and III inhibitions. This finding and the specific genes elaborated may aid the identification of mitochondrial liabilities of chemicals in both legacy data and prospective transcriptomic studies.
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Affiliation(s)
- Giada Carta
- Division of Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, the Netherlands.
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Emma W J Scuric
- Division of Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, the Netherlands
| | - Liliana Capinha
- Division of Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, the Netherlands
| | - Johannes Delp
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp‑Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | | | - Anna Forsby
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Paul Walker
- Cyprotex Discovery Ltd., Alderley Park, Macclesfield, Cheshire, UK
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp‑Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, the Netherlands
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8
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Béquignon OM, Gómez-Tamayo JC, Lenselink EB, Wink S, Hiemstra S, Lam CC, Gadaleta D, Roncaglioni A, Norinder U, Water BVD, Pastor M, van Westen GJP. Collaborative SAR Modeling and Prospective In Vitro Validation of Oxidative Stress Activation in Human HepG2 Cells. J Chem Inf Model 2023; 63:5433-5445. [PMID: 37616385 PMCID: PMC10498489 DOI: 10.1021/acs.jcim.3c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Indexed: 08/26/2023]
Abstract
Oxidative stress is the consequence of an abnormal increase of reactive oxygen species (ROS). ROS are generated mainly during the metabolism in both normal and pathological conditions as well as from exposure to xenobiotics. Xenobiotics can, on the one hand, disrupt molecular machinery involved in redox processes and, on the other hand, reduce the effectiveness of the antioxidant activity. Such dysregulation may lead to oxidative damage when combined with oxidative stress overpassing the cell capacity to detoxify ROS. In this work, a green fluorescent protein (GFP)-tagged nuclear factor erythroid 2-related factor 2 (NRF2)-regulated sulfiredoxin reporter (Srxn1-GFP) was used to measure the antioxidant response of HepG2 cells to a large series of drug and drug-like compounds (2230 compounds). These compounds were then classified as positive or negative depending on cellular response and distributed among different modeling groups to establish structure-activity relationship (SAR) models. A selection of models was used to prospectively predict oxidative stress induced by a new set of compounds subsequently experimentally tested to validate the model predictions. Altogether, this exercise exemplifies the different challenges of developing SAR models of a phenotypic cellular readout, model combination, chemical space selection, and results interpretation.
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Affiliation(s)
- Olivier
J. M. Béquignon
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Jose C. Gómez-Tamayo
- Research
Programme on Biomedical Informatics (GRIB), Department of Medicine
and Life Sciences, Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Carrer del Dr. Aiguader 88, 08002 Barcelona, Spain
| | - Eelke B. Lenselink
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Steven Wink
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Steven Hiemstra
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Chi Chung Lam
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Domenico Gadaleta
- Laboratory
of Environmental Chemistry and Toxicology, Department of Environmental
Health Sciences, IRCCS—Istituto di
Ricerche Farmacologiche Mario Negri, Via la Masa 19, 20156 Milano, Italy
| | - Alessandra Roncaglioni
- Laboratory
of Environmental Chemistry and Toxicology, Department of Environmental
Health Sciences, IRCCS—Istituto di
Ricerche Farmacologiche Mario Negri, Via la Masa 19, 20156 Milano, Italy
| | - Ulf Norinder
- MTM
Research Centre, School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden
| | - Bob van de Water
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
| | - Manuel Pastor
- Research
Programme on Biomedical Informatics (GRIB), Department of Medicine
and Life Sciences, Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Carrer del Dr. Aiguader 88, 08002 Barcelona, Spain
| | - Gerard J. P. van Westen
- Leiden
Academic Centre for Drug Research, Leiden
University, Wassenaarseweg 76, 2333 AL Leiden, The Netherlands
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9
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Schmeisser S, Miccoli A, von Bergen M, Berggren E, Braeuning A, Busch W, Desaintes C, Gourmelon A, Grafström R, Harrill J, Hartung T, Herzler M, Kass GEN, Kleinstreuer N, Leist M, Luijten M, Marx-Stoelting P, Poetz O, van Ravenzwaay B, Roggeband R, Rogiers V, Roth A, Sanders P, Thomas RS, Marie Vinggaard A, Vinken M, van de Water B, Luch A, Tralau T. New approach methodologies in human regulatory toxicology - Not if, but how and when! Environ Int 2023; 178:108082. [PMID: 37422975 PMCID: PMC10858683 DOI: 10.1016/j.envint.2023.108082] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The predominantly animal-centric approach of chemical safety assessment has increasingly come under pressure. Society is questioning overall performance, sustainability, continued relevance for human health risk assessment and ethics of this system, demanding a change of paradigm. At the same time, the scientific toolbox used for risk assessment is continuously enriched by the development of "New Approach Methodologies" (NAMs). While this term does not define the age or the state of readiness of the innovation, it covers a wide range of methods, including quantitative structure-activity relationship (QSAR) predictions, high-throughput screening (HTS) bioassays, omics applications, cell cultures, organoids, microphysiological systems (MPS), machine learning models and artificial intelligence (AI). In addition to promising faster and more efficient toxicity testing, NAMs have the potential to fundamentally transform today's regulatory work by allowing more human-relevant decision-making in terms of both hazard and exposure assessment. Yet, several obstacles hamper a broader application of NAMs in current regulatory risk assessment. Constraints in addressing repeated-dose toxicity, with particular reference to the chronic toxicity, and hesitance from relevant stakeholders, are major challenges for the implementation of NAMs in a broader context. Moreover, issues regarding predictivity, reproducibility and quantification need to be addressed and regulatory and legislative frameworks need to be adapted to NAMs. The conceptual perspective presented here has its focus on hazard assessment and is grounded on the main findings and conclusions from a symposium and workshop held in Berlin in November 2021. It intends to provide further insights into how NAMs can be gradually integrated into chemical risk assessment aimed at protection of human health, until eventually the current paradigm is replaced by an animal-free "Next Generation Risk Assessment" (NGRA).
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Affiliation(s)
| | - Andrea Miccoli
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany; National Research Council, Ancona, Italy
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | | | - Albert Braeuning
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Christian Desaintes
- European Commission (EC), Directorate General for Research and Innovation (RTD), Brussels, Belgium
| | - Anne Gourmelon
- Organisation for Economic Cooperation and Development (OECD), Environment Directorate, Paris, France
| | | | - Joshua Harrill
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health Baltimore MD USA, CAAT-Europe, University of Konstanz, Konstanz, Germany
| | - Matthias Herzler
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Nicole Kleinstreuer
- NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences (NIEHS), Durham, USA
| | - Marcel Leist
- CAAT‑Europe and Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Oliver Poetz
- NMI Natural and Medical Science Institute at the University of Tuebingen, Reutlingen, Germany; SIGNATOPE GmbH, Reutlingen, Germany
| | | | - Rob Roggeband
- European Partnership for Alternative Approaches to Animal Testing (EPAA), Procter and Gamble Services Company NV/SA, Strombeek-Bever, Belgium
| | - Vera Rogiers
- Scientific Committee on Consumer Safety (SCCS), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Adrian Roth
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Pascal Sanders
- Fougeres Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France France
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | | | | | | | - Andreas Luch
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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10
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Sanz F, Pognan F, Steger-Hartmann T, Díaz C, Asakura S, Amberg A, Bécourt-Lhote N, Blomberg N, Bosc N, Briggs K, Bringezu F, Brulle-Wohlhueter C, Brunak S, Bueters R, Callegaro G, Capella-Gutierrez S, Centeno E, Corvi J, Cronin MTD, Drew P, Duchateau-Nguyen G, Ecker GF, Escher S, Felix E, Ferreiro M, Frericks M, Furlong LI, Geiger R, George C, Grandits M, Ivanov-Draganov D, Kilgour-Christie J, Kiziloren T, Kors JA, Koyama N, Kreuchwig A, Leach AR, Mayer MA, Monecke P, Muster W, Nakazawa CM, Nicholson G, Parry R, Pastor M, Piñero J, Oberhauser N, Ramírez-Anguita JM, Rodrigo A, Smajic A, Schaefer M, Schieferdecker S, Soininen I, Terricabras E, Trairatphisan P, Turner SC, Valencia A, van de Water B, van der Lei JL, van Mulligen EM, Vock E, Wilkinson D. eTRANSAFE: data science to empower translational safety assessment. Nat Rev Drug Discov 2023; 22:605-606. [PMID: 37316648 DOI: 10.1038/d41573-023-00099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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11
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Hosseini R, Vlasveld M, Willemse J, van de Water B, Le Dévédec SE, Wolstencroft KJ. FAIR High Content Screening in Bioimaging. Sci Data 2023; 10:462. [PMID: 37460560 PMCID: PMC10352356 DOI: 10.1038/s41597-023-02367-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Affiliation(s)
- Rohola Hosseini
- Life Science Semantics, Leiden Institute of Advanced Computer Science, Leiden, The Netherlands
| | - Matthijs Vlasveld
- Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Joost Willemse
- Cell Observatory, Institute of Biology Leiden, Leiden, The Netherlands
| | - Bob van de Water
- Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
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12
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Veltman CHJ, Pennings JLA, van de Water B, Luijten M. An Adverse Outcome Pathway Network for Chemically Induced Oxidative Stress Leading to (Non)genotoxic Carcinogenesis. Chem Res Toxicol 2023. [PMID: 37156502 DOI: 10.1021/acs.chemrestox.2c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenotoxic (NGTX) carcinogens induce cancer via other mechanisms than direct DNA damage. A recognized mode of action for NGTX carcinogens is induction of oxidative stress, a state in which the amount of oxidants in a cell exceeds its antioxidant capacity, leading to regenerative proliferation. Currently, carcinogenicity assessment of environmental chemicals primarily relies on genetic toxicity end points. Since NGTX carcinogens lack genotoxic potential, these chemicals may remain undetected in such evaluations. To enhance the predictivity of test strategies for carcinogenicity assessment, a shift toward mechanism-based approaches is required. Here, we present an adverse outcome pathway (AOP) network for chemically induced oxidative stress leading to (NGTX) carcinogenesis. To develop this AOP network, we first investigated the role of oxidative stress in the various cancer hallmarks. Next, possible mechanisms for chemical induction of oxidative stress and the biological effects of oxidative damage to macromolecules were considered. This resulted in an AOP network, of which associated uncertainties were explored. Ultimately, development of AOP networks relevant for carcinogenesis in humans will aid the transition to a mechanism-based, human relevant carcinogenicity assessment that involves a substantially lower number of laboratory animals.
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Affiliation(s)
- Christina H J Veltman
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Jeroen L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
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13
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van der Noord VE, van der Stel W, Louwerens G, Verhoeven D, Kuiken HJ, Lieftink C, Grandits M, Ecker GF, Beijersbergen RL, Bouwman P, Le Dévédec SE, van de Water B. Systematic screening identifies ABCG2 as critical factor underlying synergy of kinase inhibitors with transcriptional CDK inhibitors. Breast Cancer Res 2023; 25:51. [PMID: 37147730 PMCID: PMC10161439 DOI: 10.1186/s13058-023-01648-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a subtype of breast cancer with limited treatment options and poor clinical prognosis. Inhibitors of transcriptional CDKs are currently under thorough investigation for application in the treatment of multiple cancer types, including breast cancer. These studies have raised interest in combining these inhibitors, including CDK12/13 inhibitor THZ531, with a variety of other anti-cancer agents. However, the full scope of these potential synergistic interactions of transcriptional CDK inhibitors with kinase inhibitors has not been systematically investigated. Moreover, the mechanisms behind these previously described synergistic interactions remain largely elusive. METHODS Kinase inhibitor combination screenings were performed to identify kinase inhibitors that synergize with CDK7 inhibitor THZ1 and CDK12/13 inhibitor THZ531 in TNBC cell lines. CRISPR-Cas9 knockout screening and transcriptomic evaluation of resistant versus sensitive cell lines were performed to identify genes critical for THZ531 resistance. RNA sequencing analysis after treatment with individual and combined synergistic treatments was performed to gain further insights into the mechanism of this synergy. Kinase inhibitor screening in combination with visualization of ABCG2-substrate pheophorbide A was used to identify kinase inhibitors that inhibit ABCG2. Multiple transcriptional CDK inhibitors were evaluated to extend the significance of the found mechanism to other transcriptional CDK inhibitors. RESULTS We show that a very high number of tyrosine kinase inhibitors synergize with the CDK12/13 inhibitor THZ531. Yet, we identified the multidrug transporter ABCG2 as key determinant of THZ531 resistance in TNBC cells. Mechanistically, we demonstrate that most synergistic kinase inhibitors block ABCG2 function, thereby sensitizing cells to transcriptional CDK inhibitors, including THZ531. Accordingly, these kinase inhibitors potentiate the effects of THZ531, disrupting gene expression and increasing intronic polyadenylation. CONCLUSION Overall, this study demonstrates the critical role of ABCG2 in limiting the efficacy of transcriptional CDK inhibitors and identifies multiple kinase inhibitors that disrupt ABCG2 transporter function and thereby synergize with these CDK inhibitors. These findings therefore further facilitate the development of new (combination) therapies targeting transcriptional CDKs and highlight the importance of evaluating the role of ABC transporters in synergistic drug-drug interactions in general.
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Affiliation(s)
- Vera E van der Noord
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Louwerens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Danielle Verhoeven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Hendrik J Kuiken
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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14
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Liu Q, Liu N, van der Noord V, van der Stel W, van de Water B, Danen EHJ, Le Dévédec SE. Differential response of luminal and basal breast cancer cells to acute and chronic hypoxia. Breast Cancer Res Treat 2023; 198:583-596. [PMID: 36826702 PMCID: PMC10036440 DOI: 10.1007/s10549-023-06863-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 02/25/2023]
Abstract
Hypoxia is linked to disease progression and poor prognosis in several cancers, including breast cancer. Cancer cells can encounter acute, chronic, and/or intermittent periods of oxygen deprivation and it is poorly understood how the different breast cancer subtypes respond to such hypoxia regimes. Here, we assessed the response of representative cell lines for the luminal and basal A subtype to acute (24 h) and chronic hypoxia (5 days). High throughput targeted transcriptomics analysis showed that HIF-related pathways are significantly activated in both subtypes. Indeed, HIF1⍺ nuclear accumulation and activation of the HIF1⍺ target gene CA9 were comparable. Based on the number of differentially expressed genes: (i) 5 days of exposure to hypoxia induced a more profound transcriptional reprogramming than 24 h, and (ii) basal A cells were less affected by acute and chronic hypoxia as compared to luminal cells. Hypoxia-regulated gene networks were identified of which hub genes were associated with worse survival in breast cancer patients. Notably, while chronic hypoxia altered the regulation of the cell cycle in both cell lines, it induced two distinct adaptation programs in these subtypes. Mainly genes controlling central carbon metabolism were affected in the luminal cells whereas genes controlling the cytoskeleton were affected in the basal A cells. In agreement, in response to chronic hypoxia, lactate secretion was more prominently increased in the luminal cell lines which were associated with the upregulation of the GAPDH glycolytic enzyme. This was not observed in the basal A cell lines. In contrast, basal A cells displayed enhanced cell migration associated with more F-actin stress fibers whereas luminal cells did not. Altogether, these data show distinct responses to acute and chronic hypoxia that differ considerably between luminal and basal A cells. This differential adaptation is expected to play a role in the progression of these different breast cancer subtypes.
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Affiliation(s)
- Qiuyu Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Nasi Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Vera van der Noord
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands.
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands.
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15
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Llewellyn SV, Kermanizadeh A, Ude V, Jacobsen NR, Conway GE, Shah UK, Niemeijer M, Moné MJ, van de Water B, Roy S, Moritz W, Stone V, Jenkins GJS, Doak SH. Assessing the transferability and reproducibility of 3D in vitro liver models from primary human multi-cellular microtissues to cell-line based HepG2 spheroids. Toxicol In Vitro 2022; 85:105473. [PMID: 36108805 DOI: 10.1016/j.tiv.2022.105473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022]
Abstract
To reduce, replace, and refine in vivo testing, there is increasing emphasis on the development of more physiologically relevant in vitro test systems to improve the reliability of non-animal-based methods for hazard assessment. When developing new approach methodologies, it is important to standardize the protocols and demonstrate the methods can be reproduced by multiple laboratories. The aim of this study was to assess the transferability and reproducibility of two advanced in vitro liver models, the Primary Human multicellular microtissue liver model (PHH) and the 3D HepG2 Spheroid Model, for nanomaterial (NM) and chemical hazard assessment purposes. The PHH model inter-laboratory trial showed strong consistency across the testing sites. All laboratories evaluated cytokine release and cytotoxicity following exposure to titanium dioxide (TiO2) and zinc oxide (ZnO) nanoparticles. No significant difference was observed in cytotoxicity or IL-8 release for the test materials. The data were reproducible with all three laboratories with control readouts within a similar range. The PHH model ZnO induced the greatest cytotoxicity response at 50.0 μg/mL and a dose-dependent increase in IL-8 release. For the 3D HepG2 spheroid model, all test sites were able to construct the model and demonstrated good concordance in IL-8 cytokine release and genotoxicity data. This trial demonstrates the successful transfer of new approach methodologies across multiple laboratories, with good reproducibility for several hazard endpoints.
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Affiliation(s)
- Samantha V Llewellyn
- In vitro Toxicology Group, Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Ali Kermanizadeh
- University of Derby, School of Human Sciences, Derby DE22 1GB, UK
| | - Victor Ude
- Heriot Watt University, School of Engineering and Physical Sciences, Nano Safety Research Group, Edinburgh, UK
| | - Nicklas Raun Jacobsen
- National Research Centre for the Working Environment (NRCWE), Lersø Parkallé 105, DK-2100 Copenhagen, Denmark
| | - Gillian E Conway
- In vitro Toxicology Group, Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Ume-Kulsoom Shah
- In vitro Toxicology Group, Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, the Netherlands
| | - Martijn J Moné
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, the Netherlands
| | - Shambhu Roy
- MilliporeSigma, 14920 Broschart Road, Rockville, MD 20850, USA
| | | | - Vicki Stone
- Heriot Watt University, School of Engineering and Physical Sciences, Nano Safety Research Group, Edinburgh, UK
| | - Gareth J S Jenkins
- In vitro Toxicology Group, Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, UK
| | - Shareen H Doak
- In vitro Toxicology Group, Institute of Life Sciences, Swansea University Medical School, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, UK.
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16
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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17
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Driessen M, van der Plas-Duivesteijn S, Kienhuis AS, van den Brandhof EJ, Roodbergen M, van de Water B, Spaink HP, Palmblad M, van der Ven LTM, Pennings JLA. Identification of proteome markers for drug-induced liver injury in zebrafish embryos. Toxicology 2022; 477:153262. [PMID: 35868597 DOI: 10.1016/j.tox.2022.153262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 10/17/2022]
Abstract
The zebrafish embryo (ZFE) is a promising alternative non-rodent model in toxicology, and initial studies suggested its applicability in detecting hepatic responses related to drug-induced liver injury (DILI). Here, we hypothesize that detailed analysis of underlying mechanisms of hepatotoxicity in ZFE contributes to the improved identification of hepatotoxic properties of compounds and to the reduction of rodents used for hepatotoxicity assessment. ZFEs were exposed to nine reference hepatotoxicants, targeted at induction of steatosis, cholestasis, and necrosis, and effects compared with negative controls. Protein profiles of the individual compounds were generated using LC-MS/MS. We identified differentially expressed proteins and pathways, but as these showed considerable overlap, phenotype-specific responses could not be distinguished. This led us to identify a set of common hepatotoxicity marker proteins. At the pathway level, these were mainly associated with cellular adaptive stress-responses, whereas single proteins could be linked to common hepatotoxicity-associated processes. Applying several stringency criteria to our proteomics data as well as information from other data sources resulted in a set of potential robust protein markers, notably Igf2bp1, Cox5ba, Ahnak, Itih3b.2, Psma6b, Srsf3a, Ces2b, Ces2a, Tdo2b, and Anxa1c, for the detection of adverse responses.
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Affiliation(s)
- Marja Driessen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Anne S Kienhuis
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Evert-Jan van den Brandhof
- Centre for Environmental Quality, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Marianne Roodbergen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Leo T M van der Ven
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Jeroen L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands.
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18
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Ter Braak B, Klip JE, Wink S, Hiemstra S, Cooper SL, Middleton A, White A, van de Water B. Mapping the dynamics of Nrf2 antioxidant and NFκB inflammatory responses by soft electrophilic chemicals in human liver cells defines the transition from adaptive to adverse responses. Toxicol In Vitro 2022; 84:105419. [PMID: 35724838 DOI: 10.1016/j.tiv.2022.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/19/2022] [Accepted: 06/14/2022] [Indexed: 11/15/2022]
Abstract
A comprehensive understanding of the dynamic activation and crosstalk between different cellular stress response pathways that drive cell adversity is crucial in chemical safety assessment. Various chemicals have electrophilic properties that drive cell injury responses in particular oxidative stress signaling and inflammatory signaling. Here we used bacterial artificial chromosome-based GFP cellular stress reporters with live cell confocal imaging, to systematically monitor the differential modulation of the dynamics of stress pathway activation by six different soft electrophiles: sulforaphane, andrographolide, diethyl maleate, CDDO-Me, ethacrynic acid and tert-butyl hydroquinone. The various soft electrophiles showed differential potency and dynamics of Nrf2 activation and nuclear translocation. These differences in Nrf2 dynamics correlated with distinct activation pattern of Nrf2 downstream targets SRNX1 and HMOX1. All soft electrophiles caused a strong dose dependent suppression of a cytokine-induced NFĸB response represented by suppression of NFĸB nuclear oscillation and inhibition of the downstream target gene activation A20 and ICAM1, which followed the potency of Nrf2 modulation but occurred at higher concentration close to saturation of Nrf2 activation. RNAi-based depletion of RelA resulted in a prolonged presence of Nrf2 in the nucleus after soft electrophile treatment; depletion of Nrf2 caused the induction of NFĸB signaling and activation of its downstream targets A20 and ICAM1. A systematic transcriptome analysis confirmed these effects by soft electrophiles on Nrf2 and NFκB signaling crosstalk in human induced-pluripotent stem cell-derived hepatocyte-like cells. Altogether our data indicate that modulation of Nrf2 by soft electrophiles may have consequences for efficient inflammatory signaling.
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Affiliation(s)
- Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands
| | - Janna E Klip
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands
| | - Steven Hiemstra
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands
| | | | | | | | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333, CC, Leiden, the Netherlands.
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19
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Burger GA, van de Water B, Le Dévédec SE, Beltman JB. Density-Dependent Migration Characteristics of Cancer Cells Driven by Pseudopod Interaction. Front Cell Dev Biol 2022; 10:854721. [PMID: 35547818 PMCID: PMC9084912 DOI: 10.3389/fcell.2022.854721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
The ability of cancer cells to invade neighboring tissue from primary tumors is an important determinant of metastatic behavior. Quantification of cell migration characteristics such as migration speed and persistence helps to understand the requirements for such invasiveness. One factor that may influence invasion is how local tumor cell density shapes cell migration characteristics, which we here investigate with a combined experimental and computational modeling approach. First, we generated and analyzed time-lapse imaging data on two aggressive Triple-Negative Breast Cancer (TNBC) cell lines, HCC38 and Hs578T, during 2D migration assays at various cell densities. HCC38 cells exhibited a counter-intuitive increase in speed and persistence with increasing density, whereas Hs578T did not exhibit such an increase. Moreover, HCC38 cells exhibited strong cluster formation with active pseudopod-driven migration, especially at low densities, whereas Hs578T cells maintained a dispersed positioning. In order to obtain a mechanistic understanding of the density-dependent cell migration characteristics and cluster formation, we developed realistic spatial simulations using a Cellular Potts Model (CPM) with an explicit description of pseudopod dynamics. Model analysis demonstrated that pseudopods exerting a pulling force on the cell and interacting via increased adhesion at pseudopod tips could explain the experimentally observed increase in speed and persistence with increasing density in HCC38 cells. Thus, the density-dependent migratory behavior could be an emergent property of single-cell characteristics without the need for additional mechanisms. This implies that pseudopod dynamics and interaction may play a role in the aggressive nature of cancers through mediating dispersal.
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Affiliation(s)
- Gerhard A Burger
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
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20
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van der Stel W, Yang H, le Dévédec SE, van de Water B, Beltman JB, Danen EHJ. High-content high-throughput imaging reveals distinct connections between mitochondrial morphology and functionality for OXPHOS complex I, III, and V inhibitors. Cell Biol Toxicol 2022:10.1007/s10565-022-09712-6. [PMID: 35505273 DOI: 10.1007/s10565-022-09712-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 04/07/2022] [Indexed: 11/02/2022]
Abstract
Cells can adjust their mitochondrial morphology by altering the balance between mitochondrial fission and fusion to adapt to stressful conditions. The connection between a chemical perturbation, changes in mitochondrial function, and altered mitochondrial morphology is not well understood. Here, we made use of high-throughput high-content confocal microscopy to assess the effects of distinct classes of oxidative phosphorylation (OXPHOS) complex inhibitors on mitochondrial parameters in a concentration and time resolved manner. Mitochondrial morphology phenotypes were clustered based on machine learning algorithms and mitochondrial integrity patterns were mapped. In parallel, changes in mitochondrial membrane potential (MMP), mitochondrial and cellular ATP levels, and viability were microscopically assessed. We found that inhibition of MMP, mitochondrial ATP production, and oxygen consumption rate (OCR) using sublethal concentrations of complex I and III inhibitors did not trigger mitochondrial fragmentation. Instead, complex V inhibitors that suppressed ATP and OCR but increased MMP provoked a more fragmented mitochondrial morphology. In agreement, complex V but not complex I or III inhibitors triggered proteolytic cleavage of the mitochondrial fusion protein, OPA1. The relation between increased MMP and fragmentation did not extend beyond OXPHOS complex inhibitors: increasing MMP by blocking the mPTP pore did not lead to OPA1 cleavage or mitochondrial fragmentation and the OXPHOS uncoupler FCCP was associated with OPA1 cleavage and MMP reduction. Altogether, our findings connect vital mitochondrial functions and phenotypes in a high-throughput high-content confocal microscopy approach that help understanding of chemical-induced toxicity caused by OXPHOS complex perturbing chemicals.
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Affiliation(s)
- Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands
| | - Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands
| | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg, 55, 2333 CC, Leiden, The Netherlands.
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21
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de Boer A, van der Harst J, Fehr M, Geurts L, Knipping K, Kramer N, Krul L, Tabernero Urbieta M, van de Water B, Venema K, Schütte K, Triantis V. Animal-free strategies in food safety & nutrition: What are we waiting for? Part II: Nutrition research. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Tebby C, Gao W, Delp J, Carta G, van der Stel W, Leist M, Jennings P, van de Water B, Bois FY. A quantitative AOP of mitochondrial toxicity based on data from three cell lines. Toxicol In Vitro 2022; 81:105345. [PMID: 35278637 DOI: 10.1016/j.tiv.2022.105345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/22/2022] [Accepted: 03/07/2022] [Indexed: 11/30/2022]
Abstract
Adverse Outcome Pathways (AOPs) are increasingly used to support the integration of in vitro data in hazard assessment for chemicals. Quantitative AOPs (qAOPs) use mathematical models to describe the relationship between key events (KEs). In this paper, data obtained in three cell lines, LHUMES, HepG2 and RPTEC/TERT1, using similar experimental protocols, was used to calibrate a qAOP of mitochondrial toxicity for two chemicals, rotenone and deguelin. The objectives were to determine whether the same qAOP could be used for the three cell types, and to test chemical-independence by cross-validation with a dataset obtained on eight other chemicals in LHUMES cells. Repeating the calibration approach for both chemicals in three cell lines highlighted various practical difficulties. Even when the same readouts of KEs are measured, the mathematical functions used to describe the key event relationships may not be the same. Cross-validation in LHUMES cells was attempted by estimating chemical-specific potency at the molecular initiating events and using the rest of the calibrated qAOP to predict downstream KEs: toxicity of azoxystrobin, carboxine, mepronil and thifluzamide was underestimated. Selection of most relevant readouts and accurate characterization of the molecular initiating event for cross-validation are critical when designing in vitro experiments targeted at calibrating qAOPs.
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Affiliation(s)
- Cleo Tebby
- Experimental Toxicology and Modeling (TEAM) Unit, Ineris, rue Jacques Taffanel, 60550 Verneuil-en-Halatte, France.
| | - Wang Gao
- Experimental Toxicology and Modeling (TEAM) Unit, Ineris, rue Jacques Taffanel, 60550 Verneuil-en-Halatte, France; Applied Mathematics Laboratory (LMAC EA 2222), Université Technologique de Compiègne (UTC), 57 avenue de Landshut, 60203 Compiègne Cedex, France
| | - Johannes Delp
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78464, Konstanz, Germany; Cooperative Doctorate College InViTe, University of Konstanz, Konstanz, Germany
| | - Giada Carta
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78464, Konstanz, Germany
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Frederic Y Bois
- Experimental Toxicology and Modeling (TEAM) Unit, Ineris, rue Jacques Taffanel, 60550 Verneuil-en-Halatte, France; Certara, Simcyp, Sheffield, United Kingdom
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23
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Grinberg M, Stöber RM, Edlund K, Rempel E, Godoy P, Reif R, Widera A, Madjar K, Schmidt-Heck W, Marchan R, Sachinidis A, Spitkovsky D, Hescheler J, Carmo H, Arbo MD, van de Water B, Wink S, Vinken M, Rogiers V, Escher S, Hardy B, Mitic D, Apic G, Myatt G, Waldmann T, Mardinoglu A, Damm G, Seehofer D, Nüssler A, Weiss TS, Oberemm A, Lampen A, Schaap MM, Luijten M, van Steeg H, Thasler WE, Kleinjans JCS, Stierum RH, Leist M, Rahnenführer J, Hengstler JG. Correction to: Toxicogenomics directory of chemically exposed human hepatocytes. Arch Toxicol 2022; 96:945-946. [PMID: 35099568 DOI: 10.1007/s00204-021-03206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Regina M Stöber
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Eugen Rempel
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Patricio Godoy
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Raymond Reif
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Agata Widera
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Katrin Madjar
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK), Cologne, Germany
| | - Dimitry Spitkovsky
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK), Cologne, Germany
| | - Jürgen Hescheler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK), Cologne, Germany
| | - Helena Carmo
- Laboratório de Toxicologia, Departamento de Ciências Biológicas, Universidade do Porto, Porto, Portugal
| | - Marcelo D Arbo
- Laboratório de Toxicologia, Departamento de Ciências Biológicas, Universidade do Porto, Porto, Portugal
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mathieu Vinken
- Department of Toxicology, Dermato-Cosmetology and Pharmacognosy (FAFY), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Vera Rogiers
- Department of Toxicology, Dermato-Cosmetology and Pharmacognosy (FAFY), Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sylvia Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Barry Hardy
- Douglas Connect and OpenTox, Zeiningen, Switzerland
| | | | - Gordana Apic
- Cell Networks GmbH, Lutherstr. 59, 69120, Heidelberg, Germany
| | | | - Tanja Waldmann
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Adil Mardinoglu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Georg Damm
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, Berlin, Germany
| | - Daniel Seehofer
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, Berlin, Germany
| | - Andreas Nüssler
- Department of Traumatology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Thomas S Weiss
- Department of Pediatrics and Juvenile Medicine, University of Regensburg Hospital, Regensburg, Germany
| | - Axel Oberemm
- Federal Institute for Risk Assessment, Berlin, Germany
| | - Alfons Lampen
- Federal Institute for Risk Assessment, Berlin, Germany
| | - Mirjam M Schaap
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry van Steeg
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Jos C S Kleinjans
- Department of Health Risk Analysis and Toxicology, Maastricht University, Maastricht, The Netherlands
| | | | - Marcel Leist
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
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24
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Escher SE, Aguayo-Orozco A, Benfenati E, Bitsch A, Braunbeck T, Brotzmann K, Bois F, van der Burg B, Castel J, Exner T, Gadaleta D, Gardner I, Goldmann D, Hatley O, Golbamaki N, Graepel R, Jennings P, Limonciel A, Long A, Maclennan R, Mombelli E, Norinder U, Jain S, Capinha LS, Taboureau OT, Tolosa L, Vrijenhoek NG, van Vugt-Lussenburg BMA, Walker P, van de Water B, Wehr M, White A, Zdrazil B, Fisher C. A read-across case study on chronic toxicity of branched carboxylic acids (1): Integration of mechanistic evidence from new approach methodologies (NAMs) to explore a common mode of action. Toxicol In Vitro 2021; 79:105269. [PMID: 34757180 DOI: 10.1016/j.tiv.2021.105269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/17/2021] [Accepted: 10/27/2021] [Indexed: 02/04/2023]
Abstract
This read-across case study characterises thirteen, structurally similar carboxylic acids demonstrating the application of in vitro and in silico human-based new approach methods, to determine biological similarity. Based on data from in vivo animal studies, the read-across hypothesis is that all analogues are steatotic and so should be considered hazardous. Transcriptomic analysis to determine differentially expressed genes (DEGs) in hepatocytes served as first tier testing to confirm a common mode-of-action and identify differences in the potency of the analogues. An adverse outcome pathway (AOP) network for hepatic steatosis, informed the design of an in vitro testing battery, targeting AOP relevant MIEs and KEs, and Dempster-Shafer decision theory was used to systematically quantify uncertainty and to define the minimal testing scope. The case study shows that the read-across hypothesis is the critical core to designing a robust, NAM-based testing strategy. By summarising the current mechanistic understanding, an AOP enables the selection of NAMs covering MIEs, early KEs, and late KEs. Experimental coverage of the AOP in this way is vital since MIEs and early KEs alone are not confirmatory of progression to the AO. This strategy exemplifies the workflow previously published by the EUTOXRISK project driving a paradigm shift towards NAM-based NGRA.
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Affiliation(s)
- Sylvia E Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Germany.
| | | | - Emilio Benfenati
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Annette Bitsch
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Germany
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology Group, Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Katharina Brotzmann
- Aquatic Ecology and Toxicology Group, Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Frederic Bois
- Certara UK Ltd, Simcyp Division, Sheffield, United Kingdom
| | | | - Jose Castel
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | | | - Domenico Gadaleta
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Iain Gardner
- Certara UK Ltd, Simcyp Division, Sheffield, United Kingdom
| | - Daria Goldmann
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Vienna, Austria
| | - Oliver Hatley
- Certara UK Ltd, Simcyp Division, Sheffield, United Kingdom
| | | | - Rabea Graepel
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Paul Jennings
- Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | | | | | | | - Sankalp Jain
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Vienna, Austria
| | | | | | - Laia Tolosa
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Nanette G Vrijenhoek
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | | | | | - Bob van de Water
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Matthias Wehr
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Germany
| | - Andrew White
- Unilever Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom
| | - Barbara Zdrazil
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Vienna, Austria
| | - Ciarán Fisher
- Certara UK Ltd, Simcyp Division, Sheffield, United Kingdom
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25
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van der Stel W, Yang H, Vrijenhoek NG, Schimming JP, Callegaro G, Carta G, Darici S, Delp J, Forsby A, White A, le Dévédec S, Leist M, Jennings P, Beltman JB, van de Water B, Danen EHJ. Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation. Arch Toxicol 2021; 96:259-285. [PMID: 34642769 PMCID: PMC8748354 DOI: 10.1007/s00204-021-03160-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022]
Abstract
Mitochondrial perturbation is a key event in chemical-induced organ toxicities that is incompletely understood. Here, we studied how electron transport chain (ETC) complex I, II, or III (CI, CII and CIII) inhibitors affect mitochondrial functionality, stress response activation, and cell viability using a combination of high-content imaging and TempO-Seq in HepG2 hepatocyte cells. CI and CIII inhibitors perturbed mitochondrial membrane potential (MMP) and mitochondrial and cellular ATP levels in a concentration- and time-dependent fashion and, under conditions preventing a switch to glycolysis attenuated cell viability, whereas CII inhibitors had no effect. TempO-Seq analysis of changes in mRNA expression pointed to a shared cellular response to CI and CIII inhibition. First, to define specific ETC inhibition responses, a gene set responsive toward ETC inhibition (and not to genotoxic, oxidative, or endoplasmic reticulum stress) was identified using targeted TempO-Seq in HepG2. Silencing of one of these genes, NOS3, exacerbated the impact of CI and CIII inhibitors on cell viability, indicating its functional implication in cellular responses to mitochondrial stress. Then by monitoring dynamic responses to ETC inhibition using a HepG2 GFP reporter panel for different classes of stress response pathways and applying pathway and gene network analysis to TempO-Seq data, we looked for downstream cellular events of ETC inhibition and identified the amino acid response (AAR) as being triggered in HepG2 by ETC inhibition. Through in silico approaches we provide evidence indicating that a similar AAR is associated with exposure to mitochondrial toxicants in primary human hepatocytes. Altogether, we (i) unravel quantitative, time- and concentration-resolved cellular responses to mitochondrial perturbation, (ii) identify a gene set associated with adaptation to exposure to active ETC inhibitors, and (iii) show that ER stress and an AAR accompany ETC inhibition in HepG2 and primary hepatocytes.
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Affiliation(s)
- Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Nanette G Vrijenhoek
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Johannes P Schimming
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Giulia Callegaro
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Giada Carta
- Division Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Salihanur Darici
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Johannes Delp
- Chair for In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Anna Forsby
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Sylvia le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Marcel Leist
- Chair for In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Paul Jennings
- Division Molecular and Computational Toxicology, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands.
| | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands.
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26
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Yang H, van der Stel W, Lee R, Bauch C, Bevan S, Walker P, van de Water B, Danen EHJ, Beltman JB. Dynamic Modeling of Mitochondrial Membrane Potential Upon Exposure to Mitochondrial Inhibitors. Front Pharmacol 2021; 12:679407. [PMID: 34489692 PMCID: PMC8416757 DOI: 10.3389/fphar.2021.679407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are the main bioenergetic organelles of cells. Exposure to chemicals targeting mitochondria therefore generally results in the development of toxicity. The cellular response to perturbations in cellular energy production is a balance between adaptation, by reorganisation and organelle biogenesis, and sacrifice, in the form of cell death. In homeostatic conditions, aerobic mitochondrial energy production requires the maintenance of a mitochondrial membrane potential (MMP). Chemicals can perturb this MMP, and the extent of this perturbation depends both on the pharmacokinetics of the chemicals and on downstream MMP dynamics. Here we obtain a quantitative understanding of mitochondrial adaptation upon exposure to various mitochondrial respiration inhibitors by applying mathematical modeling to partially published high-content imaging time-lapse confocal imaging data, focusing on MMP dynamics in HepG2 cells over a period of 24 h. The MMP was perturbed using a set of 24 compounds, either acting as uncoupler or as mitochondrial complex inhibitor targeting complex I, II, III or V. To characterize the effect of chemical exposure on MMP dynamics, we adapted an existing differential equation model and fitted this model to the observed MMP dynamics. Complex III inhibitor data were better described by the model than complex I data. Incorporation of pharmacokinetic decay into the model was required to obtain a proper fit for the uncoupler FCCP. Furthermore, oligomycin (complex V inhibitor) model fits were improved by either combining pharmacokinetic (PK) decay and ion leakage or a concentration-dependent decay. Subsequent mass spectrometry measurements showed that FCCP had a significant decay in its PK profile as predicted by the model. Moreover, the measured oligomycin PK profile exhibited only a limited decay at high concentration, whereas at low concentrations the compound remained below the detection limit within cells. This is consistent with the hypothesis that oligomycin exhibits a concentration-dependent decay, yet awaits further experimental verification with more sensitive detection methods. Overall, we show that there is a complex interplay between PK and MMP dynamics within mitochondria and that data-driven modeling is a powerful combination to unravel such complexity.
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Affiliation(s)
- Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Randy Lee
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | | | - Sam Bevan
- Cyprotex Discovery Limited, Cheshire, United Kingdom
| | - Paul Walker
- Cyprotex Discovery Limited, Cheshire, United Kingdom
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
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27
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Snijders KE, Fehér A, Táncos Z, Bock I, Téglási A, van den Berk L, Niemeijer M, Bouwman P, Le Dévédec SE, Moné MJ, Van Rossom R, Kumar M, Wilmes A, Jennings P, Verfaillie CM, Kobolák J, Ter Braak B, Dinnyés A, van de Water B. Fluorescent tagging of endogenous Heme oxygenase-1 in human induced pluripotent stem cells for high content imaging of oxidative stress in various differentiated lineages. Arch Toxicol 2021; 95:3285-3302. [PMID: 34480604 PMCID: PMC8448683 DOI: 10.1007/s00204-021-03127-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/27/2021] [Indexed: 12/28/2022]
Abstract
Tagging of endogenous stress response genes can provide valuable in vitro models for chemical safety assessment. Here, we present the generation and application of a fluorescent human induced pluripotent stem cell (hiPSC) reporter line for Heme oxygenase-1 (HMOX1), which is considered a sensitive and reliable biomarker for the oxidative stress response. CRISPR/Cas9 technology was used to insert an enhanced green fluorescent protein (eGFP) at the C-terminal end of the endogenous HMOX1 gene. Individual clones were selected and extensively characterized to confirm precise editing and retained stem cell properties. Bardoxolone-methyl (CDDO-Me) induced oxidative stress caused similarly increased expression of both the wild-type and eGFP-tagged HMOX1 at the mRNA and protein level. Fluorescently tagged hiPSC-derived proximal tubule-like, hepatocyte-like, cardiomyocyte-like and neuron-like progenies were treated with CDDO-Me (5.62–1000 nM) or diethyl maleate (5.62–1000 µM) for 24 h and 72 h. Multi-lineage oxidative stress responses were assessed through transcriptomics analysis, and HMOX1-eGFP reporter expression was carefully monitored using live-cell confocal imaging. We found that eGFP intensity increased in a dose-dependent manner with dynamics varying amongst lineages and stressors. Point of departure modelling further captured the specific lineage sensitivities towards oxidative stress. We anticipate that the newly developed HMOX1 hiPSC reporter will become a valuable tool in understanding and quantifying critical target organ cell-specific oxidative stress responses induced by (newly developed) chemical entities.
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Affiliation(s)
- Kirsten E Snijders
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | | | | | | | | | - Linda van den Berk
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Martijn J Moné
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Rob Van Rossom
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Manoj Kumar
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Amsterdam, The Netherlands
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Amsterdam, The Netherlands
| | - Catherine M Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | | | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - András Dinnyés
- BioTalentum Ltd., 2100, Gödöllő, Hungary. .,Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary.
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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28
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Ter Braak B, Niemeijer M, Wolters L, Le Dévédec S, Bouwman P, van de Water B. Towards an advanced testing strategy for genotoxicity using image-based 2D and 3D HepG2 DNA damage response fluorescent protein reporters. Mutagenesis 2021; 37:130-142. [PMID: 34448005 PMCID: PMC9071099 DOI: 10.1093/mutage/geab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022] Open
Abstract
In vitro assessment of mutagenicity is an essential component in the chemical risk assessment. Given the diverse modes of action by which chemicals can induce DNA damage, it is essential that these in vitro assays are carefully evaluated for their possibilities and limitations. In this study, we used a fluorescent protein HepG2 reporter test system in combination with high content imaging. To measure induction of the DNA damage response (DDR), we used three different green fluorescent protein reporters for p53 pathway activation. These allowed for accurate quantification of p53, p21 and BTG2 (BTG anti-proliferation factor 2) protein expression and cell viability parameters at a single cell or spheroid resolution. The reporter lines were cultured as 2D monolayers and as 3D spheroids. Furthermore, liver maturity and cytochrome P450 enzyme expression were increased by culturing in an amino acid-rich (AAGLY) medium. We found that culture conditions that support a sustained proliferative state (2D culturing with normal DMEM medium) give superior sensitivity when genotoxic compounds are tested that do not require metabolisation and of which the mutagenic mode of action is dependent on replication. For compounds, which are metabolically converted to mutagenic metabolites, more differentiated HepG2 DDR reporters (e.g. 3D cultures) showed a higher sensitivity. This study stratifies how different culture methods of HepG2 DDR reporter cells can influence the sensitivity towards diverse genotoxicants and how this provides opportunities for a tiered genotoxicity testing strategy.
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Affiliation(s)
- Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Liesanne Wolters
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Sylvia Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
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29
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Booij TH, Leonhard WN, Bange H, Yan K, Fokkelman M, Plugge AJ, Veraar KAM, Dauwerse JG, van Westen GJP, van de Water B, Price LS, Peters DJM. In vitro 3D phenotypic drug screen identifies celastrol as an effective in vivo inhibitor of polycystic kidney disease. J Mol Cell Biol 2021; 12:644-653. [PMID: 31065693 PMCID: PMC7683017 DOI: 10.1093/jmcb/mjz029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 02/05/2019] [Accepted: 03/10/2019] [Indexed: 01/09/2023] Open
Abstract
Polycystic kidney disease (PKD) is a prevalent genetic disorder, characterized by the formation of kidney cysts that progressively lead to kidney failure. The currently available drug tolvaptan is not well tolerated by all patients and there remains a strong need for alternative treatments. The signaling rewiring in PKD that drives cyst formation is highly complex and not fully understood. As a consequence, the effects of drugs are sometimes difficult to predict. We previously established a high throughput microscopy phenotypic screening method for quantitative assessment of renal cyst growth. Here, we applied this 3D cyst growth phenotypic assay and screened 2320 small drug-like molecules, including approved drugs. We identified 81 active molecules that inhibit cyst growth. Multi-parametric phenotypic profiling of the effects on 3D cultured cysts discriminated molecules that showed preferred pharmacological effects above genuine toxicological properties. Celastrol, a triterpenoid from Tripterygium Wilfordii, was identified as a potent inhibitor of cyst growth in vitro. In an in vivo iKspCre-Pkd1lox,lox mouse model for PKD, celastrol inhibited the growth of renal cysts and maintained kidney function.
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Affiliation(s)
- Tijmen H Booij
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands.,NEXUS Personalized Health Technologies, ETH Zürich, Switzerland
| | - Wouter N Leonhard
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Kuan Yan
- OcellO B.V., Leiden, The Netherlands
| | - Michiel Fokkelman
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Anna J Plugge
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Kimberley A M Veraar
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Johannes G Dauwerse
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Gerard J P van Westen
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden, The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Leo S Price
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands.,OcellO B.V., Leiden, The Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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30
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Duijndam B, Goudriaan A, van den Hoorn T, van der Stel W, Le Dévédec S, Bouwman P, van der Laan JW, van de Water B. Physiologically Relevant Estrogen Receptor Alpha Pathway Reporters for Single-Cell Imaging-Based Carcinogenic Hazard Assessment of Estrogenic Compounds. Toxicol Sci 2021; 181:187-198. [PMID: 33769548 PMCID: PMC8163057 DOI: 10.1093/toxsci/kfab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estrogen receptor alpha (ERα) belongs to the nuclear hormone receptor family of ligand-inducible transcription factors and regulates gene networks in biological processes such as cell growth and proliferation. Disruption of these networks by chemical compounds with estrogenic activity can result in adverse outcomes such as unscheduled cell proliferation, ultimately culminating in tumor formation. To distinguish disruptive activation from normal physiological responses, it is essential to quantify relationships between different key events leading to a particular adverse outcome. For this purpose, we established fluorescent protein MCF7 reporter cell lines for ERα-induced proliferation by bacterial artificial chromosome-based tagging of 3 ERα target genes: GREB1, PGR, and TFF1. These target genes are inducible by the non-genotoxic carcinogen and ERα agonist 17β-estradiol in an ERα-dependent manner and are essential for ERα-dependent cell-cycle progression and proliferation. The 3 GFP reporter cell lines were characterized in detail and showed different activation dynamics upon exposure to 17β-estradiol. In addition, they demonstrated specific activation in response to other established reference estrogenic compounds of different potencies, with similar sensitivities as validated OECD test methods. This study shows that these fluorescent reporter cell lines can be used to monitor the spatial and temporal dynamics of ERα pathway activation at the single-cell level for more mechanistic insight, thereby allowing a detailed assessment of the potential carcinogenic activity of estrogenic compounds in humans.
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Affiliation(s)
- Britt Duijndam
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands.,Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht 3531AH, The Netherlands
| | - Annabel Goudriaan
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands
| | - Tineke van den Hoorn
- Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht 3531AH, The Netherlands
| | - Wanda van der Stel
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands
| | - Sylvia Le Dévédec
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands
| | - Jan Willem van der Laan
- Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht 3531AH, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333CC, The Netherlands
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31
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Wijaya LS, Rau C, Braun TS, Marangoz S, Spegg V, Vlasveld M, Albrecht W, Brecklinghaus T, Kamp H, Beltman JB, Hengstler JG, van de Water B, Leist M, Schildknecht S. Stimulation of de novo glutathione synthesis by nitrofurantoin for enhanced resilience of hepatocytes. Cell Biol Toxicol 2021; 38:847-864. [PMID: 34021431 PMCID: PMC9525367 DOI: 10.1007/s10565-021-09610-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 04/27/2021] [Indexed: 10/24/2022]
Abstract
Toxicity is not only a function of damage mechanisms, but is also determined by cellular resilience factors. Glutathione has been reported as essential element to counteract negative influences. The present work hence pursued the question how intracellular glutathione can be elevated transiently to render cells more resistant toward harmful conditions. The antibiotic nitrofurantoin (NFT) was identified to stimulate de novo synthesis of glutathione in the human hepatoma cell line, HepG2, and in primary human hepatocytes. In intact cells, activation of NFT yielded a radical anion, which subsequently initiated nuclear-factor-erythroid 2-related-factor-2 (Nrf2)-dependent induction of glutamate cysteine ligase (GCL). Application of siRNA-based intervention approaches confirmed the involvement of the Nrf2-GCL axis in the observed elevation of intracellular glutathione levels. Quantitative activation of Nrf2 by NFT, and the subsequent rise in glutathione, were similar as observed with the potent experimental Nrf2 activator diethyl maleate. The elevation of glutathione levels, observed even 48 h after withdrawal of NFT, rendered cells resistant to different stressors such as the mitochondrial inhibitor rotenone, the redox cycler paraquat, the proteasome inhibitors MG-132 or bortezomib, or high concentrations of NFT. Repurpose of the antibiotic NFT as activator of Nrf2 could thus be a promising strategy for a transient and targeted activation of the endogenous antioxidant machinery. Graphical abstract.
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Affiliation(s)
- Lukas S Wijaya
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300, RA, Leiden, The Netherlands
| | - Carina Rau
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, P.O. Box M657, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Theresa S Braun
- Konstanz Research School Chemical Biology (KoRS-CB), Department of Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Serif Marangoz
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, P.O. Box M657, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Vincent Spegg
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, P.O. Box M657, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Matthijs Vlasveld
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300, RA, Leiden, The Netherlands
| | - Wiebke Albrecht
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Tim Brecklinghaus
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Hennicke Kamp
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen am Rhein, Germany
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300, RA, Leiden, The Netherlands
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2300, RA, Leiden, The Netherlands
| | - Marcel Leist
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, P.O. Box M657, Universitätsstr. 10, 78457, Konstanz, Germany
| | - Stefan Schildknecht
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, P.O. Box M657, Universitätsstr. 10, 78457, Konstanz, Germany. .,Albstadt-Sigmaringen University, Faculty of Life Sciences, 72488, Sigmaringen, Germany.
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32
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Wijaya LS, Trairatphisan P, Gabor A, Niemeijer M, Keet J, Alcalà Morera A, Snijders KE, Wink S, Yang H, Schildknecht S, Stevens JL, Bouwman P, Kamp H, Hengstler J, Beltman J, Leist M, Le Dévédec S, Saez-Rodriguez J, van de Water B. Integration of temporal single cell cellular stress response activity with logic-ODE modeling reveals activation of ATF4-CHOP axis as a critical predictor of drug-induced liver injury. Biochem Pharmacol 2021; 190:114591. [PMID: 33957093 DOI: 10.1016/j.bcp.2021.114591] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
Drug-induced liver injury (DILI) is the most prevalent adversity encountered in drug development and clinical settings leading to urgent needs to understand the underlying mechanisms. In this study, we have systematically investigated the dynamics of the activation of cellular stress response pathways and cell death outcomes upon exposure of a panel of liver toxicants using live cell imaging of fluorescent reporter cell lines. We established a comprehensive temporal dynamic response profile of a large set of BAC-GFP HepG2 cell lines representing the following components of stress signaling: i) unfolded protein response (UPR) [ATF4, XBP1, BIP and CHOP]; ii) oxidative stress [NRF2, SRXN1, HMOX1]; iii) DNA damage [P53, P21, BTG2, MDM2]; and iv) NF-κB pathway [A20, ICAM1]. We quantified the single cell GFP expression as a surrogate for endogenous protein expression using live cell imaging over > 60 h upon exposure to 14 DILI compounds at multiple concentrations. Using logic-based ordinary differential equation (Logic-ODE), we modelled the dynamic profiles of the different stress responses and extracted specific descriptors potentially predicting the progressive outcomes. We identified the activation of ATF4-CHOP axis of the UPR as the key pathway showing the highest correlation with cell death upon DILI compound perturbation. Knocking down main components of the UPR provided partial protection from compound-induced cytotoxicity, indicating a complex interplay among UPR components as well as other stress pathways. Our results suggest that a systematic analysis of the temporal dynamics of ATF4-CHOP axis activation can support the identification of DILI risk for new candidate drugs.
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Affiliation(s)
- Lukas Surya Wijaya
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Panuwat Trairatphisan
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120 Heidelberg, Germany
| | - Attila Gabor
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120 Heidelberg, Germany
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Jason Keet
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Ariadna Alcalà Morera
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Kirsten E Snijders
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Stefan Schildknecht
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - James L Stevens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Hennicke Kamp
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen am Rhein, Germany
| | - Jan Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Joost Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Marcel Leist
- In vitro Toxicology and Biomedicine, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sylvia Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120 Heidelberg, Germany; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands.
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Llewellyn SV, Niemeijer M, Nymark P, Moné MJ, van de Water B, Conway GE, Jenkins GJS, Doak SH. In Vitro Three-Dimensional Liver Models for Nanomaterial DNA Damage Assessment. Small 2021; 17:e2006055. [PMID: 33448117 DOI: 10.1002/smll.202006055] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Whilst the liver possesses the ability to repair and restore sections of damaged tissue following acute injury, prolonged exposure to engineered nanomaterials (ENM) may induce repetitive injury leading to chronic liver disease. Screening ENM cytotoxicity using 3D liver models has recently been performed, but a significant challenge has been the application of such in vitro models for evaluating ENM associated genotoxicity; a vital component of regulatory human health risk assessment. This review considers the benefits, limitations, and adaptations of specific in vitro approaches to assess DNA damage in the liver, whilst identifying critical advancements required to support a multitude of biochemical endpoints, focusing on nano(geno)toxicology (e.g., secondary genotoxicity, DNA damage, and repair following prolonged or repeated exposures).
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Affiliation(s)
- Samantha V Llewellyn
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Penny Nymark
- Division of Toxicology, Misvik Biology, Karjakatu 35 B, Turku, FI-20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Nobels väg 13, Stockholm, 17 177, Sweden
| | - Martijn J Moné
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Gillian E Conway
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Gareth J S Jenkins
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Shareen H Doak
- In vitro Toxicology Group, Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
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Pognan F, Steger-Hartmann T, Díaz C, Blomberg N, Bringezu F, Briggs K, Callegaro G, Capella-Gutierrez S, Centeno E, Corvi J, Drew P, Drewe WC, Fernández JM, Furlong LI, Guney E, Kors JA, Mayer MA, Pastor M, Piñero J, Ramírez-Anguita JM, Ronzano F, Rowell P, Saüch-Pitarch J, Valencia A, van de Water B, van der Lei J, van Mulligen E, Sanz F. The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. Pharmaceuticals (Basel) 2021; 14:ph14030237. [PMID: 33800393 PMCID: PMC7999019 DOI: 10.3390/ph14030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/25/2021] [Accepted: 02/27/2021] [Indexed: 12/19/2022] Open
Abstract
eTRANSAFE is a research project funded within the Innovative Medicines Initiative (IMI), which aims at developing integrated databases and computational tools (the eTRANSAFE ToxHub) that support the translational safety assessment of new drugs by using legacy data provided by the pharmaceutical companies that participate in the project. The project objectives include the development of databases containing preclinical and clinical data, computational systems for translational analysis including tools for data query, analysis and visualization, as well as computational models to explain and predict drug safety events.
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Affiliation(s)
- François Pognan
- Preclinical Safety/Translational Medicine, Novartis, 4057 Basel, Switzerland;
| | | | - Carlos Díaz
- Synapse Research Managers SL, 28006 Madrid, Spain;
| | | | - Frank Bringezu
- Chemical & Preclinical Safety, Merck Healthcare KGaA, 64293 Darmstadt, Germany;
| | | | - Giulia Callegaro
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 RA Leiden, The Netherlands; (G.C.); (B.v.d.W.)
| | | | - Emilio Centeno
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Javier Corvi
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
| | | | | | - José M. Fernández
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
| | - Laura I. Furlong
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
- MedBioinformatics Solutions SL, 08018 Barcelona, Spain
| | - Emre Guney
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Jan A. Kors
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Miguel Angel Mayer
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Manuel Pastor
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Janet Piñero
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Juan Manuel Ramírez-Anguita
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Francesco Ronzano
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Philip Rowell
- Lhasa Limited, Leeds LS11 5PS, UK; (K.B.); (W.C.D.); (P.R.)
| | - Josep Saüch-Pitarch
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.C.-G.); (J.C.); (J.M.F.); (A.V.)
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Bob van de Water
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 RA Leiden, The Netherlands; (G.C.); (B.v.d.W.)
| | - Johan van der Lei
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Erik van Mulligen
- Department of Medical Informatics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (J.A.K.); (J.v.d.L.); (E.v.M.)
| | - Ferran Sanz
- GRIB, Hospital del Mar Institute of Medical Research (IMIM), DCEXS, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (E.C.); (L.I.F.); (E.G.); (M.A.M.); (M.P.); (J.P.); (J.M.R.-A.); (F.R.); (J.S.-P.)
- Correspondence:
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Koedoot E, van Steijn E, Vermeer M, González-Prieto R, Vertegaal ACO, Martens JWM, Le Dévédec SE, van de Water B. Splicing factors control triple-negative breast cancer cell mitosis through SUN2 interaction and sororin intron retention. J Exp Clin Cancer Res 2021; 40:82. [PMID: 33648524 PMCID: PMC7919097 DOI: 10.1186/s13046-021-01863-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic opportunities. Recently, splicing factors have gained attention as potential targets for cancer treatment. Here we systematically evaluated the role of RNA splicing factors in TNBC cell proliferation. METHODS In this study, we performed an RNAi screen targeting 244 individual splicing factors to systematically evaluate their role in TNBC cell proliferation. For top candidates, mechanistic insight was gained using amongst others western blot, PCR, FACS, molecular imaging and cloning. Pulldown followed by mass spectrometry were used to determine protein-protein interactions and patient-derived RNA sequencing data was used relate splicing factor expression levels to proliferation markers. RESULTS We identified nine splicing factors, including SNRPD2, SNRPD3 and NHP2L1, of which depletion inhibited proliferation in two TNBC cell lines by deregulation of sister chromatid cohesion (SCC) via increased sororin intron 1 retention and down-regulation of SMC1, MAU2 and ESPL1. Protein-protein interaction analysis of SNRPD2, SNRPD3 and NHP2L1 identified that seven out of the nine identified splicing factors belong to the same spliceosome complex including novel component SUN2 that was also critical for efficient sororin splicing. Finally, sororin transcript levels are highly correlated to various proliferation markers in BC patients. CONCLUSION We systematically determined splicing factors that control proliferation of breast cancer cells through a mechanism that involves effective sororin splicing and thereby appropriate sister chromatid cohesion. Moreover, we identified SUN2 as an important new spliceosome complex interacting protein that is critical in this process. We anticipate that deregulating sororin levels through targeting of the relevant splicing factors might be a potential strategy to treat TNBC.
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Affiliation(s)
- Esmee Koedoot
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Eline van Steijn
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marjolein Vermeer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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Béquignon OJ, Pawar G, van de Water B, Cronin MT, van Westen GJ. Computational Approaches for Drug-Induced Liver Injury (DILI) Prediction: State of the Art and Challenges. Systems Medicine 2021. [DOI: 10.1016/b978-0-12-801238-3.11535-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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de Boer A, Krul L, Fehr M, Geurts L, Kramer N, Tabernero Urbieta M, van der Harst J, van de Water B, Venema K, Schütte K, Hepburn PA. Animal-free strategies in food safety & nutrition: What are we waiting for? Part I: Food safety. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gupta R, Schrooders Y, Hauser D, van Herwijnen M, Albrecht W, Ter Braak B, Brecklinghaus T, Castell JV, Elenschneider L, Escher S, Guye P, Hengstler JG, Ghallab A, Hansen T, Leist M, Maclennan R, Moritz W, Tolosa L, Tricot T, Verfaillie C, Walker P, van de Water B, Kleinjans J, Caiment F. Comparing in vitro human liver models to in vivo human liver using RNA-Seq. Arch Toxicol 2020; 95:573-589. [PMID: 33106934 PMCID: PMC7870774 DOI: 10.1007/s00204-020-02937-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023]
Abstract
The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Yannick Schrooders
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Duncan Hauser
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Wiebke Albrecht
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Tim Brecklinghaus
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Jose V Castell
- Instituto de Investigación Sanitaria La Fe, Experimental Hepatology Unit, Valencia, Spain
| | - Leroy Elenschneider
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Sylvia Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Patrick Guye
- InSphero AG, Wagistrasse 27, 8952, Schlieren, Switzerland
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Tanja Hansen
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated, Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Richard Maclennan
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | | | - Laia Tolosa
- Instituto de Investigación Sanitaria La Fe, Unidad Hepatología Experimental, Valencia, Spain
| | - Tine Tricot
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Paul Walker
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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Mav D, Phadke DP, Balik-Meisner MR, Merrick BA, Auerbach S, Niemeijer M, Huppelschoten S, Baze A, Parmentier C, Richert L, van de Water B, Shah RR, Paules RS. Utility of Extrapolating Human S1500+ Genes to the Whole Transcriptome: Tunicamycin Case Study. Bioinform Biol Insights 2020; 14:1177932220952742. [PMID: 33088175 PMCID: PMC7545517 DOI: 10.1177/1177932220952742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 08/04/2020] [Indexed: 01/07/2023] Open
Abstract
The TempO-Seq S1500+ platform(s), now available for human, mouse, rat, and zebrafish, measures a discrete number of genes that are representative of biological and pathway co-regulation across the entire genome in a given species. While measurement of these genes alone provides a direct assessment of gene expression activity, extrapolating expression values to the whole transcriptome (~26 000 genes in humans) can estimate measurements of non-measured genes of interest and increases the power of pathway analysis algorithms by using a larger background gene expression space. Here, we use data from primary hepatocytes of 54 donors that were treated with the endoplasmic reticulum (ER) stress inducer tunicamycin and then measured on the human S1500+ platform containing ~3000 representative genes. Measurements for the S1500+ genes were then used to extrapolate expression values for the remaining human transcriptome. As a case study of the improved downstream analysis achieved by extrapolation, the “measured only” and “whole transcriptome” (measured + extrapolated) gene sets were compared. Extrapolation increased the number of significant genes by 49%, bringing to the forefront many that are known to be associated with tunicamycin exposure. The extrapolation procedure also correctly identified established tunicamycin-related functional pathways reflected by coordinated changes in interrelated genes while maintaining the sample variability observed from the “measured only” genes. Extrapolation improved the gene- and pathway-level biological interpretations for a variety of downstream applications, including differential expression analysis, gene set enrichment pathway analysis, DAVID keyword analysis, Ingenuity Pathway Analysis, and NextBio correlated compound analysis. The extrapolated data highlight the role of metabolism/metabolic pathways, the ER, immune response, and the unfolded protein response, each of which are key activities associated with tunicamycin exposure that were unrepresented or underrepresented in one or more of the analyses of the original “measured only” dataset. Furthermore, the inclusion of the extrapolated genes raised “tunicamycin” from third to first upstream regulator in Ingenuity Pathway Analysis and from sixth to second most correlated compound in NextBio analysis. Therefore, our case study suggests an approach to extend and enhance data from the S1500+ platform for improved insight into biological mechanisms and functional outcomes of diseases, drugs, and other perturbations.
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Affiliation(s)
- Deepak Mav
- Sciome LLC, Research Triangle Park, NC, USA
| | | | | | - B Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Scott Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Marije Niemeijer
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Suzanna Huppelschoten
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | - Richard S Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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Kruidering M, van de Water B, de Heer E, Mulder GJ, Nagelkerke JF. The Use of Porcine Proximal Tubular Cells for Studying NephrotoxicityIn Vitro:The Role of Oxidative Stress in Cisplatin-induced Cell Death. Altern Lab Anim 2020. [DOI: 10.1177/026119299602400207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The effects of a widely used antitumour drug, cisplatin, on freshly isolated porcine proximal tubular cells (PPTC) in suspension were investigated. Incubation of the PPTC with 5-500μM cisplatin resulted in a decrease in mitochondrial membrane potential (MMP) and in cell death. In addition, the formation of reactive oxygen species (ROS) was observed within 20 minutes. Prevention of ROS formation with the antioxidants diphenyl- p-phenylene-diamine (DPPD) or desferrioxamine had no effect on the cisplatin-induced effects on MMP and cell death, implying that cisplatin-induced ROS formation is not a cause of cell death. In order to investigate whether the ROS formation was related to mitochondrial damage, we determined the effects of cisplatin on the enzymatic activities of NADP:ubiquinone reductase (Complex I) and succinate:ubiquinone reductase (Complex II) of the respiratory chain. Exposure of the PPTC to cisplatin resulted in a time-dependent and dose-dependent inhibition of the activities of both Complex I and Complex II. The inhibition of these activities and the depletion of ATP could not be prevented by the antioxidants, indicating that these effects are not a consequence of ROS formation. We propose that damage to the mitochondria could be a key event in cisplatin-induced cell death.
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Affiliation(s)
- Marieke Kruidering
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, P.O. Box 9503
| | - Bob van de Water
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, P.O. Box 9503
| | - Emile de Heer
- Department of Pathology, P.O. Box 9603, University of Leiden, 2300 RC Leiden, The Netherlands
| | - Gerard J. Mulder
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, P.O. Box 9503
| | - J. Fred Nagelkerke
- Division of Toxicology, Leiden/Amsterdam Center for Drug Research, P.O. Box 9503
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van der Stel W, Carta G, Eakins J, Darici S, Delp J, Forsby A, Bennekou SH, Gardner I, Leist M, Danen EHJ, Walker P, van de Water B, Jennings P. Correction to: Multiparametric assessment of mitochondrial respiratory inhibition in HepG2 and RPTEC/TERT1 cells using a panel of mitochondrial targeting agrochemicals. Arch Toxicol 2020; 94:2731-2732. [PMID: 32720191 DOI: 10.1007/s00204-020-02849-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the original publication of the article.
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Affiliation(s)
- Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Giada Carta
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan, 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Julie Eakins
- Cyprotex Discovery Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Salihanur Darici
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | | | - Anna Forsby
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | | | | | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Paul Walker
- Cyprotex Discovery Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan, 1108, 1081 HZ, Amsterdam, The Netherlands.
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van der Stel W, Carta G, Eakins J, Darici S, Delp J, Forsby A, Bennekou SH, Gardner I, Leist M, Danen EHJ, Walker P, van de Water B, Jennings P. Multiparametric assessment of mitochondrial respiratory inhibition in HepG2 and RPTEC/TERT1 cells using a panel of mitochondrial targeting agrochemicals. Arch Toxicol 2020; 94:2707-2729. [PMID: 32607615 PMCID: PMC7395062 DOI: 10.1007/s00204-020-02792-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/20/2020] [Indexed: 12/21/2022]
Abstract
Evidence is mounting for the central role of mitochondrial dysfunction in several pathologies including metabolic diseases, accelerated ageing, neurodegenerative diseases and in certain xenobiotic-induced organ toxicity. Assessing mitochondrial perturbations is not trivial and the outcomes of such investigations are dependent on the cell types used and assays employed. Here we systematically investigated the effect of electron transport chain (ETC) inhibitors on multiple mitochondrial-related parameters in two human cell types, HepG2 and RPTEC/TERT1. Cells were exposed to a broad range of concentrations of 20 ETC-inhibiting agrochemicals and capsaicin, consisting of inhibitors of NADH dehydrogenase (Complex I, CI), succinate dehydrogenase (Complex II, CII) and cytochrome bc1 complex (Complex III, CIII). A battery of tests was utilised, including viability assays, lactate production, mitochondrial membrane potential (MMP) and the Seahorse bioanalyser, which simultaneously measures extracellular acidification rate [ECAR] and oxygen consumption rate [OCR]. CI inhibitors caused a potent decrease in OCR, decreased mitochondrial membrane potential, increased ECAR and increased lactate production in both cell types. Twenty-fourhour exposure to CI inhibitors decreased viability of RPTEC/TERT1 cells and 3D spheroid-cultured HepG2 cells in the presence of glucose. CI inhibitors decreased 2D HepG2 viability only in the absence of glucose. CII inhibitors had no notable effects in intact cells up to 10 µM. CIII inhibitors had similar effects to the CI inhibitors. Antimycin A was the most potent CIII inhibitor, with activity in the nanomolar range. The proposed CIII inhibitor cyazofamid demonstrated a mitochondrial uncoupling signal in both cell types. The study presents a comprehensive example of a mitochondrial assessment workflow and establishes measurable key events of ETC inhibition.
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Affiliation(s)
- Wanda van der Stel
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Giada Carta
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De
Boelelaan, 1108, 1081 HZ Amsterdam, The Netherlands
| | - Julie Eakins
- Cyprotex Discovery Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Salihanur Darici
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Anna Forsby
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | | | | | - Erik H. J. Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Paul Walker
- Cyprotex Discovery Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De
Boelelaan, 1108, 1081 HZ Amsterdam, The Netherlands
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43
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Sampadi B, Pines A, Munk S, Mišovic B, de Groot AJ, van de Water B, Olsen JV, Mullenders LHF, Vrieling H. Quantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action. Arch Toxicol 2020; 94:1655-1671. [PMID: 32189037 PMCID: PMC7261734 DOI: 10.1007/s00204-020-02712-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/09/2020] [Indexed: 12/02/2022]
Abstract
Damage to cellular macromolecules and organelles by chemical exposure evokes activation of various stress response pathways. To what extent different chemical stressors activate common and stressor-specific pathways is largely unknown. Here, we used quantitative phosphoproteomics to compare the signaling events induced by four stressors with different modes of action: the DNA damaging agent: cisplatin (CDDP), the topoisomerase II inhibitor: etoposide (ETO), the pro-oxidant: diethyl maleate (DEM) and the immunosuppressant: cyclosporine A (CsA) administered at an equitoxic dose to mouse embryonic stem cells. We observed major differences between the stressors in the number and identity of responsive phosphosites and the amplitude of phosphorylation. Kinase motif and pathway analyses indicated that the DNA damage response (DDR) activation by CDDP occurs predominantly through the replication-stress-related Atr kinase, whereas ETO triggers the DDR through Atr as well as the DNA double-strand-break-associated Atm kinase. CsA shares with ETO activation of CK2 kinase. Congruent with their known modes of action, CsA-mediated signaling is related to down-regulation of pathways that control hematopoietic differentiation and immunity, whereas oxidative stress is the most prominent initiator of DEM-modulated stress signaling. This study shows that even at equitoxic doses, different stressors induce distinctive and complex phosphorylation signaling cascades.
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Affiliation(s)
- Bharath Sampadi
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Alex Pines
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Stephanie Munk
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Branislav Mišovic
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Anton J de Groot
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
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44
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Giustarini G, Huppelschoten S, Barra M, Oppelt A, Wagenaar L, Weaver RJ, Bol-Schoenmakers M, Smit JJ, van de Water B, Klingmüller U, Pieters RHH. The hepatotoxic fluoroquinolone trovafloxacin disturbs TNF- and LPS-induced p65 nuclear translocation in vivo and in vitro. Toxicol Appl Pharmacol 2020; 391:114915. [PMID: 32035082 DOI: 10.1016/j.taap.2020.114915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 01/10/2020] [Accepted: 02/05/2020] [Indexed: 01/26/2023]
Abstract
Idiosyncratic drug-induced liver injury (IDILI) is a severe disease that cannot be detected during drug development. It has been shown that hepatotoxicity of some compounds associated with IDILI becomes apparent when these are combined in vivo and in vitro with LPS or TNF. Among these compounds trovafloxacin (TVX) induced apoptosis in the liver and increased pro-inflammatory cytokines in mice exposed to LPS/TNF. The hepatocyte survival and the cytokine release after TNF/LPS stimulation relies on a pulsatile activation of NF-κB. We set out to evaluate the dynamic activation of NF-κB in response to TVX + TNF or LPS models, both in mouse and human cells. Remarkably, TVX prolonged the first translocation of NF-κB induced by TNF both in vivo and in vitro. The prolonged p65 translocation caused by TVX was associated with an increased phosphorylation of IKK and MAPKs and accumulation of inhibitors of NF-κB such as IκBα and A20 in HepG2. Coherently, TVX suppressed further TNF-induced NF-κB translocations in HepG2 leading to decreased transcription of ICAM-1 and inhibitors of apoptosis. TVX prolonged LPS-induced NF-κB translocation in RAW264.7 macrophages increasing the secretion of TNF. In summary, this study presents new, relevant insights into the mechanism of TVX-induced liver injury underlining the resemblance between mouse and human models. In this study we convincingly show that regularly used toxicity models provide a coherent view of relevant pathways for IDILI. We propose that assessment of the kinetics of activation of NF-κB and MAPKs is an appropriate tool for the identification of hepatotoxic compounds during drug development.
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Affiliation(s)
- Giulio Giustarini
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Suzanna Huppelschoten
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Marco Barra
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands; University of Pisa, Department of Pharmacy, Italy
| | - Angela Oppelt
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Wagenaar
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Richard J Weaver
- Biopharmacy, Institut de Recherches Internationales Servier (I.R.I.S.), Suresnes 92284, France
| | - Marianne Bol-Schoenmakers
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Joost J Smit
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raymond H H Pieters
- Immunotoxicology, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
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45
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Yang H, Niemeijer M, van de Water B, Beltman JB. ATF6 Is a Critical Determinant of CHOP Dynamics during the Unfolded Protein Response. iScience 2020; 23:100860. [PMID: 32058971 PMCID: PMC7005498 DOI: 10.1016/j.isci.2020.100860] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/09/2019] [Accepted: 01/16/2020] [Indexed: 11/12/2022] Open
Abstract
The unfolded protein response (UPR) pathway senses unfolded proteins and regulates proteostasis and cell fate through activity of the transcription factors ATF4, ATF6, and XBP1 within a complex network of three main branches. Here, we investigated contributions of the three branches to UPR activity in single cells using microscopy-based quantification and dynamic modeling. BAC-GFP HepG2 reporter cell lines were exposed to tunicamycin, and activation of various UPR components was monitored for 24 h. We constructed a dynamic model to describe the adaptive UPR signaling network, for which incorporation of all three branches was required to match the data. Our calibrated model suggested that ATF6 shapes the early dynamics of pro-apoptotic CHOP. We confirmed this hypothesis by measurements beyond 24 h, by perturbing single siRNA knockdowns and by ATF6 measurements. Overall, our work indicates that ATF6 is an important regulator of CHOP, which in turn regulates cell fate decisions. A mathematical model of the unfolded protein response describes microscopy data Integration of modeling and experimental work offers insights into UPR regulation ATF6 shapes the early dynamics of the CHOP response
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Affiliation(s)
- Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
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46
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Drakvik E, Altenburger R, Aoki Y, Backhaus T, Bahadori T, Barouki R, Brack W, Cronin MTD, Demeneix B, Hougaard Bennekou S, van Klaveren J, Kneuer C, Kolossa-Gehring M, Lebret E, Posthuma L, Reiber L, Rider C, Rüegg J, Testa G, van der Burg B, van der Voet H, Warhurst AM, van de Water B, Yamazaki K, Öberg M, Bergman Å. Statement on advancing the assessment of chemical mixtures and their risks for human health and the environment. Environ Int 2020; 134:105267. [PMID: 31704565 PMCID: PMC6979318 DOI: 10.1016/j.envint.2019.105267] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/01/2019] [Accepted: 10/13/2019] [Indexed: 05/20/2023]
Abstract
The number of anthropogenic chemicals, manufactured, by-products, metabolites and abiotically formed transformation products, counts to hundreds of thousands, at present. Thus, humans and wildlife are exposed to complex mixtures, never one chemical at a time and rarely with only one dominating effect. Hence there is an urgent need to develop strategies on how exposure to multiple hazardous chemicals and the combination of their effects can be assessed. A workshop, "Advancing the Assessment of Chemical Mixtures and their Risks for Human Health and the Environment" was organized in May 2018 together with Joint Research Center in Ispra, EU-funded research projects and Commission Services and relevant EU agencies. This forum for researchers and policy-makers was created to discuss and identify gaps in risk assessment and governance of chemical mixtures as well as to discuss state of the art science and future research needs. Based on the presentations and discussions at this workshop we want to bring forward the following Key Messages.
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Affiliation(s)
- Elina Drakvik
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, SE-171 77 Stockholm, Sweden; Stockholm University, ACES, SE-106 91 Stockholm, Sweden.
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Yasunobu Aoki
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Thomas Backhaus
- University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, SE-405 30 Gothenburg, Sweden
| | - Tina Bahadori
- US Environmental Protection Agency, 1200 Pennsylvania Ave, NW, MC 8201R, Washington, DC 20460, USA
| | - Robert Barouki
- Université de Paris, Inserm Unit 1124, 45 rue des Saints Pères, 75006 Paris, France
| | - Werner Brack
- Helmholtz Centre for Environmental Research UFZ, Permoserstr. 15, 04318 Leipzig, Germany; RWTH Aachen University Institute for Environmental Research, ABBt-aachen Biology, Worringerweg 1, 52074 Aachen, Germany
| | - Mark T D Cronin
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Byrom Street, Liverpool L3 3AF, UK
| | - Barbara Demeneix
- Muséum National d'Histoire Naturelle (MNHN) UMR 7221 (CNRS/MNHN), 7 rue Cuvier, 75005 Paris, France
| | | | - Jacob van Klaveren
- National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, the Netherlands
| | - Carsten Kneuer
- German Federal Institute for Risk Assessment, Pesticide Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | | | - Erik Lebret
- National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, the Netherlands; Institute of Risk Assessment Sciences - IRAS, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Leo Posthuma
- National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, the Netherlands; Radboud University, Department of Environmental Science, Institute for Water and Wetland Research, Nijmegen, the Netherlands
| | - Lena Reiber
- German Environment Agency (UBA), Corrensplatz 1, 14195 Berlin, Germany
| | - Cynthia Rider
- National Toxicology Program, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, PO Box 12233, MD:K2-12, Research Triangle Park, NC 27709, USA
| | - Joëlle Rüegg
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, SE-171 77 Stockholm, Sweden; Uppsala University, Department of Organismal Biology, Norbyvägen 18A, SE-752 36 Uppsala, Sweden
| | - Giuseppe Testa
- University of Milan, Department of Oncology, Via S. Sofia, 9/1, 20122 Milan, Italy; IEO European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Bart van der Burg
- BioDetection Systems, Science Park 406, 1098XH Amsterdam, the Netherlands
| | - Hilko van der Voet
- Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | | | - Bob van de Water
- Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Kunihiko Yamazaki
- Ministry of the Environment, Japan, 1-2-2 Kasumigaseki, Chiyoda-ku, Tokyo 100-8975, Japan
| | - Mattias Öberg
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, SE-171 77 Stockholm, Sweden
| | - Åke Bergman
- Stockholm University, ACES, SE-106 91 Stockholm, Sweden; Örebro University, Department of Science and Technology, SE-701 82 Örebro, Sweden; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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47
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Koenders SA, Wijaya LS, Erkelens MN, Bakker AT, van der Noord VE, van Rooden EJ, Burggraaff L, Putter PC, Botter E, Wals K, van den Elst H, den Dulk H, Florea BI, van de Water B, van Westen GJP, Mebius RE, Overkleeft HS, Le Dévédec SE, van der Stelt M. Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells. ACS Cent Sci 2019; 5:1965-1974. [PMID: 31893226 PMCID: PMC6936097 DOI: 10.1021/acscentsci.9b01022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 05/13/2023]
Abstract
Retinaldehyde dehydrogenases belong to a superfamily of enzymes that regulate cell differentiation and are responsible for detoxification of anticancer drugs. Chemical tools and methods are of great utility to visualize and quantify aldehyde dehydrogenase (ALDH) activity in health and disease. Here, we present the discovery of a first-in-class chemical probe based on retinal, the endogenous substrate of retinal ALDHs. We unveil the utility of this probe in quantitating ALDH isozyme activity in a panel of cancer cells via both fluorescence and chemical proteomic approaches. We demonstrate that our probe is superior to the widely used ALDEFLUOR assay to explain the ability of breast cancer (stem) cells to produce all-trans retinoic acid. Furthermore, our probe revealed the cellular selectivity profile of an advanced ALDH1A1 inhibitor, thereby prompting us to investigate the nature of its cytotoxicity. Our results showcase the application of substrate-based probes in interrogating pathologically relevant enzyme activities. They also highlight the general power of chemical proteomics in driving the discovery of new biological insights and its utility to guide drug discovery efforts.
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Affiliation(s)
- Sebastiaan
T. A. Koenders
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
| | - Lukas S. Wijaya
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Martje N. Erkelens
- Department
of Molecular Cell Biology and Immunology, Amsterdam University Medical Centra, Amsterdam 1081 HV, The Netherlands
| | - Alexander T. Bakker
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Vera E. van der Noord
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Eva J. van Rooden
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Lindsey Burggraaff
- Computational
Drug Discovery, Division of Drug Discovery and Safety, Leiden Academic
Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Pasquale C. Putter
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Else Botter
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Kim Wals
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
| | - Hans van den Elst
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Hans den Dulk
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Bob van de Water
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Gerard J. P. van Westen
- Computational
Drug Discovery, Division of Drug Discovery and Safety, Leiden Academic
Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Reina E. Mebius
- Department
of Molecular Cell Biology and Immunology, Amsterdam University Medical Centra, Amsterdam 1081 HV, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
| | - Sylvia E. Le Dévédec
- Cancer
Therapeutics and Drug Safety, Division of Drug Discovery and Safety,
Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300 RA, The Netherlands
| | - Mario van der Stelt
- Department
of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden 2300 RA, The Netherlands
- Oncode Institute, Utrecht 3521 AL, The Netherlands
- E-mail:
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48
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Liu S, González-Prieto R, Zhang M, Geurink PP, Kooij R, Iyengar PV, van Dinther M, Bos E, Zhang X, Le Dévédec SE, van de Water B, Koning RI, Zhu HJ, Mesker WE, Vertegaal ACO, Ovaa H, Zhang L, Martens JWM, Ten Dijke P. Deubiquitinase Activity Profiling Identifies UCHL1 as a Candidate Oncoprotein That Promotes TGFβ-Induced Breast Cancer Metastasis. Clin Cancer Res 2019; 26:1460-1473. [PMID: 31857432 DOI: 10.1158/1078-0432.ccr-19-1373] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Therapies directed to specific molecular targets are still unmet for patients with triple-negative breast cancer (TNBC). Deubiquitinases (DUB) are emerging drug targets. The identification of highly active DUBs in TNBC may lead to novel therapies. EXPERIMENTAL DESIGN Using DUB activity probes, we profiled global DUB activities in 52 breast cancer cell lines and 52 patients' tumor tissues. To validate our findings in vivo, we employed both zebrafish and murine breast cancer xenograft models. Cellular and molecular mechanisms were elucidated using in vivo and in vitro biochemical methods. A specific inhibitor was synthesized, and its biochemical and biological functions were assessed in a range of assays. Finally, we used patient sera samples to investigate clinical correlations. RESULTS Two DUB activity profiling approaches identified UCHL1 as being highly active in TNBC cell lines and aggressive tumors. Functionally, UCHL1 promoted metastasis in zebrafish and murine breast cancer xenograft models. Mechanistically, UCHL1 facilitates TGFβ signaling-induced metastasis by protecting TGFβ type I receptor and SMAD2 from ubiquitination. We found that these responses are potently suppressed by the specific UCHL1 inhibitor, 6RK73. Furthermore, UCHL1 levels were significantly increased in sera of patients with TNBC, and highly enriched in sera exosomes as well as TNBC cell-conditioned media. UCHL1-enriched exosomes stimulated breast cancer migration and extravasation, suggesting that UCHL1 may act in a paracrine manner to promote tumor progression. CONCLUSIONS Our DUB activity profiling identified UCHL1 as a candidate oncoprotein that promotes TGFβ-induced breast cancer metastasis and may provide a potential target for TNBC treatment.
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Affiliation(s)
- Sijia Liu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mengdi Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Raymond Kooij
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Prasanna Vasudevan Iyengar
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten van Dinther
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik Bos
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Xiaobing Zhang
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, the Netherlands
| | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hong-Jian Zhu
- Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - Wilma E Mesker
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | | | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands. .,Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
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49
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de Jong Y, Bennani F, van Oosterwijk JG, Alberti G, Baranski Z, Wijers-Koster P, Venneker S, Briaire-de Bruijn IH, van de Akker BE, Baelde H, Cleton-Jansen AM, van de Water B, Danen EH, Bovée JV. A screening-based approach identifies cell cycle regulators AURKA, CHK1 and PLK1 as targetable regulators of chondrosarcoma cell survival. J Bone Oncol 2019; 19:100268. [PMID: 31832331 PMCID: PMC6889735 DOI: 10.1016/j.jbo.2019.100268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Chondrosarcomas are malignant cartilage tumors that are relatively resistant towards conventional therapeutic approaches. Kinase inhibitors have been investigated and shown successful for several different cancer types. In this study we aimed at identifying kinase inhibitors that inhibit the survival of chondrosarcoma cells and thereby serve as new potential therapeutic strategies to treat chondrosarcoma patients. An siRNA screen targeting 779 different kinases was conducted in JJ012 chondrosarcoma cells in parallel with a compound screen consisting of 273 kinase inhibitors in JJ012, SW1353 and CH2879 chondrosarcoma cell lines. AURKA, CHK1 and PLK1 were identified as most promising targets and validated further in a more comprehensive panel of chondrosarcoma cell lines. Dose response curves were performed using tyrosine kinase inhibitors: MK-5108 (AURKA), LY2603618 (CHK1) and Volasertib (PLK1) using viability assays and cell cycle analysis. Apoptosis was measured at 24 h after treatment using a caspase 3/7 assay. Finally, chondrosarcoma patient samples (N = =34) were used to examine the correlation between AURKA, CHK1 and PLK1 RNA expression and documented patient survival. Dose dependent decreases in viability were observed in chondrosarcoma cell lines after treatment with MK-5108, LY2603618 and volasertib, with cell lines showing highest sensitivity to PLK1 inhibition. In addition increased sensitivity to conventional chemotherapy was observed after CHK1 inhibition in a subset of the cell lines. Interestingly, whereas AURKA and CHK1 were both expressed in chondrosarcoma patient samples, PLK1 expression was found to be low compared to normal cartilage. Analysis of patient samples revealed that high CHK1 RNA expression correlated with a worse overall survival. AURKA, CHK1 and PLK1 are identified as important survival genes in chondrosarcoma cell lines. Although further research is needed to validate these findings, inhibiting CHK1 seems to be the most promising potential therapeutic target for patients with chondrosarcoma.
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Affiliation(s)
- Yvonne de Jong
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Fairuz Bennani
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Jolieke G. van Oosterwijk
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Gaia Alberti
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Zuzanna Baranski
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Pauline Wijers-Koster
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Sanne Venneker
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Inge H. Briaire-de Bruijn
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Brendy E. van de Akker
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Hans Baelde
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Anne-Marie Cleton-Jansen
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Erik H.J. Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Judith V.M.G. Bovée
- Department of Pathology, Leiden University Medical Centre, P.O. Box 9600, L1-Q, 2300 RC Leiden, the Netherlands
- Corresponding author.
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He J, Wink S, de Bont H, Le Dévédec S, Zhang Y, van de Water B. FRET biosensor-based kinase inhibitor screen for ERK and AKT activity reveals differential kinase dependencies for proliferation in TNBC cells. Biochem Pharmacol 2019; 169:113640. [DOI: 10.1016/j.bcp.2019.113640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
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