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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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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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Niemeijer M. S-20-02 An all iPSC liver model for advanced risk assessment. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.155] [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: 10/14/2022]
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Shi S, Verstegen MMA, Roest HP, Ardisasmita AI, Cao W, Roos FJM, de Ruiter PE, Niemeijer M, Pan Q, IJzermans JNM, van der Laan LJW. Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids. Cell Mol Gastroenterol Hepatol 2021; 13:541-564. [PMID: 34700031 PMCID: PMC8688721 DOI: 10.1016/j.jcmgh.2021.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Liver and bile duct diseases often are associated with extensive cell death of cholangiocytes. Necroptosis represents a common mode of programmed cell death in cholangiopathy, however, detailed mechanistic knowledge is limited owing to the lack of appropriate in vitro models. To address this void, we investigated whether human intrahepatic cholangiocyte organoids (ICOs) can recapitulate cholangiopathy-associated necroptosis and whether this model can be used for drug screening. METHODS We evaluated the clinical relevance of necroptosis in end-stage liver diseases and liver transplantation by immunohistochemistry. Cholangiopathy-associated programmed cell death was evoked in ICOs derived from healthy donors or patients with primary sclerosing cholangitis or alcoholic liver diseases by the various stimuli. RESULTS The expression of key necroptosis mediators, receptor-interacting protein 3 and phosphorylated mixed lineage kinase domain-like, in cholangiocytes during end-stage liver diseases was confirmed. The phosphorylated mixed lineage kinase domain-like expression was etiology-dependent. Gene expression analysis confirmed that primary cholangiocytes are more prone to necroptosis compared with primary hepatocytes. Both apoptosis and necroptosis could be specifically evoked using tumor necrosis factor α and second mitochondrial-derived activator of caspases mimetic, with or without caspase inhibition in healthy and patient-derived ICOs. Necroptosis also was induced by ethanol metabolites or human bile in ICOs from donors and patients. The organoid cultures further uncovered interdonor variable and species-specific drug responses. Dabrafenib was identified as a potent necroptosis inhibitor and showed a protective effect against ethanol metabolite toxicity. CONCLUSIONS Human ICOs recapitulate cholangiopathy-associated necroptosis and represent a useful in vitro platform for the study of biliary cytotoxicity and preclinical drug evaluation.
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Affiliation(s)
- Shaojun Shi
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Henk P Roest
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Arif I Ardisasmita
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wanlu Cao
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Department of Oncology, Shanghai East Hospital, Tongji University, Shanghai, P. R. China
| | - Floris J M Roos
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Petra E de Ruiter
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marije Niemeijer
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
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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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Niemeijer M, Wiecek W, Huppelschoten S, Baze A, Parmentier C, Richert L, Bois F, Paules R, van de Water B. Transcriptomic profiling of the inter-individual variability of chemical-induced cellular stress response activation in primary human hepatocytes. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00312-x] [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: 11/28/2022]
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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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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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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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11
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Kunst RF, Niemeijer M, van der Laan LJW, Spee B, van de Graaf SFJ. From fatty hepatocytes to impaired bile flow: Matching model systems for liver biology and disease. Biochem Pharmacol 2020; 180:114173. [PMID: 32717228 DOI: 10.1016/j.bcp.2020.114173] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023]
Abstract
A large variety of model systems are used in hepatobiliary research. In this review, we aim to provide an overview of established and emerging models for specific research questions. We specifically discuss the value and limitations of these models for research on metabolic associated fatty liver disease (MAFLD), (previously named non-alcoholic fatty liver diseases/non-alcoholic steatohepatitis (NAFLD/NASH)) and cholestasis-related diseases such as primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). The entire range of models is discussed varying from immortalized cell lines, mature or pluripotent stem cell-based models including organoids/spheroids, to animal models and human ex vivo models such as normothermic machine perfusion of livers and living liver slices. Finally, the pros and cons of each model are discussed as well as the need in the scientific community for continuous innovation in model development to better mimic the human (patho)physiology.
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Affiliation(s)
- Roni F Kunst
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Marije Niemeijer
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands.
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12
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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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13
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Abstract
Exposure to oxidative radical species and cytokine-mediated inflammatory stress are established contributors to hepatocyte cell death during cholestasis. Cellular counter measures against those stressors are called adaptive stress response pathways. While in early stages of the disease adaptive stress pathways protect the hepatocytes, in later stages during prolonged stressed conditions they fail. The quantitative imaging-based assessment of cellular stress response pathways using the HepG2 BAC-GFP response reporter platform is a powerful strategy to evaluate the impact of chemical substances and gene knockdown on activation of adaptive stress response pathways, hence allowing systematic screening for positive or negative influences on cholestasis progression. This protocol allows the application of a highly versatile screening tool for a systematic evaluation of the effect of compounds having cholestasis liability and affected genes during cholestatic injury on cellular adaptive stress pathway activation. The approach involves high-throughput live-cell visualization of GFP-tagged key proteins of the oxidative stress response/Nrf2 pathway and inflammatory cytokine signaling. Quantitative image analysis of temporal responses of individual cells is followed by informatics analysis. The overall practical approaches are discussed in this chapter.
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Affiliation(s)
- Johannes P Schimming
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Marije Niemeijer
- 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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14
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Scarfe L, Brillant N, Kumar JD, Ali N, Alrumayh A, Amali M, Barbellion S, Jones V, Niemeijer M, Potdevin S, Roussignol G, Vaganov A, Barbaric I, Barrow M, Burton NC, Connell J, Dazzi F, Edsbagge J, French NS, Holder J, Hutchinson C, Jones DR, Kalber T, Lovatt C, Lythgoe MF, Patel S, Patrick PS, Piner J, Reinhardt J, Ricci E, Sidaway J, Stacey GN, Starkey Lewis PJ, Sullivan G, Taylor A, Wilm B, Poptani H, Murray P, Goldring CEP, Park BK. Preclinical imaging methods for assessing the safety and efficacy of regenerative medicine therapies. NPJ Regen Med 2017; 2:28. [PMID: 29302362 PMCID: PMC5677988 DOI: 10.1038/s41536-017-0029-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/30/2017] [Accepted: 07/24/2017] [Indexed: 02/08/2023] Open
Abstract
Regenerative medicine therapies hold enormous potential for a variety of currently incurable conditions with high unmet clinical need. Most progress in this field to date has been achieved with cell-based regenerative medicine therapies, with over a thousand clinical trials performed up to 2015. However, lack of adequate safety and efficacy data is currently limiting wider uptake of these therapies. To facilitate clinical translation, non-invasive in vivo imaging technologies that enable careful evaluation and characterisation of the administered cells and their effects on host tissues are critically required to evaluate their safety and efficacy in relevant preclinical models. This article reviews the most common imaging technologies available and how they can be applied to regenerative medicine research. We cover details of how each technology works, which cell labels are most appropriate for different applications, and the value of multi-modal imaging approaches to gain a comprehensive understanding of the responses to cell therapy in vivo.
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Affiliation(s)
- Lauren Scarfe
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.,Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Nathalie Brillant
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.,Medical Research Council Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - J Dinesh Kumar
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Noura Ali
- College of Health Science, University of Duhok, Duhok, Iraq
| | - Ahmed Alrumayh
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Mohammed Amali
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Stephane Barbellion
- Medical Research Council Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Vendula Jones
- GlaxoSmithKline, David Jack Centre for Research and Development, Ware, UK
| | - Marije Niemeijer
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Sophie Potdevin
- SANOFI Research and Development, Disposition, Safety and Animal Research, Alfortville, France
| | - Gautier Roussignol
- SANOFI Research and Development, Disposition, Safety and Animal Research, Alfortville, France
| | - Anatoly Vaganov
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Michael Barrow
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | | | - John Connell
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Francesco Dazzi
- Department of Haemato-Oncology, King's College London, London, UK
| | | | - Neil S French
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Julie Holder
- Roslin Cells, University of Cambridge, Cambridge, UK
| | - Claire Hutchinson
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.,Medical Research Council Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - David R Jones
- Medicines and Healthcare Products Regulatory Agency, London, UK
| | - Tammy Kalber
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Cerys Lovatt
- GlaxoSmithKline, David Jack Centre for Research and Development, Ware, UK
| | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Sara Patel
- ReNeuron Ltd, Pencoed Business Park, Pencoed, Bridgend, UK
| | - P Stephen Patrick
- Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Jacqueline Piner
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, UK
| | | | - Emanuelle Ricci
- Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | | | - Glyn N Stacey
- UK Stem Cell Bank, Division of Advanced Therapies, National Institute for Biological Standards Control, Medicines and Healthcare Products Regulatory Agency, London, UK
| | - Philip J Starkey Lewis
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Gareth Sullivan
- Department of Biochemistry, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Norwegian Center for Stem Cell Research, Blindern, Oslo, Norway.,Institute of Immunology, Oslo University Hospital-Rikshospitalet, Nydalen, Oslo, Norway.,Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Arthur Taylor
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.,Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Bettina Wilm
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.,Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Harish Poptani
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.,Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Patricia Murray
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.,Centre for Preclinical Imaging, University of Liverpool, Liverpool, UK
| | - Chris E P Goldring
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.,Medical Research Council Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.,Medical Research Council Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
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15
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Hiemstra S, Niemeijer M, Koedoot E, Wink S, Klip JE, Vlasveld M, de Zeeuw E, van Os B, White A, Water BVD. Comprehensive Landscape of Nrf2 and p53 Pathway Activation Dynamics by Oxidative Stress and DNA Damage. Chem Res Toxicol 2016; 30:923-933. [PMID: 27982581 DOI: 10.1021/acs.chemrestox.6b00322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A quantitative dynamics pathway map of the Nrf2-mediated oxidative stress response and p53-related DNA damage response pathways as well as the cross-talk between these pathways has not systematically been defined. To allow the dynamic single cell evaluation of these pathways, we have used BAC-GFP recombineering to tag for each pathway's three key components: for the oxidative stress response, Keap1-GFP, Nrf2-GFP, and Srxn1-GFP; for the DNA damage response, 53bp1-GFP, p53-GFP, and p21-GFP. The dynamic activation of these individual components was assessed using quantitative high throughput confocal microscopy after treatment with a broad concentration range of diethyl maleate (DEM; to induce oxidative stress) and etoposide (to induce DNA damage). DEM caused a rapid activation of Nrf2, which returned to baseline levels at low concentrations but remained sustained at high concentrations. Srxn1-GFP induction and Keap1-GFP translocation to autophagosomes followed later, with upper boundaries reached at high concentrations, close to the onset of cell death. Etoposide caused rapid accumulation of 53bp1-GFP in DNA damage foci, which was later followed by the concentration dependent nuclear accumulation of p53-GFP and subsequent induction of p21-GFP. While etoposide caused activation of Srxn1-GFP, a modest activation of DNA damage reporters was observed for DEM at high concentrations. Interestingly, Nrf2 knockdown caused an inhibition of the DNA damage response at high concentrations of etoposide, while Keap1 knockdown caused an enhancement of the DNA damage response already at low concentrations of etoposide. Knockdown of p53 did not affect the oxidative stress response. Altogether, the current stress response landscapes provide insight in the time course responses of and cross-talk between oxidative stress and DNA-damage and defines the tipping points where cell injury may switch from adaptation to injury.
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Affiliation(s)
- Steven Hiemstra
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marije Niemeijer
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Esmee Koedoot
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Janna E Klip
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Matthijs Vlasveld
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elisabeth de Zeeuw
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bram van Os
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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16
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Wink S, Hiemstra S, Huppelschoten S, Danen E, Niemeijer M, Hendriks G, Vrieling H, Herpers B, van de Water B. Quantitative high content imaging of cellular adaptive stress response pathways in toxicity for chemical safety assessment. Chem Res Toxicol 2014; 27:338-55. [PMID: 24450961 DOI: 10.1021/tx4004038] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past decade, major leaps forward have been made on the mechanistic understanding and identification of adaptive stress response landscapes underlying toxic insult using transcriptomics approaches. However, for predictive purposes of adverse outcome several major limitations in these approaches exist. First, the limited number of samples that can be analyzed reduces the in depth analysis of concentration-time course relationships for toxic stress responses. Second these transcriptomics analysis have been based on the whole cell population, thereby inevitably preventing single cell analysis. Third, transcriptomics is based on the transcript level, totally ignoring (post)translational regulation. We believe these limitations are circumvented with the application of high content analysis of relevant toxicant-induced adaptive stress signaling pathways using bacterial artificial chromosome (BAC) green fluorescent protein (GFP) reporter cell-based assays. The goal is to establish a platform that incorporates all adaptive stress pathways that are relevant for toxicity, with a focus on drug-induced liver injury. In addition, cellular stress responses typically follow cell perturbations at the subcellular organelle level. Therefore, we complement our reporter line panel with reporters for specific organelle morphometry and function. Here, we review the approaches of high content imaging of cellular adaptive stress responses to chemicals and the application in the mechanistic understanding and prediction of chemical toxicity at a systems toxicology level.
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Affiliation(s)
- Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University , The Netherlands
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17
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Abstract
The detection of the position of the normal anatomy in color fundus photographs is an important step in the automated analysis of retinal images. An automatic system for the detection of the position of the optic disc and the fovea is presented. The method integrates the use of local vessel geometry and image intensity features to find the correct positions in the image. A kNN regressor is used to accomplish the integration. Evaluation was performed on a set of 250 digital color fundus photographs and the detection performance for the optic disc and the fovea were 99.2% and 96.4% respectively.
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Affiliation(s)
- M Niemeijer
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, USA.
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