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von Coburg E, Wedler M, Muino JM, Wolff C, Körber N, Dunst S, Liu S. Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles. Nat Commun 2025; 16:3857. [PMID: 40274798 PMCID: PMC12022024 DOI: 10.1038/s41467-025-58765-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 04/02/2025] [Indexed: 04/26/2025] Open
Abstract
Phenotypic changes in the morphology and internal organization of cells can indicate perturbations in cell functions. Therefore, imaging-based high-throughput phenotypic profiling (HTPP) applications such as Cell Painting (CP) play an important role in basic and translational research, drug discovery, and regulatory toxicology. Here we present the Cell Painting PLUS (CPP) assay, an efficient, robust and broadly applicable approach that further expands the versatility of available HTPP methods and offers additional options for addressing mode-of-action specific research questions. An iterative staining-elution cycle allows multiplexing of at least seven fluorescent dyes that label nine different subcellular compartments and organelles including the plasma membrane, actin cytoskeleton, cytoplasmic RNA, nucleoli, lysosomes, nuclear DNA, endoplasmic reticulum, mitochondria, and Golgi apparatus. In this way, CPP significantly expands the flexibility, customizability, and multiplexing capacity of the original CP method and, importantly, also improves the organelle-specificity and diversity of the phenotypic profiles due to the separate imaging and analysis of single dyes in individual channels.
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Affiliation(s)
- Elena von Coburg
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Department of Food Chemistry, University of Potsdam, Potsdam, Germany
| | - Marlene Wedler
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Jose M Muino
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Institute of Clinical Pharmacology and Toxicology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christopher Wolff
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Nils Körber
- Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Berlin, Germany
| | - Sebastian Dunst
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany.
| | - Shu Liu
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany.
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2
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Piergiovanni M, Mennecozzi M, Barale-Thomas E, Danovi D, Dunst S, Egan D, Fassi A, Hartley M, Kainz P, Koch K, Le Dévédec SE, Mangas I, Miranda E, Nyffeler J, Pesenti E, Ricci F, Schmied C, Schreiner A, Stokar-Regenscheit N, Swedlow JR, Uhlmann V, Wieland FC, Wilson A, Whelan M. Bridging imaging-based in vitro methods from biomedical research to regulatory toxicology. Arch Toxicol 2025; 99:1271-1285. [PMID: 39945818 PMCID: PMC11968550 DOI: 10.1007/s00204-024-03922-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 11/26/2024] [Indexed: 04/04/2025]
Abstract
Imaging technologies are being increasingly used in biomedical research and experimental toxicology to gather morphological and functional information from cellular models. There is a concrete opportunity of incorporating imaging-based in vitro methods in international guidelines to respond to regulatory requirements with human relevant data. To translate these methods from R&D to international regulatory acceptance, the community needs to implement test methods under quality management systems, assess inter-laboratory transferability, and demonstrate data reliability and robustness. This article summarises current challenges associated with image acquisition, image analysis, including artificial intelligence, and data management of imaging-based methods, with examples from the developmental neurotoxicity in vitro battery and phenotypic profiling assays. The article includes considerations on specific needs and potential solutions to design and implement future validation and transferability studies.
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Affiliation(s)
| | | | - Erio Barale-Thomas
- Preclinical Sciences and Translational Safety, Janssen Pharmaceuticals, Beerse, Belgium
| | - Davide Danovi
- Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Sebastian Dunst
- German Centre for the Protection of Laboratory Animals (Bf3R), Department Experimental Toxicology and ZEBET, German Federal Institute for Risk Assessment, Berlin, Germany
| | - David Egan
- Core Life Analytics BV, 57 Kabelweg, 1014 BA, Amsterdam, The Netherlands
| | - Aurora Fassi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | | | - Katharina Koch
- IUF - Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
- DNTOX GmbH, Duesseldorf, Germany
| | - Sylvia E Le Dévédec
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333, Leiden, Netherlands
| | - Iris Mangas
- European Food Safety Authority (EFSA), Parma, Italy
| | | | - Jo Nyffeler
- Department of Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Enrico Pesenti
- Crown Bioscience Inc, 16550 West Bernardo Drive, Building 5, Suite 525, San Diego, CA, 92127, USA
| | | | - Christopher Schmied
- EU-OPENSCREEN ERIC, Campus Berlin-Buch, Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | | | - Nadine Stokar-Regenscheit
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Jason R Swedlow
- Divisions of Computational Biology and Molecular, Cell and Developmental Biology, School of Life Sciences, National Phenotypic Screening Centre, University of Dundee, Dundee, UK
| | | | - Fredrik C Wieland
- Life Science Business Europe, Yokogawa Deutschland GmbH, Ratingen, Germany
| | - Amy Wilson
- Safety Sciences, Clinical Pharmacology and Safety Sciences, AstraZeneca, Cambridge, UK
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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von Coburg E, Dunst S. The adverse outcome pathway for breast cancer: a knowledge management framework bridging biomedicine and toxicology. Discov Oncol 2023; 14:223. [PMID: 38051394 DOI: 10.1007/s12672-023-00840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/26/2023] [Indexed: 12/07/2023] Open
Abstract
Breast cancer is the most common cancer worldwide, with an estimated 2.3 million new cases diagnosed every year. Effective measures for cancer prevention and cancer therapy require a detailed understanding of the individual key disease mechanisms involved and their interactions at the molecular, cellular, tissue, organ, and organism level. In that regard, the rapid progress of biomedical and toxicological research in recent years now allows the pursuit of new approaches based on non-animal methods that provide greater mechanistic insight than traditional animal models and therefore facilitate the development of Adverse Outcome Pathways (AOPs) for human diseases. We performed a systematic review of the current state of published knowledge with regard to breast cancer to identify relevant key mechanisms for inclusion into breast cancer AOPs, i.e. decreased cell stiffness and decreased cell adhesion, and to concurrently map non-animal methods addressing these key events. We conclude that the broader sharing of expertise and methods between biomedical research and toxicology enabled by the AOP knowledge management framework can help to coordinate global research efforts and accelerate the transition to advanced non-animal methods, which, when combined into powerful method batteries, closely mimic human physiology and disease states without the need for animal testing.
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Affiliation(s)
- Elena von Coburg
- German Centre for the Protection of Laboratory Animals (Bf3R), Department Experimental Toxicology and ZEBET, German Federal Institute for Risk Assessment, Berlin, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Sebastian Dunst
- German Centre for the Protection of Laboratory Animals (Bf3R), Department Experimental Toxicology and ZEBET, German Federal Institute for Risk Assessment, Berlin, Germany.
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Audebert M, Assmann AS, Azqueta A, Babica P, Benfenati E, Bortoli S, Bouwman P, Braeuning A, Burgdorf T, Coumoul X, Debizet K, Dusinska M, Ertych N, Fahrer J, Fetz V, Le Hégarat L, López de Cerain A, Heusinkveld HJ, Hogeveen K, Jacobs MN, Luijten M, Raitano G, Recoules C, Rundén-Pran E, Saleh M, Sovadinová I, Stampar M, Thibol L, Tomkiewicz C, Vettorazzi A, Van de Water B, El Yamani N, Zegura B, Oelgeschläger M. New approach methodologies to facilitate and improve the hazard assessment of non-genotoxic carcinogens-a PARC project. FRONTIERS IN TOXICOLOGY 2023; 5:1220998. [PMID: 37492623 PMCID: PMC10364052 DOI: 10.3389/ftox.2023.1220998] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
Carcinogenic chemicals, or their metabolites, can be classified as genotoxic or non-genotoxic carcinogens (NGTxCs). Genotoxic compounds induce DNA damage, which can be detected by an established in vitro and in vivo battery of genotoxicity assays. For NGTxCs, DNA is not the primary target, and the possible modes of action (MoA) of NGTxCs are much more diverse than those of genotoxic compounds, and there is no specific in vitro assay for detecting NGTxCs. Therefore, the evaluation of the carcinogenic potential is still dependent on long-term studies in rodents. This 2-year bioassay, mainly applied for testing agrochemicals and pharmaceuticals, is time-consuming, costly and requires very high numbers of animals. More importantly, its relevance for human risk assessment is questionable due to the limited predictivity for human cancer risk, especially with regard to NGTxCs. Thus, there is an urgent need for a transition to new approach methodologies (NAMs), integrating human-relevant in vitro assays and in silico tools that better exploit the current knowledge of the multiple processes involved in carcinogenesis into a modern safety assessment toolbox. Here, we describe an integrative project that aims to use a variety of novel approaches to detect the carcinogenic potential of NGTxCs based on different mechanisms and pathways involved in carcinogenesis. The aim of this project is to contribute suitable assays for the safety assessment toolbox for an efficient and improved, internationally recognized hazard assessment of NGTxCs, and ultimately to contribute to reliable mechanism-based next-generation risk assessment for chemical carcinogens.
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Affiliation(s)
- Marc Audebert
- INRAE: Toxalim, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Ann-Sophie Assmann
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, UNAV: University of Navarra, Pamplona, Spain
| | - Pavel Babica
- RECETOX: RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Emilio Benfenati
- IRFMN: Istituto di Ricerche Farmacologiche Mario Negri—IRCCS, Milan, Italy
| | - Sylvie Bortoli
- INSERM: INSERM UMR-S 1124 T3S—Université Paris Cité, Paris, France
| | - Peter Bouwman
- UL-LACDR: Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Albert Braeuning
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
| | - Tanja Burgdorf
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
| | - Xavier Coumoul
- INSERM: INSERM UMR-S 1124 T3S—Université Paris Cité, Paris, France
| | - Kloé Debizet
- INSERM: INSERM UMR-S 1124 T3S—Université Paris Cité, Paris, France
| | - Maria Dusinska
- Health Effects Laboratory, NILU: The Climate and Environmental Research Institute, Kjeller, Norway
| | - Norman Ertych
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jörg Fahrer
- Department of Chemistry, RPTU: Division of Food Chemistry and Toxicology, Kaiserslautern, Germany
| | - Verena Fetz
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ludovic Le Hégarat
- ANSES: French Agency for Food, Environmental and Occupational Health and Safety, Fougères Laboratory, Toxicology of Contaminants Unit, Fougères, France
| | - Adela López de Cerain
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, UNAV: University of Navarra, Pamplona, Spain
| | - Harm J. Heusinkveld
- RIVM: National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Kevin Hogeveen
- ANSES: French Agency for Food, Environmental and Occupational Health and Safety, Fougères Laboratory, Toxicology of Contaminants Unit, Fougères, France
| | - Miriam N. Jacobs
- Radiation, Chemical and Environmental Hazards, UKHSA: UK Health Security Agency, Chilton, Oxfordshire, United Kingdom
| | - Mirjam Luijten
- RIVM: National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Giuseppa Raitano
- IRFMN: Istituto di Ricerche Farmacologiche Mario Negri—IRCCS, Milan, Italy
| | - Cynthia Recoules
- INRAE: Toxalim, INRAE, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, Toulouse, France
| | - Elise Rundén-Pran
- Health Effects Laboratory, NILU: The Climate and Environmental Research Institute, Kjeller, Norway
| | - Mariam Saleh
- ANSES: French Agency for Food, Environmental and Occupational Health and Safety, Fougères Laboratory, Toxicology of Contaminants Unit, Fougères, France
| | - Iva Sovadinová
- RECETOX: RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martina Stampar
- Department of Genetic Toxicology and Cancer Biology, NIB: National Institute of Biology, Ljubljana, Slovenia
| | - Lea Thibol
- Department of Chemistry, RPTU: Division of Food Chemistry and Toxicology, Kaiserslautern, Germany
| | | | - Ariane Vettorazzi
- Department of Pharmacology and Toxicology, School of Pharmacy and Nutrition, UNAV: University of Navarra, Pamplona, Spain
| | - Bob Van de Water
- UL-LACDR: Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Naouale El Yamani
- Health Effects Laboratory, NILU: The Climate and Environmental Research Institute, Kjeller, Norway
| | - Bojana Zegura
- Department of Genetic Toxicology and Cancer Biology, NIB: National Institute of Biology, Ljubljana, Slovenia
| | - Michael Oelgeschläger
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R) and Department Food Safety, BfR: German Federal Institute for Risk Assessment, Berlin, Germany
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Jeong J, Kim D, Choi J. Application of ToxCast/Tox21 data for toxicity mechanism-based evaluation and prioritization of environmental chemicals: Perspective and limitations. Toxicol In Vitro 2022; 84:105451. [PMID: 35921976 DOI: 10.1016/j.tiv.2022.105451] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/28/2022] [Indexed: 01/28/2023]
Abstract
In response to the need to minimize the use of experimental animals, new approach methodologies (NAMs) using advanced technology have emerged in the 21st century. ToxCast/Tox21 aims to evaluate the adverse effects of chemicals quickly and efficiently using a high-throughput screening and to transform the paradigm of toxicity assessment into mechanism-based toxicity prediction. The ToxCast/Tox21 database, which contains extensive data from over 1400 assays with numerous biological targets and activity data for over 9000 chemicals, can be used for various purposes in the field of chemical prioritization and toxicity prediction. In this study, an overview of the database was explored to aid mechanism-based chemical prioritization and toxicity prediction. Implications for the utilization of the ToxCast/Tox21 database in chemical prioritization and toxicity prediction were derived. The research trends in ToxCast/Tox21 assay data were reviewed in the context of toxicity mechanism identification, chemical priority, environmental monitoring, assay development, and toxicity prediction. Finally, the potential applications and limitations of using ToxCast/Tox21 assay data in chemical risk assessment were discussed. The analysis of the toxicity mechanism-based assays of ToxCast/Tox21 will help in chemical prioritization and regulatory applications without the use of laboratory animals.
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Affiliation(s)
- Jaeseong Jeong
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Donghyeon Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul 02504, Republic of Korea.
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Luijten M, Sprong RC, Rorije E, van der Ven LTM. Prioritization of chemicals in food for risk assessment by integrating exposure estimates and new approach methodologies: A next generation risk assessment case study. FRONTIERS IN TOXICOLOGY 2022; 4:933197. [PMID: 36199824 PMCID: PMC9527283 DOI: 10.3389/ftox.2022.933197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/02/2022] [Indexed: 11/15/2022] Open
Abstract
Next generation risk assessment is defined as a knowledge-driven system that allows for cost-efficient assessment of human health risk related to chemical exposure, without animal experimentation. One of the key features of next generation risk assessment is to facilitate prioritization of chemical substances that need a more extensive toxicological evaluation, in order to address the need to assess an increasing number of substances. In this case study focusing on chemicals in food, we explored how exposure data combined with the Threshold of Toxicological Concern (TTC) concept could be used to prioritize chemicals, both for existing substances and new substances entering the market. Using a database of existing chemicals relevant for dietary exposure we calculated exposure estimates, followed by application of the TTC concept to identify substances of higher concern. Subsequently, a selected set of these priority substances was screened for toxicological potential using high-throughput screening (HTS) approaches. Remarkably, this approach resulted in alerts for a selection of substances that are already on the market and represent relevant exposure in consumers. Taken together, the case study provides proof-of-principle for the approach taken to identify substances of concern, and this approach can therefore be considered a supportive element to a next generation risk assessment strategy.
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Affiliation(s)
- Mirjam Luijten
- Centre for Health Protection, Bilthoven, Netherlands
- *Correspondence: Mirjam Luijten,
| | - R. Corinne Sprong
- Centre for Nutrition, Prevention and Health Services, Bilthoven, Netherlands
| | - Emiel Rorije
- Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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von Coburg E, Liu S, Dunst S. P12-14 Adaptation of the E-Morph Assay to serum-free cell culture conditions for CellPainting-based phenotypic screening of environmental estrogens. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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