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Viant MR, Amstalden E, Athersuch T, Bouhifd M, Camuzeaux S, Crizer DM, Driemert P, Ebbels T, Ekman D, Flick B, Giri V, Gómez-Romero M, Haake V, Herold M, Kende A, Lai F, Leonards PEG, Lim PP, Lloyd GR, Mosley J, Namini C, Rice JR, Romano S, Sands C, Smith MJ, Sobanski T, Southam AD, Swindale L, van Ravenzwaay B, Walk T, Weber RJM, Zickgraf FM, Kamp H. Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice. Arch Toxicol 2024; 98:1111-1123. [PMID: 38368582 PMCID: PMC10944399 DOI: 10.1007/s00204-024-03680-y] [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: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
While grouping/read-across is widely used to fill data gaps, chemical registration dossiers are often rejected due to weak category justifications based on structural similarity only. Metabolomics provides a route to robust chemical categories via evidence of shared molecular effects across source and target substances. To gain international acceptance, this approach must demonstrate high reliability, and best-practice guidance is required. The MetAbolomics ring Trial for CHemical groupING (MATCHING), comprising six industrial, government and academic ring-trial partners, evaluated inter-laboratory reproducibility and worked towards best-practice. An independent team selected eight substances (WY-14643, 4-chloro-3-nitroaniline, 17α-methyl-testosterone, trenbolone, aniline, dichlorprop-p, 2-chloroaniline, fenofibrate); ring-trial partners were blinded to their identities and modes-of-action. Plasma samples were derived from 28-day rat tests (two doses per substance), aliquoted, and distributed to partners. Each partner applied their preferred liquid chromatography-mass spectrometry (LC-MS) metabolomics workflows to acquire, process, quality assess, statistically analyze and report their grouping results to the European Chemicals Agency, to ensure the blinding conditions of the ring trial. Five of six partners, whose metabolomics datasets passed quality control, correctly identified the grouping of eight test substances into three categories, for both male and female rats. Strikingly, this was achieved even though a range of metabolomics approaches were used. Through assessing intrastudy quality-control samples, the sixth partner observed high technical variation and was unable to group the substances. By comparing workflows, we conclude that some heterogeneity in metabolomics methods is not detrimental to consistent grouping, and that assessing data quality prior to grouping is essential. We recommend development of international guidance for quality-control acceptance criteria. This study demonstrates the reliability of metabolomics for chemical grouping and works towards best-practice.
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Affiliation(s)
- Mark R Viant
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - E Amstalden
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - T Athersuch
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - M Bouhifd
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - S Camuzeaux
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - D M Crizer
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - P Driemert
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - T Ebbels
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - D Ekman
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - B Flick
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- NUVISAN ICB GmbH, Toxicology, 13353, Berlin, Germany
| | - V Giri
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - M Gómez-Romero
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - V Haake
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - M Herold
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - A Kende
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - F Lai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - P E G Leonards
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - P P Lim
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - G R Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Namini
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - J R Rice
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - S Romano
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Sands
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - M J Smith
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - T Sobanski
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - A D Southam
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - L Swindale
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - B van Ravenzwaay
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- Environmental Sciences Consulting, 67122, Altrip, Germany
| | - T Walk
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - R J M Weber
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - F M Zickgraf
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - H Kamp
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
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Kamp H, Kocabas NA, Faulhammer F, Synhaeve N, Rushton E, Flick B, Giri V, Sperber S, Higgins LG, Penman MG, van Ravenzwaay B, Rooseboom M. Utility of in vivo metabolomics to support read-across for UVCB substances under REACH. Arch Toxicol 2024; 98:755-768. [PMID: 38265474 PMCID: PMC10861390 DOI: 10.1007/s00204-023-03638-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 01/25/2024]
Abstract
Structure-based grouping of chemicals for targeted testing and read-across is an efficient way to reduce resources and animal usage. For substances of unknown or variable composition, complex reaction products, or biological materials (UVCBs), structure-based grouping is virtually impossible. Biology-based approaches such as metabolomics could provide a solution. Here, 15 steam-cracked distillates, registered in the EU through the Lower Olefins Aromatics Reach Consortium (LOA), as well as six of the major substance constituents, were tested in a 14-day rat oral gavage study, in line with the fundamental elements of the OECD 407 guideline, in combination with plasma metabolomics. Beyond signs of clinical toxicity, reduced body weight (gain), and food consumption, pathological investigations demonstrated the liver, thyroid, kidneys (males only), and hematological system to be the target organs. These targets were confirmed by metabolome pattern recognition, with no additional targets being identified. While classical toxicological parameters did not allow for a clear distinction between the substances, univariate and multivariate statistical analysis of the respective metabolomes allowed for the identification of several subclusters of biologically most similar substances. These groups were partly associated with the dominant (> 50%) constituents of these UVCBs, i.e., indene and dicyclopentadiene. Despite minor differences in clustering results based on the two statistical analyses, a proposal can be made for the grouping of these UVCBs. Both analyses correctly clustered the chemically most similar compounds, increasing the confidence that this biological approach may provide a solution for the grouping of UVCBs.
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Affiliation(s)
- H Kamp
- BASF Metabolome Solutions GmbH, Berlin, Germany
| | | | | | | | - E Rushton
- LyondellBasell, Rotterdam, The Netherlands
| | - B Flick
- BASF SE, Ludwigshafen, Germany
- NUVISAN ICB GmbH, Toxicology, 13353, Berlin, Germany
| | - V Giri
- BASF SE, Ludwigshafen, Germany
| | | | - L G Higgins
- LOA C/O Penman Consulting Ltd, Brussels, Belgium
| | - M G Penman
- LOA C/O Penman Consulting Ltd, Brussels, Belgium
| | | | - M Rooseboom
- Shell Global Solution International B.V, The Hague, The Netherlands
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Ramirez-Hincapie S, Giri V, Keller J, Kamp H, Haake V, Richling E, van Ravenzwaay B. Influence of pregnancy and non-fasting conditions on the plasma metabolome in a rat prenatal toxicity study. Arch Toxicol 2021; 95:2941-2959. [PMID: 34327559 DOI: 10.1007/s00204-021-03105-0] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/17/2021] [Indexed: 11/25/2022]
Abstract
The current parameters for determining maternal toxicity (e.g. clinical signs, food consumption, body weight development) lack specificity and may underestimate the extent of effects of test compounds on the dams. Previous reports have highlighted the use of plasma metabolomics for an improved and mechanism-based identification of maternal toxicity. To establish metabolite profiles of healthy pregnancies and evaluate the influence of food consumption as a confounding factor, metabolite profiling of rat plasma was performed by gas- and liquid-chromatography-tandem mass spectrometry techniques. Metabolite changes in response to pregnancy, food consumption prior to blood sampling (non-fasting) as well as the interaction of both conditions were studied. In dams, both conditions, non-fasting and pregnancy, had a marked influence on the plasma metabolome and resulted in distinct individual patterns of changed metabolites. Non-fasting was characterized by increased plasma concentrations of amino acids and diet related compounds and lower levels of ketone bodies. The metabolic profile of pregnant rats was characterized by lower amino acids and glucose levels and higher concentrations of plasma fatty acids, triglycerides and hormones, capturing the normal biochemical changes undergone during pregnancy. The establishment of metabolic profiles of pregnant non-fasted rats serves as a baseline to create metabolic fingerprints for prenatal and maternal toxicity studies.
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Affiliation(s)
- S Ramirez-Hincapie
- Experimental Toxicology and Ecology, BASF SE, 67056, Ludwigshafen, Germany
| | - V Giri
- Experimental Toxicology and Ecology, BASF SE, 67056, Ludwigshafen, Germany
| | - J Keller
- Experimental Toxicology and Ecology, BASF SE, 67056, Ludwigshafen, Germany
| | - H Kamp
- Experimental Toxicology and Ecology, BASF SE, 67056, Ludwigshafen, Germany
| | - V Haake
- BASF Metabolome Solution GmbH, Berlin, Germany
| | - E Richling
- Food Chemistry and Toxicology, Department of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - B van Ravenzwaay
- Experimental Toxicology and Ecology, BASF SE, 67056, Ludwigshafen, Germany.
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Bajaj J, Maliekal TT, Vivien E, Pattabiraman C, Srivastava S, Krishnamurthy H, Giri V, Subramanyam D, Krishna S. Notch signaling in CD66+ cells drives the progression of human cervical cancers. Cancer Res 2011; 71:4888-97. [PMID: 21646470 DOI: 10.1158/0008-5472.can-11-0543] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human epithelial tumor progression and metastasis involve cellular invasion, dissemination in the vasculature, and regrowth at metastatic sites. Notch signaling has been implicated in metastatic progression but its roles have yet to be fully understood. Here we report the important role of Notch signaling in maintaining cells expressing the carcinoembryonic antigen cell adhesion molecule CEACAM (CD66), a known mediator of metastasis. CD66 and Notch1 were studied in clinical specimens and explants of human cervical cancer, including specimens grown in a pathophysiologically relevant murine model. Gene expression profiling of CD66(+) cells from primary tumors showed enhanced features of Notch signaling, metastasis, and stemness. Significant differences were also seen in invasion, colony formation, and tumor forming efficiency between CD66(+) and CD66(-) cancer cells. Notably, CD66(+) cells showed a marked sensitivity to a Notch small molecule inhibitor. In support of studies in established cell lines, we documented the emergence of a tumorigenic CD66(+) cell subset within a metastatic lesion-derived cervical-cancer cell line. Similar to primary cancers, CD66 expression in the cell line was blocked by chemical and genetic inhibitors of ligand-dependent nuclear Notch signaling. Collectively, our work on the oncogenic properties of CD66(+) cells in epithelial cancers provides insights into the nature of tumor progression and offers a mechanistic rationale to inhibit the Notch signaling pathway as a generalized therapeutic strategy to treat metastatic cancers.
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MESH Headings
- Animals
- Antigens, CD/biosynthesis
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Adhesion Molecules/biosynthesis
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Disease Progression
- Female
- Flow Cytometry
- Gene Expression Profiling
- Humans
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Receptors, Notch/biosynthesis
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Signal Transduction
- Spheroids, Cellular
- Transplantation, Heterologous
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/pathology
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Affiliation(s)
- Jeevisha Bajaj
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus and Department of Radiotherapy, Kidwai Memorial Institute of Oncology, Bangalore, India
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