1
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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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2
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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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3
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Wilhelmi P, Haake V, Zickgraf FM, Giri V, Ternes P, Driemert P, Nöth J, Scholz S, Barenys M, Flick B, Birk B, Kamp H, Landsiedel R, Funk-Weyer D. Molecular signatures of angiogenesis inhibitors: a single-embryo untargeted metabolomics approach in zebrafish. Arch Toxicol 2024; 98:943-956. [PMID: 38285066 PMCID: PMC10861732 DOI: 10.1007/s00204-023-03655-5] [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: 10/20/2023] [Accepted: 11/29/2023] [Indexed: 01/30/2024]
Abstract
Angiogenesis is a key process in embryonic development, a disruption of this process can lead to severe developmental defects, such as limb malformations. The identification of molecular perturbations representative of antiangiogenesis in zebrafish embryo (ZFE) may guide the assessment of developmental toxicity from an endpoint- to a mechanism-based approach, thereby improving the extrapolation of findings to humans. Thus, the aim of the study was to discover molecular changes characteristic of antiangiogenesis and developmental toxicity. We exposed ZFEs to two antiangiogenic drugs (SU4312, sorafenib) and two developmental toxicants (methotrexate, rotenone) with putative antiangiogenic action. Molecular changes were measured by performing untargeted metabolomics in single embryos. The metabolome response was accompanied by the occurrence of morphological alterations. Two distinct metabolic effect patterns were observed. The first pattern comprised common effects of two specific angiogenesis inhibitors and the known teratogen methotrexate, strongly suggesting a shared mode of action of antiangiogenesis and developmental toxicity. The second pattern involved joint effects of methotrexate and rotenone, likely related to disturbances in energy metabolism. The metabolites of the first pattern, such as phosphatidylserines, pterines, retinol, or coenzyme Q precursors, represented potential links to antiangiogenesis and related developmental toxicity. The metabolic effect pattern can contribute to biomarker identification for a mechanism-based toxicological testing.
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Affiliation(s)
- Pia Wilhelmi
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany.
- University of Barcelona, Research Group in Toxicology-GRET, 08028, Barcelona, Spain.
| | - Volker Haake
- BASF Metabolome Solutions, 10589, Berlin, Germany
| | - Franziska M Zickgraf
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany.
| | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany
| | | | | | - Julia Nöth
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Stefan Scholz
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Marta Barenys
- University of Barcelona, Research Group in Toxicology-GRET, 08028, Barcelona, Spain
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Burkhard Flick
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany
- Preclinical Compound Profiling, Toxicology, NUVISAN ICB GmbH, 13353, Berlin, Germany
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany
| | | | - Robert Landsiedel
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany
- Institute of Pharmacy, Pharmacology and Toxicology, Free University of Berlin, 14195, Berlin, Germany
| | - Dorothee Funk-Weyer
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Strasse 38, 67056, Ludwigshafen Am Rhein, Germany
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4
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van Ravenzwaay B, Kocabas NA, Faulhammer F, Flick B, Giri V, Sperber S, Penman MG, Higgins LG, Kamp H, Rooseboom M. The short-term toxicity and metabolome of dicyclopentadiene. Toxicol Lett 2024; 393:57-68. [PMID: 38219808 DOI: 10.1016/j.toxlet.2024.01.005] [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: 10/13/2023] [Revised: 12/25/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Dicyclopentadiene (DCPD) was investigated in a 14-day oral rat toxicity study based on the OECD 407 guideline in combination with plasma metabolomics. Wistar rats received the compound daily via gavage at dose levels of 0, 50 and 150 mg/kg bw. The high dose induced transient clinical signs of toxicity and in males only reduced body weight gain. High dose liver changes were characterized by altered clinical chemistry parameters in both sexes and pathological changes in females. In high dose males an accumulation of alpha-2 u-globulin in the kidney was noted. Comparing the DCPD metabolome with previously established specific metabolome patterns in the MetaMap® Tox data base suggested that the high dose would result in liver enzyme induction leading to increased breakdown of thyroid hormones for males and females. An indication for liver toxicity in males was also noted. Metabolomics also suggested an effect on the functionality of the adrenals in high dose males, which together with published data, is suggestive of a stress related effect in this organ. The results of the present 14-day combined toxicity and metabolome investigations were qualitatively in line with literature data from subchronic oral studies in rats with DCPD. Importantly no other types of organ toxicity, or hormone dysregulation beyond the ones associated with liver enzyme induction and stress were indicated, again in line with results of published 90-day studies. It is therefore suggested that short term "smart" studies, combining classical toxicity with 'omics technologies, could be a 2 R (refine and reduce) new approach method allowing for the reduction of in vivo toxicity testing.
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Affiliation(s)
| | | | | | | | | | | | - Michael G Penman
- Lower Olefins and Aromatics Consortium Services Team, Penman Consulting bvba, Brussels, Belgium
| | - Larry G Higgins
- Lower Olefins and Aromatics Consortium Services Team, Penman Consulting bvba, Brussels, Belgium.
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5
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Golden E, Allen D, Amberg A, Anger LT, Baker E, Baran SW, Bringezu F, Clark M, Duchateau-Nguyen G, Escher SE, Giri V, Grevot A, Hartung T, Li D, Lotfi L, Muster W, Snyder K, Wange R, Steger-Hartmann T. Toward implementing virtual control groups in nonclinical safety studies. ALTEX 2023; 41:282-301. [PMID: 38043132 DOI: 10.14573/altex.2310041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Historical data from control groups in animal toxicity studies is currently mainly used for comparative purposes to assess validity and robustness of study results. Due to the highly controlled environment in which the studies are performed and the homogeneity of the animal collectives it has been proposed to use the historical data for building so-called virtual control groups, which could replace partly or entirely the concurrent control. This would constitute a substantial contribution to the reduction of animal use in safety studies. Before the concept can be implemented, the prerequisites regarding data collection, curation and statistical evaluation together with a validation strategy need to be identified to avoid any impairment of the study outcome and subsequent consequences for human risk assessment. To further assess and develop the concept of virtual control groups the transatlantic think tank for toxicology (t⁴) sponsored a workshop with stakeholders from the pharmaceutical and chemical industry, academia, FDA, pharmaceutical, contract research organizations (CROs), and non-governmental organizations in Washington, which took place in March 2023. This report summarizes the current efforts of a European initiative to share, collect and curate animal control data in a centralized database and the first approaches to identify optimal matching criteria between virtual controls and the treatment arms of a study as well as first reflections about strategies for a qualification procedure and potential pitfalls of the concept.
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Affiliation(s)
- Emily Golden
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | - Elizabeth Baker
- Physicians Committee for Responsible Medicine, Washington, DC, USA
| | | | - Frank Bringezu
- Merck Healthcare KGaA, Chemical & Preclinical Safety, Darmstadt, Germany
| | - Matthew Clark
- Charles River Laboratories, now KALOS Technologies, Philadelphia, PA, USA
| | - Guillemette Duchateau-Nguyen
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | | | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, 67056 Ludwigshafen am Rhein, Germany
| | - Armelle Grevot
- Novartis Institute for Biomedical Research, Novartis AG, Basel, Switzerland
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- CAAT-Europe, University of Konstanz, Konstanz, Germany
| | - Dingzhou Li
- Pfizer, Global Biometrics and Data Management, Groton, CT, USA
| | | | - Wolfgang Muster
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Kevin Snyder
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA
| | - Ronald Wange
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA
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6
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Ramirez-Hincapie S, Birk B, Ternes P, Giri V, Haake V, Herold M, Zickgraf FM, Verlohner A, Huener HA, Kamp H, Driemert P, Landsiedel R, Richling E, Funk-Weyer D, van Ravenzwaay B. A high-throughput metabolomics in vitro platform for the characterization of hepatotoxicity. Cell Biol Toxicol 2023; 39:2899-2917. [PMID: 37138123 PMCID: PMC10693528 DOI: 10.1007/s10565-023-09809-6] [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: 12/14/2022] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
Cell-based metabolomics provides multiparametric physiologically relevant readouts that can be highly advantageous for improved, biologically based decision making in early stages of compound development. Here, we present the development of a 96-well plate LC-MS/MS-based targeted metabolomics screening platform for the classification of liver toxicity modes of action (MoAs) in HepG2 cells. Different parameters of the workflow (cell seeding density, passage number, cytotoxicity testing, sample preparation, metabolite extraction, analytical method, and data processing) were optimized and standardized to increase the efficiency of the testing platform. The applicability of the system was tested with seven substances known to be representative of three different liver toxicity MoAs (peroxisome proliferation, liver enzyme induction, and liver enzyme inhibition). Five concentrations per substance, aimed at covering the complete dose-response curve, were analyzed and 221 uniquely identified metabolites were measured, annotated, and allocated in 12 different metabolite classes such as amino acids, carbohydrates, energy metabolism, nucleobases, vitamins and cofactors, and diverse lipid classes. Multivariate and univariate analyses showed a dose response of the metabolic effects, a clear differentiation between liver toxicity MoAs and resulted in the identification of metabolite patterns specific for each MoA. Key metabolites indicative of both general and mechanistic specific hepatotoxicity were identified. The method presented here offers a multiparametric, mechanistic-based, and cost-effective hepatotoxicity screening that provides MoA classification and sheds light into the pathways involved in the toxicological mechanism. This assay can be implemented as a reliable compound screening platform for improved safety assessment in early compound development pipelines.
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Affiliation(s)
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | | | | | | | | | | | | | - Robert Landsiedel
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
- Free University of Berlin, Pharmacy, Pharmacology and Toxicology, Berlin, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern, Germany
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7
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Ramirez-Hincapie S, Birk B, Ternes P, Giri V, Zickgraf FM, Haake V, Herold M, Kamp H, Driemert P, Landsiedel R, Richling E, Funk-Weyer D, van Ravenzwaay B. Application of high throughput in vitro metabolomics for hepatotoxicity mode of action characterization and mechanistic-anchored point of departure derivation: a case study with nitrofurantoin. Arch Toxicol 2023; 97:2903-2917. [PMID: 37665362 PMCID: PMC10504224 DOI: 10.1007/s00204-023-03572-7] [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: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023]
Abstract
Omics techniques have been increasingly recognized as promising tools for Next Generation Risk Assessment. Targeted metabolomics offer the advantage of providing readily interpretable mechanistic information about perturbed biological pathways. In this study, a high-throughput LC-MS/MS-based broad targeted metabolomics system was applied to study nitrofurantoin metabolic dynamics over time and concentration and to provide a mechanistic-anchored approach for point of departure (PoD) derivation. Upon nitrofurantoin exposure at five concentrations (7.5 µM, 15 µM, 20 µM, 30 µM and 120 µM) and four time points (3, 6, 24 and 48 h), the intracellular metabolome of HepG2 cells was evaluated. In total, 256 uniquely identified metabolites were measured, annotated, and allocated in 13 different metabolite classes. Principal component analysis (PCA) and univariate statistical analysis showed clear metabolome-based time and concentration effects. Mechanistic information evidenced the differential activation of cellular pathways indicative of early adaptive and hepatotoxic response. At low concentrations, effects were seen mainly in the energy and lipid metabolism, in the mid concentration range, the activation of the antioxidant cellular response was evidenced by increased levels of glutathione (GSH) and metabolites from the de novo GSH synthesis pathway. At the highest concentrations, the depletion of GSH, together with alternations reflective of mitochondrial impairments, were indicative of a hepatotoxic response. Finally, a metabolomics-based PoD was derived by multivariate PCA using the whole set of measured metabolites. This approach allows using the entire dataset and derive PoD that can be mechanistically anchored to established key events. Our results show the suitability of high throughput targeted metabolomics to investigate mechanisms of hepatoxicity and derive point of departures that can be linked to existing adverse outcome pathways and contribute to the development of new ones.
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Affiliation(s)
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | | | | | | | | | | | - Robert Landsiedel
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
- Pharmacy, Pharmacology and Toxicology, Free University of Berlin, Berlin, Germany
| | - Elke Richling
- Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
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8
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Wilhelmi P, Giri V, Zickgraf FM, Haake V, Henkes S, Driemert P, Michaelis P, Busch W, Scholz S, Flick B, Barenys M, Birk B, Kamp H, Landsiedel R, Funk-Weyer D. A metabolomics approach to reveal the mechanism of developmental toxicity in zebrafish embryos exposed to 6-propyl-2-thiouracil. Chem Biol Interact 2023; 382:110565. [PMID: 37236578 DOI: 10.1016/j.cbi.2023.110565] [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: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
A crucial component of a substance registration and regulation is the evaluation of human prenatal developmental toxicity. Current toxicological tests are based on mammalian models, but these are costly, time consuming and may pose ethical concerns. The zebrafish embryo has evolved as a promising alternative model to study developmental toxicity. However, the implementation of the zebrafish embryotoxicity test is challenged by lacking information on the relevance of observed morphological alterations in fish for human developmental toxicity. Elucidating the mechanism of toxicity could help to overcome this limitation. Through LC-MS/MS and GC-MS metabolomics, we investigated whether changes to the endogenous metabolites can indicate pathways associated with developmental toxicity. To this aim, zebrafish embryos were exposed to different concentrations of 6-propyl-2-thiouracil (PTU), a compound known to induce developmental toxicity. The reproducibility and the concentration-dependence of the metabolome response and its association with morphological alterations were studied. Major morphological findings were reduced eye size, and other craniofacial anomalies; major metabolic changes included increased tyrosine, pipecolic acid and lysophosphatidylcholine levels, decreased methionine levels, and disturbance of the 'Phenylalanine, tyrosine and tryptophan biosynthesis' pathway. This pathway, and the changes in tyrosine and pipecolic acid levels could be linked to the mode of action of PTU, i.e., inhibition of thyroid peroxidase (TPO). The other findings suggested neurodevelopmental impairments. This proof-of-concept study demonstrated that metabolite changes in zebrafish embryos are robust and provide mechanistic information associated with the mode of action of PTU.
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Affiliation(s)
- Pia Wilhelmi
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany; University of Barcelona, Research Group in Toxicology-GRET, 08028, Barcelona, Spain.
| | - Varun Giri
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany.
| | | | - Volker Haake
- BASF Metabolome Solutions, 10589, Berlin, Germany
| | | | | | - Paul Michaelis
- Helmholtz Centre for Environmental Research-UFZ, Department of Bioanalytical Ecotoxicology, 04318, Leipzig, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research-UFZ, Department of Bioanalytical Ecotoxicology, 04318, Leipzig, Germany
| | - Stefan Scholz
- Helmholtz Centre for Environmental Research-UFZ, Department of Bioanalytical Ecotoxicology, 04318, Leipzig, Germany
| | - Burkhard Flick
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany
| | - Marta Barenys
- University of Barcelona, Research Group in Toxicology-GRET, 08028, Barcelona, Spain; German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany
| | | | - Robert Landsiedel
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany; Free University of Berlin, Institute of Pharmacy, Pharmacology and Toxicology, 14195, Berlin, Germany
| | - Dorothee Funk-Weyer
- BASF SE, Experimental Toxicology and Ecology, 67056, Ludwigshafen am Rhein, Germany
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Murali A, Giri V, Zickgraf FM, Ternes P, Cameron HJ, Sperber S, Haake V, Driemert P, Kamp H, Funk-Weyer D, Sturla SJ, Rietjens IMCM, van Ravenzwaay B. Connecting Gut Microbial Diversity with Plasma Metabolome and Fecal Bile Acid Changes Induced by the Antibiotics Tobramycin and Colistin Sulfate. Chem Res Toxicol 2023; 36:598-616. [PMID: 36972423 DOI: 10.1021/acs.chemrestox.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The diversity of microbial species in the gut has a strong influence on health and development of the host. Further, there are indications that the variation in expression of gut bacterial metabolic enzymes is less diverse than the taxonomic profile, underlying the importance of microbiome functionality, particularly from a toxicological perspective. To address these relationships, the gut bacterial composition of Wistar rats was altered by a 28 day oral treatment with the antibiotics tobramycin or colistin sulfate. On the basis of 16S marker gene sequencing data, tobramycin was found to cause a strong reduction in the diversity and relative abundance of the microbiome, whereas colistin sulfate had only a marginal impact. Associated plasma and fecal metabolomes were characterized by targeted mass spectrometry-based profiling. The fecal metabolome of tobramycin-treated animals had a high number of significant alterations in metabolite levels compared to controls, particularly in amino acids, lipids, bile acids (BAs), carbohydrates, and energy metabolites. The accumulation of primary BAs and significant reduction of secondary BAs in the feces indicated that the microbial alterations induced by tobramycin inhibit bacterial deconjugation reactions. The plasma metabolome showed less, but still many alterations in the same metabolite groups, including reductions in indole derivatives and hippuric acid, and furthermore, despite marginal effects of colistin sulfate treatment, there were nonetheless systemic alterations also in BAs. Aside from these treatment-based differences, we also uncovered interindividual differences particularly centering on the loss of Verrucomicrobiaceae in the microbiome, but with no apparent associated metabolite alterations. Finally, by comparing the data set from this study with metabolome alterations in the MetaMapTox database, key metabolite alterations were identified as plasma biomarkers indicative of altered gut microbiomes resulting from a wide activity spectrum of antibiotics.
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Affiliation(s)
| | - Varun Giri
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | | | - Philipp Ternes
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hunter James Cameron
- BASF Corporation Computational Biology (RTP), Research Triangle Park, 3500 Paramount Parkway, Morrisvile, North Carolina 27560, United States
| | - Saskia Sperber
- BASF SE, Ludwigshafen am Rhein 67056, Rheinland-Pfalz, Germany
| | - Volker Haake
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Peter Driemert
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | - Hennicke Kamp
- Metanomics (BASF Metabolome Solutions) GmbH, Tegeler Weg 33, Berlin 10589, Germany
| | | | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zurich CH 8092, Switzerland
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Murali A, Zickgraf FM, Ternes P, Giri V, Cameron HJ, Sperber S, Haake V, Driemert P, Kamp H, Weyer DF, Sturla SJ, Rietjens IMGM, van Ravenzwaay B. Gut Microbiota as Well as Metabolomes of Wistar Rats Recover within Two Weeks after Doripenem Antibiotic Treatment. Microorganisms 2023; 11:microorganisms11020533. [PMID: 36838498 PMCID: PMC9959319 DOI: 10.3390/microorganisms11020533] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
An understanding of the changes in gut microbiome composition and its associated metabolic functions is important to assess the potential implications thereof on host health. Thus, to elucidate the connection between the gut microbiome and the fecal and plasma metabolomes, two poorly bioavailable carbapenem antibiotics (doripenem and meropenem), were administered in a 28-day oral study to male and female Wistar rats. Additionally, the recovery of the gut microbiome and metabolomes in doripenem-exposed rats were studied one and two weeks after antibiotic treatment (i.e., doripenem-recovery groups). The 16S bacterial community analysis revealed an altered microbial population in all antibiotic treatments and a recovery of bacterial diversity in the doripenem-recovery groups. A similar pattern was observed in the fecal metabolomes of treated animals. In the recovery group, particularly after one week, an over-compensation was observed in fecal metabolites, as they were significantly changed in the opposite direction compared to previously changed metabolites upon 28 days of antibiotic exposure. Key plasma metabolites known to be diagnostic of antibiotic-induced microbial shifts, including indole derivatives, hippuric acid, and bile acids were also affected by the two carbapenems. Moreover, a unique increase in the levels of indole-3-acetic acid in plasma following meropenem treatment was observed. As was observed for the fecal metabolome, an overcompensation of plasma metabolites was observed in the recovery group. The data from this study provides insights into the connectivity of the microbiome and fecal and plasma metabolomes and demonstrates restoration post-antibiotic treatment not only for the microbiome but also for the metabolomes. The importance of overcompensation reactions for health needs further studies.
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Affiliation(s)
- Aishwarya Murali
- BASF SE, 67056 Ludwigshafen, Germany
- Correspondence: (A.M.); (B.v.R.)
| | | | | | | | | | | | - Volker Haake
- BASF Metabolome Solutions GmbH, 10589 Berlin, Germany
| | | | - Hennicke Kamp
- BASF Metabolome Solutions GmbH, 10589 Berlin, Germany
| | | | - Shana J. Sturla
- ETH Zürich, Department of Health Sciences and Technology, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | | | - Bennard van Ravenzwaay
- Department of Toxicology, Wageningen University & Research, 6703 HE Wageningen, The Netherlands
- Correspondence: (A.M.); (B.v.R.)
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11
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Wilhelmi P, Giri V, Henkes S, Walk T, Haake V, Scholz S, Busch W, Barenys M, Zickgraf F, Landsiedel R, Funk-Weyer D, Birk B, Flick B. P20-05 A targeted metabolomics approach for unraveling different modes of embryotoxicity in zebrafish. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.671] [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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Murali A, Giri V, Cameron HJ, Sperber S, Zickgraf FM, Haake V, Driemert P, Walk T, Kamp H, Rietjens IMCM, van Ravenzwaay B. Investigating the gut microbiome and metabolome following treatment with artificial sweeteners acesulfame potassium and saccharin in young adult Wistar rats. Food Chem Toxicol 2022; 165:113123. [DOI: 10.1016/j.fct.2022.113123] [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] [Received: 01/27/2022] [Revised: 04/07/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022]
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13
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Ramirez Hincapie S, Herold M, Sperber S, Birk B, Haake V, Giri V, Huener HA, Verlohner A, Kamp H, Landsiedel R, Richling E, Van Ravenzwaay B. Miniaturization of in vitro liver metabolomics - a screening approach to predict the mode of action of liver toxicants in HepG2 cells. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00470-7] [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: 11/17/2022]
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14
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Murali A, Giri V, Cameron H, Sperber S, Kamp H, Haake V, Walk T, Rietjens I, van Ravenzwaay B. The safety of artificial sweeteners examined by an integrated metabolomics and gut bacterial profiling approach of Acesulfame K and Saccharin treated Wistar rats. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00777-3] [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: 11/25/2022]
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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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Sivakumar TV, Giri V, Park JH, Kim TY, Bhaduri A. ReactPRED: a tool to predict and analyze biochemical reactions. Bioinformatics 2016; 32:3522-3524. [DOI: 10.1093/bioinformatics/btw491] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/24/2016] [Accepted: 07/19/2016] [Indexed: 01/19/2023] Open
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Giri V, Sivakumar TV, Cho KM, Kim TY, Bhaduri A. RxnSim: a tool to compare biochemical reactions. Bioinformatics 2015; 31:3712-4. [PMID: 26187943 DOI: 10.1093/bioinformatics/btv416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/13/2015] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED : Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patterns. We describe a tool, RxnSim, which computes reaction similarity based on the molecular signatures of participating molecules. The tool is able to compare reactions based on similarities of substrates and products in addition to their transformation. It allows masking of user-defined chemical moieties for weighted similarity computations. AVAILABILITY AND IMPLEMENTATION RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http://cran.r-project.org/web/packages/RxnSim/). CONTACT anirban.b@samsung.com or ty76.kim@samsung.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Varun Giri
- Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and
| | - Tadi Venkata Sivakumar
- Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and
| | - Kwang Myung Cho
- Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea
| | - Tae Yong Kim
- Biomaterials Lab, Materials Center, Samsung Advanced Institute of Technology, Gyeonggi-do 443803, Korea
| | - Anirban Bhaduri
- Bioinformatics Lab, Samsung Advanced Institute of Technology, Bangalore 560037, India and
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Affiliation(s)
- Milind Baldi
- Department of Chest Medicine and Environmental Pollution Research Centre, Seth Gordhandas Sunderdas Medical College and King Edward Memorial Hospital, Mumbai, Maharashtra, India E-mail:
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Singh S, Samal A, Giri V, Krishna S, Raghuram N, Jain S. Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 87:052708. [PMID: 23767567 DOI: 10.1103/physreve.87.052708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 03/23/2013] [Indexed: 06/02/2023]
Abstract
Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of three microorganisms. We apply flux balance analysis to study the optimal growth states of these organisms in different environments. By investigating the differential usage of reactions across flux patterns for different environments, we observe a striking bimodal distribution in the activity of reactions. Motivated by this, we propose a simple algorithm to decompose the metabolic network into three subnetworks. It turns out that our reaction classifier, which is blind to the biochemical role of pathways, leads to three functionally relevant subnetworks that correspond to input, output, and intermediate parts of the metabolic network with distinct structural characteristics. Our decomposition method unveils a functional bow-tie organization of metabolic networks that is different from the bow-tie structure determined by graph-theoretic methods that do not incorporate functionality.
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Affiliation(s)
- Shalini Singh
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India
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20
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Pradhan P, Nandi D, Pradhan S, Jaisankar P, Giri V. An Unusual Diastereoselective Pictet–Spengler Reaction: Synthesis of Novel Tetrahydro-β-Carboline Glycosides. Synlett 2012. [DOI: 10.1055/s-0032-1317632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Debkumar Nandi
- Chemistry Department, Indian Institute of Chemical Biology
| | | | | | - V. Giri
- Chemistry Department, Indian Institute of Chemical Biology
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21
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Abstract
Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the ‘food set’, being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying ‘nested ACSs’, a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.
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Affiliation(s)
- Varun Giri
- Department of Physics and Astrophysics, University of Delhi, Delhi, India
| | - Sanjay Jain
- Department of Physics and Astrophysics, University of Delhi, Delhi, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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22
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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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23
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Maliekal TT, Bajaj J, Giri V, Subramanyam D, Krishna S. The role of Notch signaling in human cervical cancer: implications for solid tumors. Oncogene 2008; 27:5110-4. [PMID: 18758479 DOI: 10.1038/onc.2008.224] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The detection of intracellular forms of Notch1 in human cervical cancers more than a decade ago prompted an investigation into the possible role of this pathway in driving these cancers. These tumors are consistently characterized by features of deregulated ligand-dependent signaling. Although Notch signaling complements the function of papillomavirus oncogenes in transformation assays of human keratinocytes, there are dose-dependent effects, which inhibit growth of established cervical cancer cell lines. Two pro-oncogenic effector mechanisms that have been suggested to operate in this context by Notch signaling are the activation of PI3K/Akt pathway and the upregulation of c-Myc. Collectively, there is a complex interplay between Notch signaling and papillomaviruses in the context of cervical carcinogenesis. Better animal model systems and identification of human cervical cancer stem cells should help clarify the possible stage specific and pleiotropic effects and regulation of Notch signaling.
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Affiliation(s)
- T T Maliekal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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24
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Gower DJ, Dharne M, Bhatta G, Giri V, Vyas R, Govindappa V, Oommen OV, George J, Shouche Y, Wilkinson M. Remarkable genetic homogeneity in unstriped, long-tailedIchthyophisalong 1500 km of the Western Ghats, India. J Zool (1987) 2007. [DOI: 10.1111/j.1469-7998.2006.00266.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Samal A, Singh S, Giri V, Krishna S, Raghuram N, Jain S. Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics 2006; 7:118. [PMID: 16524470 PMCID: PMC1434774 DOI: 10.1186/1471-2105-7-118] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 03/08/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently there has been a lot of interest in identifying modules at the level of genetic and metabolic networks of organisms, as well as in identifying single genes and reactions that are essential for the organism. A goal of computational and systems biology is to go beyond identification towards an explanation of specific modules and essential genes and reactions in terms of specific structural or evolutionary constraints. RESULTS In the metabolic networks of Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus, we identified metabolites with a low degree of connectivity, particularly those that are produced and/or consumed in just a single reaction. Using flux balance analysis (FBA) we also determined reactions essential for growth in these metabolic networks. We find that most reactions identified as essential in these networks turn out to be those involving the production or consumption of low degree metabolites. Applying graph theoretic methods to these metabolic networks, we identified connected clusters of these low degree metabolites. The genes involved in several operons in E. coli are correctly predicted as those of enzymes catalyzing the reactions of these clusters. Furthermore, we find that larger sized clusters are over-represented in the real network and are analogous to a 'network motif. Using FBA for the above mentioned three organisms we independently identified clusters of reactions whose fluxes are perfectly correlated. We find that the composition of the latter 'functional clusters' is also largely explained in terms of clusters of low degree metabolites in each of these organisms. CONCLUSION Our findings mean that most metabolic reactions that are essential can be tagged by one or more low degree metabolites. Those reactions are essential because they are the only ways of producing or consuming their respective tagged metabolites. Furthermore, reactions whose fluxes are strongly correlated can be thought of as 'glued together' by these low degree metabolites. The methods developed here could be used in predicting essential reactions and metabolic modules in other organisms from the list of metabolic reactions.
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Affiliation(s)
- Areejit Samal
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India
| | - Shalini Singh
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India
| | - Varun Giri
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India
| | - Sandeep Krishna
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560065, India
- Niels Bohr Institute for Astronomy, Physics and Geophysics, Blegdamsvej 17, Copenhagen DK-2100, Denmark
| | - Nandula Raghuram
- School of Biotechnology, GGS Indraprastha University, Delhi 110006, India
| | - Sanjay Jain
- Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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