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Cheng SL, Hedges M, Keski-Rahkonen P, Chatziioannou AC, Scalbert A, Chung KF, Sinharay R, Green DC, de Kok TMCM, Vlaanderen J, Kyrtopoulos SA, Kelly F, Portengen L, Vineis P, Vermeulen RCH, Chadeau-Hyam M, Dagnino S. Multiomic Signatures of Traffic-Related Air Pollution in London Reveal Potential Short-Term Perturbations in Gut Microbiome-Related Pathways. Environ Sci Technol 2024. [PMID: 38728551 DOI: 10.1021/acs.est.3c09148] [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] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
This randomized crossover study investigated the metabolic and mRNA alterations associated with exposure to high and low traffic-related air pollution (TRAP) in 50 participants who were either healthy or were diagnosed with chronic pulmonary obstructive disease (COPD) or ischemic heart disease (IHD). For the first time, this study combined transcriptomics and serum metabolomics measured in the same participants over multiple time points (2 h before, and 2 and 24 h after exposure) and over two contrasted exposure regimes to identify potential multiomic modifications linked to TRAP exposure. With a multivariate normal model, we identified 78 metabolic features and 53 mRNA features associated with at least one TRAP exposure. Nitrogen dioxide (NO2) emerged as the dominant pollutant, with 67 unique associated metabolomic features. Pathway analysis and annotation of metabolic features consistently indicated perturbations in the tryptophan metabolism associated with NO2 exposure, particularly in the gut-microbiome-associated indole pathway. Conditional multiomics networks revealed complex and intricate mechanisms associated with TRAP exposure, with some effects persisting 24 h after exposure. Our findings indicate that exposure to TRAP can alter important physiological mechanisms even after a short-term exposure of a 2 h walk. We describe for the first time a potential link between NO2 exposure and perturbation of the microbiome-related pathways.
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Affiliation(s)
- Sibo Lucas Cheng
- NIHR HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K
| | - Michael Hedges
- MRC Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K
| | | | | | - Augustin Scalbert
- International Agency for Research on Cancer (IARC), Lyon 69366 Cedex, France
| | - Kian Fan Chung
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, U.K
- Royal Brompton & Harefield NHS Trust, London SW3 6NP, U.K
| | - Rudy Sinharay
- National Heart & Lung Institute, Imperial College London, London SW7 2AZ, U.K
- Imperial College Healthcare NHS Trust, London W2 1NY, U.K
| | - David C Green
- NIHR HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K
- MRC Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229 ER, The Netherlands
| | - Jelle Vlaanderen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | | | - Frank Kelly
- NIHR HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K
- MRC Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K
| | - Lützen Portengen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Paolo Vineis
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K
| | - Roel C H Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Marc Chadeau-Hyam
- NIHR HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K
| | - Sonia Dagnino
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K
- Transporters in Imaging and Radiotherapy in Oncology (TIRO), School of Medicine, Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Fréderic Joliot, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Côte d'Azur (UniCA), Nice 06107, France
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2
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He Y, DeBenedictis JN, Caiment F, van Breda SGJ, de Kok TMCM. Author Correction: Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx. Sci Rep 2024; 14:5096. [PMID: 38429310 PMCID: PMC10907571 DOI: 10.1038/s41598-024-53927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024] Open
Affiliation(s)
- Yueqin He
- Department of Toxicogenomics, GROW ‑ School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Julia Nicole DeBenedictis
- Department of Toxicogenomics, GROW ‑ School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW ‑ School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW ‑ School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW ‑ School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
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O’Donovan SD, Cavill R, Wimmenauer F, Lukas A, Stumm T, Smirnov E, Lenz M, Ertaylan G, Jennen DGJ, van Riel NAW, Driessens K, Peeters RLM, de Kok TMCM. Application of transfer learning to predict drug-induced human in vivo gene expression changes using rat in vitro and in vivo data. PLoS One 2023; 18:e0292030. [PMID: 38032940 PMCID: PMC10688741 DOI: 10.1371/journal.pone.0292030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/11/2023] [Indexed: 12/02/2023] Open
Abstract
The liver is the primary site for the metabolism and detoxification of many compounds, including pharmaceuticals. Consequently, it is also the primary location for many adverse reactions. As the liver is not readily accessible for sampling in humans; rodent or cell line models are often used to evaluate potential toxic effects of a novel compound or candidate drug. However, relating the results of animal and in vitro studies to relevant clinical outcomes for the human in vivo situation still proves challenging. In this study, we incorporate principles of transfer learning within a deep artificial neural network allowing us to leverage the relative abundance of rat in vitro and in vivo exposure data from the Open TG-GATEs data set to train a model to predict the expected pattern of human in vivo gene expression following an exposure given measured human in vitro gene expression. We show that domain adaptation has been successfully achieved, with the rat and human in vitro data no longer being separable in the common latent space generated by the network. The network produces physiologically plausible predictions of human in vivo gene expression pattern following an exposure to a previously unseen compound. Moreover, we show the integration of the human in vitro data in the training of the domain adaptation network significantly improves the temporal accuracy of the predicted rat in vivo gene expression pattern following an exposure to a previously unseen compound. In this way, we demonstrate the improvements in prediction accuracy that can be achieved by combining data from distinct domains.
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Affiliation(s)
- Shauna D. O’Donovan
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Artificial Intelligence Systems Institute (EAISI), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Rachel Cavill
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Florian Wimmenauer
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Alexander Lukas
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Tobias Stumm
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Evgueni Smirnov
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Michael Lenz
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
- Preventive Cardiology and Preventative Medicine – Center for Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Gokhan Ertaylan
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Danyel G. J. Jennen
- Dept. of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Natal A. W. van Riel
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Artificial Intelligence Systems Institute (EAISI), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Kurt Driessens
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Ralf L. M. Peeters
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Theo M. C. M. de Kok
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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4
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He Y, DeBenedictis JN, Caiment F, van Breda SGJ, de Kok TMCM. Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx. Sci Rep 2023; 13:18281. [PMID: 37880448 PMCID: PMC10600214 DOI: 10.1038/s41598-023-45582-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023] Open
Abstract
Diet is an important determinant of overall health, and has been linked to the risk of various cancers. To understand the mechanisms involved, transcriptomic responses from human intervention studies are very informative. However, gene expression analysis of human biopsy material only represents the average profile of a mixture of cell types that can mask more subtle, but relevant cell-specific changes. Here, we use the CIBERSORTx algorithm to generate single-cell gene expression from human multicellular colon tissue. We applied the CIBERSORTx to microarray data from the PHYTOME study, which investigated the effects of different types of meat on transcriptional and biomarker changes relevant to colorectal cancer (CRC) risk. First, we used single-cell mRNA sequencing data from healthy colon tissue to generate a novel signature matrix in CIBERSORTx, then we determined the proportions and gene expression of each separate cell type. After comparison, cell proportion analysis showed a continuous upward trend in the abundance of goblet cells and stem cells, and a continuous downward trend in transit amplifying cells after the addition of phytochemicals in red meat products. The dietary intervention influenced the expression of genes involved in the growth and division of stem cells, the metabolism and detoxification of enterocytes, the translation and glycosylation of goblet cells, and the inflammatory response of innate lymphoid cells. These results show that our approach offers novel insights into the heterogeneous gene expression responses of different cell types in colon tissue during a dietary intervention.
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Affiliation(s)
- Yueqin He
- Department of Toxicogenomics, GROW - School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Julia Nicole DeBenedictis
- Department of Toxicogenomics, GROW - School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW - School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW - School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW - School for Oncology and Reproduction, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
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O’Donovan SD, Driessens K, Lopatta D, Wimmenauer F, Lukas A, Neeven J, Stumm T, Smirnov E, Lenz M, Ertaylan G, Jennen DGJ, van Riel NAW, Cavill R, Peeters RLM, de Kok TMCM. Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes. PLoS One 2020; 15:e0236392. [PMID: 32780735 PMCID: PMC7418976 DOI: 10.1371/journal.pone.0236392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/06/2020] [Indexed: 11/19/2022] Open
Abstract
In clinical trials, animal and cell line models are often used to evaluate the potential toxic effects of a novel compound or candidate drug before progressing to human trials. However, relating the results of animal and in vitro model exposures to relevant clinical outcomes in the human in vivo system still proves challenging, relying on often putative orthologs. In recent years, multiple studies have demonstrated that the repeated dose rodent bioassay, the current gold standard in the field, lacks sufficient sensitivity and specificity in predicting toxic effects of pharmaceuticals in humans. In this study, we evaluate the potential of deep learning techniques to translate the pattern of gene expression measured following an exposure in rodents to humans, circumventing the current reliance on orthologs, and also from in vitro to in vivo experimental designs. Of the applied deep learning architectures applied in this study the convolutional neural network (CNN) and a deep artificial neural network with bottleneck architecture significantly outperform classical machine learning techniques in predicting the time series of gene expression in primary human hepatocytes given a measured time series of gene expression from primary rat hepatocytes following exposure in vitro to a previously unseen compound across multiple toxicologically relevant gene sets. With a reduction in average mean absolute error across 76 genes that have been shown to be predictive for identifying carcinogenicity from 0.0172 for a random regression forest to 0.0166 for the CNN model (p < 0.05). These deep learning architecture also perform well when applied to predict time series of in vivo gene expression given measured time series of in vitro gene expression for rats.
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Affiliation(s)
- Shauna D. O’Donovan
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Kurt Driessens
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Daniel Lopatta
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Florian Wimmenauer
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Alexander Lukas
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Jelmer Neeven
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Tobias Stumm
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Evgueni Smirnov
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Michael Lenz
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
- Preventive Cardiology and Preventative Medicine—Center for Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Gokhan Ertaylan
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Danyel G. J. Jennen
- Dept. of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Natal A. W. van Riel
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Rachel Cavill
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Ralf L. M. Peeters
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Theo M. C. M. de Kok
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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O’Donovan SD, Lenz M, Vink RG, Roumans NJT, de Kok TMCM, Mariman ECM, Peeters RLM, van Riel NAW, van Baak MA, Arts ICW. A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data. PLoS Comput Biol 2019; 15:e1007400. [PMID: 31581241 PMCID: PMC6890259 DOI: 10.1371/journal.pcbi.1007400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 12/03/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Given the association of disturbances in non-esterified fatty acid (NEFA) metabolism with the development of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease, computational models of glucose-insulin dynamics have been extended to account for the interplay with NEFA. In this study, we use arteriovenous measurement across the subcutaneous adipose tissue during a mixed meal challenge test to evaluate the performance and underlying assumptions of three existing models of adipose tissue metabolism and construct a new, refined model of adipose tissue metabolism. Our model introduces new terms, explicitly accounting for the conversion of glucose to glyceraldehye-3-phosphate, the postprandial influx of glycerol into the adipose tissue, and several physiologically relevant delays in insulin signalling in order to better describe the measured adipose tissues fluxes. We then applied our refined model to human adipose tissue flux data collected before and after a diet intervention as part of the Yoyo study, to quantify the effects of caloric restriction on postprandial adipose tissue metabolism. Significant increases were observed in the model parameters describing the rate of uptake and release of both glycerol and NEFA. Additionally, decreases in the model's delay in insulin signalling parameters indicates there is an improvement in adipose tissue insulin sensitivity following caloric restriction.
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Affiliation(s)
- Shauna D. O’Donovan
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Division of Human Health and Nurtrition, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Michael Lenz
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
- Preventive Cardiology and Preventative Medicine - Center for Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Roel G. Vink
- Dept. Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Nadia J. T. Roumans
- Dept. Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Theo M. C. M. de Kok
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Edwin C. M. Mariman
- Dept. Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Ralf L. M. Peeters
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Natal A. W. van Riel
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Marleen A. van Baak
- Dept. Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Ilja C. W. Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- Dept. Epidemiology, CARIM School for Cardiovascular Disease, Maastricht University, Maastricht, The Netherlands
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Georgiadis P, Gavriil M, Rantakokko P, Ladoukakis E, Botsivali M, Kelly RS, Bergdahl IA, Kiviranta H, Vermeulen RCH, Spaeth F, Hebbels DGAJ, Kleinjans JCS, de Kok TMCM, Palli D, Vineis P, Kyrtopoulos SA. DNA methylation profiling implicates exposure to PCBs in the pathogenesis of B-cell chronic lymphocytic leukemia. Environ Int 2019; 126:24-36. [PMID: 30776747 PMCID: PMC7063446 DOI: 10.1016/j.envint.2019.01.068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/17/2019] [Accepted: 01/28/2019] [Indexed: 05/03/2023]
Abstract
OBJECTIVES To characterize the impact of PCB exposure on DNA methylation in peripheral blood leucocytes and to evaluate the corresponding changes in relation to possible health effects, with a focus on B-cell lymphoma. METHODS We conducted an epigenome-wide association study on 611 adults free of diagnosed disease, living in Italy and Sweden, in whom we also measured plasma concentrations of 6 PCB congeners, DDE and hexachlorobenzene. RESULTS We identified 650 CpG sites whose methylation correlates strongly (FDR < 0.01) with plasma concentrations of at least one PCB congener. Stronger effects were observed in males and in Sweden. This epigenetic exposure profile shows extensive and highly statistically significant overlaps with published profiles associated with the risk of future B-cell chronic lymphocytic leukemia (CLL) as well as with clinical CLL (38 and 28 CpG sites, respectively). For all these sites, the methylation changes were in the same direction for increasing exposure and for higher disease risk or clinical disease status, suggesting an etiological link between exposure and CLL. Mediation analysis reinforced the suggestion of a causal link between exposure, changes in DNA methylation and disease. Disease connectivity analysis identified multiple additional diseases associated with differentially methylated genes, including melanoma for which an etiological link with PCB exposure is established, as well as developmental and neurological diseases for which there is corresponding epidemiological evidence. Differentially methylated genes include many homeobox genes, suggesting that PCBs target stem cells. Furthermore, numerous polycomb protein target genes were hypermethylated with increasing exposure, an effect known to constitute an early marker of carcinogenesis. CONCLUSIONS This study provides mechanistic evidence in support of a link between exposure to PCBs and the etiology of CLL and underlines the utility of omic profiling in the evaluation of the potential toxicity of environmental chemicals.
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Affiliation(s)
- Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Marios Gavriil
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Panu Rantakokko
- National Institute for Health and Welfare, Department of Health Security, Environmental Health unit, P.O. Box 95, Kuopio, Finland
| | - Efthymios Ladoukakis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Maria Botsivali
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Rachel S Kelly
- MRC-HPA Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, UK
| | - Ingvar A Bergdahl
- Department of Biobank Research, and Occupational and Environmental Medicine, Department of Public Health and Clinical Medicine, Umeå University, Sweden
| | - Hannu Kiviranta
- MRC-HPA Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, UK
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Florentin Spaeth
- Department of Radiation Sciences, Oncology, Umeå University, Sweden
| | | | | | | | - Domenico Palli
- The Institute for Cancer Research and Prevention, Florence, Italy
| | - Paolo Vineis
- MRC-HPA Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, UK
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece.
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8
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Campanella G, Gunter MJ, Polidoro S, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Fiorito G, Guarrera S, Iacoviello L, Bergdahl IA, Melin B, Lenner P, de Kok TMCM, Georgiadis P, Kleinjans JCS, Kyrtopoulos SA, Bueno-de-Mesquita HB, Lillycrop KA, May AM, Onland-Moret NC, Murray R, Riboli E, Verschuren M, Lund E, Mode N, Sandanger TM, Fiano V, Trevisan M, Matullo G, Froguel P, Elliott P, Vineis P, Chadeau-Hyam M. Epigenome-wide association study of adiposity and future risk of obesity-related diseases. Int J Obes (Lond) 2018; 42:2022-2035. [PMID: 29713043 DOI: 10.1038/s41366-018-0064-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Obesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction. METHODS DNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population. RESULTS We identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10-8 to 3.27×10-18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10-7), higher triglyceride levels (P = 5.37×10-9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10-10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P < 1.6×10-3) and one intergenic locus on chromosome 1 was inversely associated with myocardial infarction (P < 1.25×10-3), independently of obesity and established risk factors. CONCLUSION Our results suggest that epigenetic changes, in particular altered DNA methylation patterns, may be an intermediate biomarker at the intersection of obesity and obesity-related diseases, and could offer clues as to underlying biological mechanisms.
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Affiliation(s)
- Gianluca Campanella
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Vittorio Krogh
- Fondazione IRCCS-Istituto Nazionale dei Tumori, Milan, Italy
| | - Domenico Palli
- Istituto per lo Studio e la Prevenzione Oncologica (ISPO Toscana), Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Carlotta Sacerdote
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, Azienda Ospedaliera "Civile-M.P. Arezzo", Ragusa, Italy
| | - Giovanni Fiorito
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simonetta Guarrera
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
| | | | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Per Lenner
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Theo M C M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Panagiotis Georgiadis
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Soterios A Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - H Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
- Department of Social and Preventive Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Karen A Lillycrop
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Anne M May
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Charlotte Onland-Moret
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Robert Murray
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Monique Verschuren
- Centre for Prevention and Health Services Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Eiliv Lund
- Department of Community Medicine, University of Tromsø (UiT)-The Artic University of Norway, Tromsø, Norway
| | - Nicolle Mode
- Department of Community Medicine, University of Tromsø (UiT)-The Artic University of Norway, Tromsø, Norway
| | - Torkjel M Sandanger
- Department of Community Medicine, University of Tromsø (UiT)-The Artic University of Norway, Tromsø, Norway
| | - Valentina Fiano
- Department of Medical Sciences, Unit of Cancer Epidemiology-CERMS, University of Turin, Turin, Italy
| | - Morena Trevisan
- Department of Medical Sciences, Unit of Cancer Epidemiology-CERMS, University of Turin, Turin, Italy
| | - Giuseppe Matullo
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Philippe Froguel
- CNRS UMR8199, Pasteur Institute of Lille, Lille University, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.
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9
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Espín-Pérez A, Krauskopf J, Chadeau-Hyam M, van Veldhoven K, Chung F, Cullinan P, Piepers J, van Herwijnen M, Kubesch N, Carrasco-Turigas G, Nieuwenhuijsen M, Vineis P, Kleinjans JCS, de Kok TMCM. Short-term transcriptome and microRNAs responses to exposure to different air pollutants in two population studies. Environ Pollut 2018; 242:182-190. [PMID: 29980036 DOI: 10.1016/j.envpol.2018.06.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/17/2018] [Accepted: 06/17/2018] [Indexed: 05/18/2023]
Abstract
Diesel vehicle emissions are the major source of genotoxic compounds in ambient air from urban areas. These pollutants are linked to risks of cardiovascular diseases, lung cancer, respiratory infections and adverse neurological effects. Biological events associated with exposure to some air pollutants are widely unknown but applying omics techniques may help to identify the molecular processes that link exposure to disease risk. Most data on health risks are related to long-term exposure, so the aim of this study is to investigate the impact of short-term exposure (two hours) to air pollutants on the blood transcriptome and microRNA expression levels. We analyzed transcriptomics and microRNA expression using microarray technology on blood samples from volunteers participating in studies in London, the Oxford Street cohort, and, in Barcelona, the TAPAS cohort. Personal exposure levels measurements of particulate matter (PM10, PM2.5), ultrafine particles (UFPC), nitrogen oxides (NO2, NO and NOx), black carbon (BC) and carbon oxides (CO and CO2) were registered for each volunteer. Associations between air pollutant levels and gene/microRNA expression were evaluated using multivariate normal models (MVN). MVN-models identified compound-specific expression of blood cell genes and microRNAs associated with air pollution despite the low exposure levels, the short exposure periods and the relatively small-sized cohorts. Hsa-miR-197-3p, hsa-miR-29a-3p, hsa-miR-15a-5p, hsa-miR-16-5p and hsa-miR-92a-3p are found significantly expressed in association with exposures. These microRNAs target also relevant transcripts, indicating their potential relevance in the research of omics-biomarkers responding to air pollution. Furthermore, these microRNAs are also known to be associated with diseases previously linked to air pollution exposure including several cancers such lung cancer and Alzheimer's disease. In conclusion, we identified in this study promising compound-specific mRNA and microRNA biomarkers after two hours of exposure to low levels of air pollutants during two hours that suggest increased cancer risks.
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Affiliation(s)
- Almudena Espín-Pérez
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands.
| | - Julian Krauskopf
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Karin van Veldhoven
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Fan Chung
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Paul Cullinan
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jolanda Piepers
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Nadine Kubesch
- Centre for Epidemiology and Screening, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
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10
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Espín-Pérez A, Portier C, Chadeau-Hyam M, van Veldhoven K, Kleinjans JCS, de Kok TMCM. Comparison of statistical methods and the use of quality control samples for batch effect correction in human transcriptome data. PLoS One 2018; 13:e0202947. [PMID: 30161168 PMCID: PMC6117018 DOI: 10.1371/journal.pone.0202947] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/13/2018] [Indexed: 01/26/2023] Open
Abstract
Batch effects are technical sources of variation introduced by the necessity of conducting gene expression analyses on different dates due to the large number of biological samples in population-based studies. The aim of this study is to evaluate the performances of linear mixed models (LMM) and Combat in batch effect removal. We also assessed the utility of adding quality control samples in the study design as technical replicates. In order to do so, we simulated gene expression data by adding “treatment” and batch effects to a real gene expression dataset. The performances of LMM and Combat, with and without quality control samples, are assessed in terms of sensitivity and specificity while correcting for the batch effect using a wide range of effect sizes, statistical noise, sample sizes and level of balanced/unbalanced designs. The simulations showed small differences among LMM and Combat. LMM identifies stronger relationships between big effect sizes and gene expression than Combat, while Combat identifies in general more true and false positives than LMM. However, these small differences can still be relevant depending on the research goal. When any of these methods are applied, quality control samples did not reduce the batch effect, showing no added value for including them in the study design.
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Affiliation(s)
- Almudena Espín-Pérez
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- * E-mail:
| | - Chris Portier
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Karin van Veldhoven
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Jos C. S. Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Theo M. C. M. de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
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11
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Vermeulen R, Saberi Hosnijeh F, Bodinier B, Portengen L, Liquet B, Garrido-Manriquez J, Lokhorst H, Bergdahl IA, Kyrtopoulos SA, Johansson AS, Georgiadis P, Melin B, Palli D, Krogh V, Panico S, Sacerdote C, Tumino R, Vineis P, Castagné R, Chadeau-Hyam M, Botsivali M, Chatziioannou A, Valavanis I, Kleinjans JCS, de Kok TMCM, Keun HC, Athersuch TJ, Kelly R, Lenner P, Hallmans G, Stephanou EG, Myridakis A, Kogevinas M, Fazzo L, De Santis M, Comba P, Bendinelli B, Kiviranta H, Rantakokko P, Airaksinen R, Ruokojarvi P, Gilthorpe M, Fleming S, Fleming T, Tu YK, Lundh T, Chien KL, Chen WJ, Lee WC, Kate Hsiao C, Kuo PH, Hung H, Liao SF. Pre-diagnostic blood immune markers, incidence and progression of B-cell lymphoma and multiple myeloma: Univariate and functionally informed multivariate analyses. Int J Cancer 2018; 143:1335-1347. [PMID: 29667176 PMCID: PMC6100111 DOI: 10.1002/ijc.31536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 12/13/2022]
Abstract
Recent prospective studies have shown that dysregulation of the immune system may precede the development of B‐cell lymphomas (BCL) in immunocompetent individuals. However, to date, the studies were restricted to a few immune markers, which were considered separately. Using a nested case–control study within two European prospective cohorts, we measured plasma levels of 28 immune markers in samples collected a median of 6 years before diagnosis (range 2.01–15.97) in 268 incident cases of BCL (including multiple myeloma [MM]) and matched controls. Linear mixed models and partial least square analyses were used to analyze the association between levels of immune marker and the incidence of BCL and its main histological subtypes and to investigate potential biomarkers predictive of the time to diagnosis. Linear mixed model analyses identified associations linking lower levels of fibroblast growth factor‐2 (FGF‐2 p = 7.2 × 10−4) and transforming growth factor alpha (TGF‐α, p = 6.5 × 10−5) and BCL incidence. Analyses stratified by histological subtypes identified inverse associations for MM subtype including FGF‐2 (p = 7.8 × 10−7), TGF‐α (p = 4.08 × 10−5), fractalkine (p = 1.12 × 10−3), monocyte chemotactic protein‐3 (p = 1.36 × 10−4), macrophage inflammatory protein 1‐alpha (p = 4.6 × 10−4) and vascular endothelial growth factor (p = 4.23 × 10−5). Our results also provided marginal support for already reported associations between chemokines and diffuse large BCL (DLBCL) and cytokines and chronic lymphocytic leukemia (CLL). Case‐only analyses showed that Granulocyte‐macrophage colony stimulating factor levels were consistently higher closer to diagnosis, which provides further evidence of its role in tumor progression. In conclusion, our study suggests a role of growth‐factors in the incidence of MM and of chemokine and cytokine regulation in DLBCL and CLL. What's new? B‐cell lymphomas (BCL) are frequent in immunocompromised individuals, but most BCL cases are thought to occur as a consequence of minor immune perturbations in otherwise immunocompetent individuals. Here the authors prospectively examined a panel of immune markers in the blood from 268 patients afflicted with BCL and paired controls. The data uncover a functional role for growth factors (i.e. FGF‐2, TGF‐alpha) in the incidence and progression of multiple myeloma, a BCL subtype, and underscore the importance of chemokine and cytokine regulation in diffuse large B‐cell lymphoma and chronic lymphocytic leukemia.
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Affiliation(s)
- Roel Vermeulen
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Fatemeh Saberi Hosnijeh
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,Immunology Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Bodinier
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Lützen Portengen
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Benoît Liquet
- Laboratoire de Mathématiques et de leurs Applications, Université de Pau et des Pays de l'Adour, UMR CNRS, Pau, France.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, Australia
| | - Javiera Garrido-Manriquez
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Henk Lokhorst
- Department of Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ingvar A Bergdahl
- Department of Public Health and Clinical Medicine, and Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | | | - Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Domenico Palli
- The Institute for Cancer Research and Prevention, Florence, Italy
| | - Vittorio Krogh
- Fondazione IRCCS-Instituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Frederico II, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Cancer registry and Histopathology Unit, Azienda Ospedaliera 'Civile-M.P.Arezzo', Ragusa, Italy
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,HuGeF Foundation, Torino, Italy
| | - Raphaële Castagné
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Marc Chadeau-Hyam
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | | | - Maria Botsivali
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ioannis Valavanis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Hector C Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Institute of Reproductive and Developmental Biology (IRDB), Hammersmith Hospital, London, United Kingdom
| | - Toby J Athersuch
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rachel Kelly
- Immunology Department, Erasmus University Medical Center, Rotterdam, The Netherlands.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Per Lenner
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Goran Hallmans
- Nutrition Research, Department of Public Health and Clinical Medicine, and Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Antonis Myridakis
- Environmental Chemical Processes Laboratory, University of Crete, Heraklion, Greece
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Yu-Kang Tu
- University of Leeds, Leeds, United Kingdom
| | | | | | - Wei J Chen
- National Taiwan University, Taipei, Taiwan
| | | | | | | | - Hung Hung
- National Taiwan University, Taipei, Taiwan
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12
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van Breda SGJ, de Kok TMCM. Smart Combinations of Bioactive Compounds in Fruits and Vegetables May Guide New Strategies for Personalized Prevention of Chronic Diseases. Mol Nutr Food Res 2017; 62. [PMID: 29108107 DOI: 10.1002/mnfr.201700597] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/19/2017] [Indexed: 12/24/2022]
Abstract
There is ample scientific evidence suggesting that the health benefits of eating the right amounts of a variety of vegetables and fruit are the consequence of the combined action of different phytochemicals. The present review provides an update of the scientific literature on additive and synergistic effects of mixtures of phytochemicals. Most research has been carried out in in vitro systems in which synergistic or additive effects have been established on the level of cell proliferation, apoptosis, antioxidant capacity, and tumor incidence, accompanied by changes in gene and protein expression in relevant pathways underlying molecular mechanisms of disease prevention. The number of human dietary intervention studies investigating complex mixtures of phytochemicals is relatively small, but showing promising results. These studies have demonstrated that combining transcriptomic data with phenotypic markers provide insight into the relevant cellular processes which contribute to the antioxidant response of complex mixtures of phytochemicals. Future studies should be designed as short-term studies testing different combinations of vegetables and fruit, in which markers for disease outcome as well as molecular ('omics)-markers and genetic variability between subjects are included. This will create new opportunities for food innovation and the development of more personalized strategies for prevention of chronic diseases.
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Affiliation(s)
- Simone G J van Breda
- Department of Toxicogenomics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
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13
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Wolters JEJ, van Breda SGJ, Caiment F, Claessen SM, de Kok TMCM, Kleinjans JCS. Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes. Chem Res Toxicol 2017; 30:1847-1854. [PMID: 28853863 PMCID: PMC5645762 DOI: 10.1021/acs.chemrestox.7b00171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Valproic
acid (VPA) is one of the most widely prescribed antiepileptic
drugs in the world. Despite its pharmacological importance, it may
cause liver toxicity and steatosis through mitochondrial dysfunction.
The aim of this study is to further investigate VPA-induced mechanisms
of steatosis by analyzing changes in patterns of methylation in nuclear
DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human
hepatocytes (PHHs) were exposed to an incubation concentration of
VPA that was shown to cause steatosis without inducing overt cytotoxicity.
VPA was administered daily for 5 days, and this was followed by a
3 day washout (WO). Methylated DNA regions (DMRs) were identified
by using the methylated DNA immunoprecipitation–sequencing
(MeDIP-seq) method. The nDNA DMRs after VPA treatment could indeed
be classified into oxidative stress- and steatosis-related pathways.
In particular, networks of the steatosis-related gene EP300 provided novel insight into the mechanisms of toxicity induced by
VPA treatment. Furthermore, we suggest that VPA induces a crosstalk
between nDNA hypermethylation and mtDNA hypomethylation that plays
a role in oxidative stress and steatosis development. Although most
VPA-induced methylation patterns appeared reversible upon terminating
VPA treatment, 31 nDNA DMRs (including 5 zinc finger protein genes)
remained persistent after the WO period. Overall, we have shown that
MeDIP-seq analysis is highly informative in disclosing novel mechanisms
of VPA-induced toxicity in PHHs. Our results thus provide a prototype
for the novel generation of interesting methylation biomarkers for
repeated dose liver toxicity in vitro.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
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Vlaanderen J, Leenders M, Chadeau-Hyam M, Portengen L, Kyrtopoulos SA, Bergdahl IA, Johansson AS, Hebels DDGAJ, de Kok TMCM, Vineis P, Vermeulen RCH. Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage. BMC Genomics 2017; 18:239. [PMID: 28320322 PMCID: PMC5360061 DOI: 10.1186/s12864-017-3627-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
Background We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched controls. We hypothesized that a large fraction of these markers were likely related to early disease manifestations. Here we aim to gain a better understanding of the natural history of the identified markers by comparing results from our prediagnostic analysis, the only prediagnostic analysis to date, to results obtained from a meta-analysis of a series of publically available transcriptomics profiles obtained in incident CLL cases and controls. Results We observed considerable overlap between the results from our prediagnostic study and the clinical CLL signals (p-value for overlap Bonferroni significant markers 0.01; p-value for overlap nominal significant markers < 2.20e-16). We observed similar patterns with time to diagnosis and similar functional annotations for the markers that were identified in both settings compared to the markers that were only identified in the prediagnostic study. These results suggest that both gene sets operate in similar pathways. Conclusion An overlap exists between expression levels of genes predictive of CLL identified in prediagnostic blood and expression levels of genes associated to CLL at the clinical stage. Our analysis provides insight in a set of genes for which expression levels can be used to follow the time-course of the disease; providing an opportunity to study CLL progression in more detail in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3627-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jelle Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Max Leenders
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Marc Chadeau-Hyam
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands.,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Lützen Portengen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Soterios A Kyrtopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | | | | | - Theo M C M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Molecular and Genetic Epidemiology, Human Genetics Foundation (HuGeF), Turin, Italy
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands. .,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK. .,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
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Wolters JEJ, van Herwijnen MHM, Theunissen DHJ, Jennen DGJ, Van den Hof WFPM, de Kok TMCM, Schaap FG, van Breda SGJ, Kleinjans JCS. Integrative “-Omics” Analysis in Primary Human Hepatocytes Unravels Persistent Mechanisms of Cyclosporine A-Induced Cholestasis. Chem Res Toxicol 2016; 29:2164-2174. [DOI: 10.1021/acs.chemrestox.6b00337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jarno E. J. Wolters
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Marcel H. M. van Herwijnen
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Daniel H. J. Theunissen
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Danyel G. J. Jennen
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Wim F. P. M. Van den Hof
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Theo M. C. M. de Kok
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Frank G. Schaap
- Department of Surgery, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Simone G. J. van Breda
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Jos C. S. Kleinjans
- Department of Toxicogenomics,
GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
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van Breda SGJ, Wilms LC, Gaj S, Jennen DGJ, Briedé JJ, Kleinjans JCS, de Kok TMCM. The exposome concept in a human nutrigenomics study: evaluating the impact of exposure to a complex mixture of phytochemicals using transcriptomics signatures. Mutagenesis 2015; 30:723-31. [PMID: 25711498 DOI: 10.1093/mutage/gev008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The application of transcriptome analyses in molecular epidemiology studies has become a promising tool in order to evaluate the impact of environmental exposures. These analyses have a great value in establishing the exposome, the totality of human exposures, both by identifying the chemical nature of the exposures and the induced molecular responses. Transcriptomic signatures can be regarded as biomarker of exposure as well as markers of effect which reflect the interaction between individual genetic background and exposure levels. However, the biological interpretation of modulated gene expression profiles is a challenging task and translating affected molecular pathways into risk assessment, for instance in terms of cancer promoting or disease preventing responses, is a far from standardised process. Here, we describe the in-depth analyses of the gene expression responses in a human dietary intervention in which the interaction between genotype and exposure to a blueberry-apple juice containing a complex mixture of phytochemicals is investigated. We also describe how data on differences in genetic background combined with different effect markers can provide a better understanding of gene-environment interactions. Pathway analyses of differentially expressed genes in combination with gene were used to identify complex but strong changes in several biological processes like immune response, cell adhesion, lipid metabolism and apoptosis. These observed changes may lead to upgraded growth control, induced immunity, reduced platelet aggregation and activation, diminished production of reactive oxidative species by platelets, blood glucose homeostasis, regulation of blood lipid levels and increased apoptosis. Our findings demonstrate that applying transcriptomics to well-controlled human dietary intervention studies can provide insight into mechanistic pathways involved in disease prevention by dietary factors.
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Affiliation(s)
- Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Lonneke C Wilms
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Stan Gaj
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Jacob J Briedé
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
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Jiang J, Briedé JJ, Jennen DGJ, Van Summeren A, Saritas-Brauers K, Schaart G, Kleinjans JCS, de Kok TMCM. Increased mitochondrial ROS formation by acetaminophen in human hepatic cells is associated with gene expression changes suggesting disruption of the mitochondrial electron transport chain. Toxicol Lett 2015; 234:139-50. [PMID: 25704631 DOI: 10.1016/j.toxlet.2015.02.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/15/2015] [Accepted: 02/17/2015] [Indexed: 12/16/2022]
Abstract
Acetaminophen (APAP) overdosage results in hepatotoxicity, but the underlying molecular mechanisms are still not completely understood. In the current study, we focused on mitochondrial-specific oxidative liver injury induced by APAP exposure. Owning to genetic polymorphisms in the CYP2E1 gene or varying inducibility by xenobiotics, the CYP2E1 mRNA level and protein activity vary extensively among individuals. As CYP2E1 is a known ROS generating enzyme, we chose HepG2 to minimize CYP2E1-induced ROS formation, which will help us better understand the APAP induced mitochondrial-specific hepatotoxicity in a subpopulation with low CYP2E1 activity. HepG2 cells were exposed to a low and toxic dose (0.5 and 10mM) of APAP and analyzed at four time points for genome-wide gene expression. Mitochondria were isolated and electron spin resonance spectroscopy was performed to measure the formation of mitochondrial ROS. The yield of ATP was measured to confirm the impact of the toxic dose of APAP on cellular energy production. Our results indicate that 10mM APAP significantly influences the expression of mitochondrial protein-encoding genes in association with an increase in mitochondrial ROS formation. Additionally, 10mM APAP affects the expression of genes encoding the subunits of electron transport chain (ETC) complexes, which may alter normal mitochondrial functions by disrupting the assembly, stability, and structural integrity of ETC complexes, leading to a measurable depletion of ATP, and cell death. The expression of mitochondrium-specific antioxidant enzyme, SOD2, is reduced which may limit the ROS scavenging ability and cause imbalance of the mitochondrial ROS homeostasis. Overall, transcriptome analysis reveals the molecular processes involved in the observed APAP-induced increase of mitochondrial ROS formation and the associated APAP-induced oxidative stress.
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Affiliation(s)
- Jian Jiang
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands.
| | - Jacob J Briedé
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Anke Van Summeren
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Karen Saritas-Brauers
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Gert Schaart
- Department of Human Movement Sciences, School of nutrition, Toxicology and metabolism (NUTRIM) Maastricht University Medical Centre, 6200 MD Maastricht, the Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, the Netherlands
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Hebels DGAJ, van Herwijnen MHM, Brauers KJJ, de Kok TMCM, Chalkiadaki G, Kyrtopoulos SA, Kleinjans JCS. Elimination of heparin interference during microarray processing of fresh and biobank-archived blood samples. Environ Mol Mutagen 2014; 55:482-91. [PMID: 24740823 DOI: 10.1002/em.21869] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
In the context of environmental health research, biobank blood samples have recently been identified as suitable for high-throughput omics analyses enabling the identification of new biomarkers of exposure and disease. However, blood samples containing the anti-coagulant heparin could complicate transcriptomic analysis because heparin may inhibit RNA polymerase causing inefficient cRNA synthesis and fluorophore labelling. We investigated the inhibitory effect of heparin and the influence of storage conditions (0 or 3 hr bench times, storage at room temperature or -80°C) on fluorophore labelling in heparinized fresh human buffy coat and whole blood biobank samples during the mRNA work-up protocol for microarray analysis. Subsequently, we removed heparin by lithium chloride (LiCl) treatment and performed a quality control analysis of LiCl-treated biobank sample microarrays to prove their suitability for downstream data analysis. Both fresh and biobank samples experienced varying degrees of heparin-induced inhibition of fluorophore labelling, making most samples unusable for microarray analysis. RNA derived from EDTA and citrate blood was not inhibited. No effect of bench time was observed but room temperature storage gave slightly better results. Strong correlations were observed between original blood sample RNA yield and the amount of synthesized cRNA. LiCl treatment restored sample quality to normal standards in both fresh and biobank samples and the previously identified correlations disappeared. Microarrays hybridized with LiCl-treated biobank samples were of excellent quality with no identifiable influence of heparin. We conclude that, to obtain high quality results, in most cases heparin removal is essential in blood-derived RNA samples intended for microarray analysis.
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Affiliation(s)
- Dennie G A J Hebels
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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van Breda SGJ, Wilms LC, Gaj S, Jennen DGJ, Briedé JJ, Helsper JP, Kleinjans JCS, de Kok TMCM. Can transcriptomics provide insight into the chemopreventive mechanisms of complex mixtures of phytochemicals in humans? Antioxid Redox Signal 2014; 20:2107-13. [PMID: 24328558 PMCID: PMC3994912 DOI: 10.1089/ars.2013.5528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Blueberries contain relatively large amounts of different phytochemicals, which are suggested to have chemopreventive properties, but little information is available on the underlying molecular modes of action. This study investigates whole genome gene expression changes in lymphocytes of 143 humans after a 4-week blueberry-apple juice dietary intervention. Differentially expressed genes and genes correlating with the extent of antioxidant protection were identified in four subgroups. The magnitude of the preventive effect after the intervention differed between these four subgroups. Furthermore, subjects in two groups carried genetic polymorphisms that were previously found to influence the chemopreventive response. Pathway analysis of the identified genes showed strong but complex gene expression changes in pathways signaling for apoptosis, immune response, cell adhesion, and lipid metabolism. These pathways indicate increased apoptosis, upgraded growth control, induced immunity, reduced platelet aggregation and activation, blood glucose homeostasis, and regulation of fatty acid metabolism. Based on these observations, we hypothesize that combining transcriptomic data with phenotypic markers of oxidative stress may provide insight into the relevant cellular processes and genetic pathways, which contribute to the antioxidant response of complex mixtures of phytochemicals, such as found in blueberry-apple juice.
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Affiliation(s)
- Simone G J van Breda
- 1 Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , Maastricht, The Netherlands
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Hogervorst JGF, de Bruijn-Geraets D, Schouten LJ, van Engeland M, de Kok TMCM, Goldbohm RA, van den Brandt PA, Weijenberg MP. Dietary acrylamide intake and the risk of colorectal cancer with specific mutations in KRAS and APC. Carcinogenesis 2014; 35:1032-8. [PMID: 24398672 DOI: 10.1093/carcin/bgu002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acrylamide, a probable human carcinogen, is present in heat-treated carbohydrate-rich foods. Epidemiological studies have not shown a clear association between acrylamide intake and colorectal cancer (CRC) risk. This may be due to the molecular heterogeneity in colorectal tumors, which was not taken into consideration before. Since the acrylamide metabolite glycidamide induces specific DNA mutations in rodents, we investigated whether acrylamide is associated with CRC risk characterized by mutations in Kirsten-ras (KRAS) and adenomatous polyposis coli (APC); key genes in colorectal carcinogenesis. This case-cohort analysis, within the Netherlands Cohort Study on diet and cancer, was based on 7.3 years of follow-up. Acrylamide intake was assessed with a food frequency questionnaire. Mutation analysis of codons 1286-1520 in exon 15 in APC and codons 12 and 13 in exon 1 in KRAS was performed on tumor tissue of 733 cases. Hazard ratios (HR) were calculated using Cox proportional hazards analysis. Among men, acrylamide intake was statistically significantly associated with an increased risk of particularly tumors with an activating KRAS mutation {HR fourth versus first quartile: 2.12 [95% confidence interval (CI): 1.16-3.87], P trend: 0.01}. Among women, acrylamide intake was statistically significantly associated with a decreased risk of particularly tumors with a truncating APC mutation (fourth versus first quartile: 0.47 (95% CI: 0.23-0.94), P trend: 0.02), but only in the highest quartile of intake. This is the first study to show that acrylamide might be associated with CRC with specific somatic mutations, differentially in men and women. More research is needed to corroborate or refute these findings.
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Hebels DGAJ, Georgiadis P, Keun HC, Athersuch TJ, Vineis P, Vermeulen R, Portengen L, Bergdahl IA, Hallmans G, Palli D, Bendinelli B, Krogh V, Tumino R, Sacerdote C, Panico S, Kleinjans JCS, de Kok TMCM, Smith MT, Kyrtopoulos SA. Performance in omics analyses of blood samples in long-term storage: opportunities for the exploitation of existing biobanks in environmental health research. Environ Health Perspect 2013; 121:480-487. [PMID: 23384616 PMCID: PMC3620742 DOI: 10.1289/ehp.1205657] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 02/04/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. OBJECTIVES We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. METHODS We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at -80oC or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. RESULTS Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of time-in-storage was observed in samples stored over a period of 13-17 years. CONCLUSIONS Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.
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Affiliation(s)
- Dennie G A J Hebels
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
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Kok TMCMD, Breda SGJV, Briedé JJ. Genomics-based identification of molecular mechanisms behind the cancer preventive action of phytochemicals: potential and challenges. Curr Pharm Biotechnol 2012; 13:255-64. [PMID: 21466423 DOI: 10.2174/138920112798868601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/03/2010] [Accepted: 11/04/2010] [Indexed: 11/22/2022]
Abstract
High intake of dietary phytochemicals, non-nutritive compounds found in vegetables and fruits, has been associated with a decreased risk of various types of cancer. With the introduction of new "omics" research approaches, technologies providing large scale and holistic data on biological responses to dietary or environmental factors, our understanding of the molecular mechanisms of the preventive action of individual phytochemicals has started to increase rapidly. This understanding contributes to the biological plausibility of the observed link between fruit and vegetable consumption and decreased cancer risk in epidemiological studies. In this mini-review, we present an overview of the characteristics of the different "omics" techniques, with emphasis on transcriptomics, epigenetics, and the analysis of single nucleotide polymorphisms, and evaluate their implications in studies on dietary phytochemicals. We focus particularly on studies in human cell cultures in vitro and in human population studies and discuss the potential and different challenges offered by each technique, as well as future perspectives on applications of these new tools in nutritional genomics research.
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Affiliation(s)
- Theo M C M de Kok
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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Hebels DGAJ, Briedé JJ, Khampang R, Kleinjans JCS, de Kok TMCM. Radical Mechanisms in Nitrosamine- and Nitrosamide-Induced Whole-Genome Gene Expression Modulations in Caco-2 Cells. Toxicol Sci 2010; 116:194-205. [DOI: 10.1093/toxsci/kfq121] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Briedé JJ, van Delft JMH, de Kok TMCM, van Herwijnen MHM, Maas LM, Gottschalk RWH, Kleinjans JCS. Global gene expression analysis reveals differences in cellular responses to hydroxyl- and superoxide anion radical-induced oxidative stress in caco-2 cells. Toxicol Sci 2009; 114:193-203. [PMID: 20044591 DOI: 10.1093/toxsci/kfp309] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reactive oxygen species-induced oxidative stress in the colon is involved in inflammatory bowel diseases and suggested to be associated with colorectal cancer risk. However, our insight in molecular responses to different oxygen radicals is still fragmentary. Therefore, we studied global gene expression by an extensive time series (0.08, 0.25, 0.5, 1, 2, 4, 8, 16, or 24 h) analyses in human colon cancer (caco-2) cells after exposure to H(2)O(2) or the superoxide anion donor menadione. Differences in gene expression were investigated by hybridization on two-color microarrays against nonexposed time-matched control cells. Next to gene expression, correlations with related phenotypic markers (8-oxodG levels and cell cycle arrest) were investigated. Gene expression analysis resulted in 1404 differentially expressed genes upon H(2)O(2) challenge and 979 genes after menadione treatment. Further analysis of gene expression data revealed how these oxidant responses can be discriminated. Time-dependent coregulated genes immediately showed a pulse-like response to H(2)O(2), while the menadione-induced expression is not restored over 24 h. Pathway analyses demonstrated that H(2)O(2) immediately influences pathways involved in the immune function, while menadione constantly regulated cell cycle-related pathways Altogether, this study offers a novel and detailed insight in the similarities and differences of the time-dependent oxidative stress responses induced by the oxidants H(2)O(2) and menadione and show that these can be discriminated regarding their modulation of particular colon carcinogenesis-related mechanisms.
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Affiliation(s)
- Jacob J Briedé
- Netherlands Toxicogenomics Centre, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6200 MD Maastricht, The Netherlands.
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de Kok TMCM, de Waard P, Wilms LC, van Breda SGJ. Antioxidative and antigenotoxic properties of vegetables and dietary phytochemicals: The value of genomics biomarkers in molecular epidemiology. Mol Nutr Food Res 2009; 54:208-17. [DOI: 10.1002/mnfr.200900288] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Hebels DGAJ, Jennen DGJ, Kleinjans JCS, de Kok TMCM. Molecular signatures of N-nitroso compounds in Caco-2 cells: implications for colon carcinogenesis. Toxicol Sci 2009; 108:290-300. [PMID: 19221148 DOI: 10.1093/toxsci/kfp035] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
N-nitroso compounds (NOC) are genotoxic, carcinogenic to animals, and may play a role in human cancer development. Because the gastro-intestinal tract is an important route of exposure through endogenous nitrosation, we hypothesize that NOC exposure targets genetic processes relevant in colon carcinogenesis. To investigate these genomic responses, we analyzed the transcriptomic effects of genotoxic concentrations of two nitrosamides, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG, 1 microM) and N-methyl-N-nitrosurea (MNU, 1 mM), and four nitrosamines, N-nitrosodiethylamine (NDEA, 50mM), N-nitrosodimethylamine (NDMA, 100 mM), N-nitrosopiperidine (NPIP, 40 mM), and N-nitrosopyrrolidine (NPYR, 100mM), in the human colon carcinoma cell line Caco-2. Gene Ontology gene group, consensus motif gene group and biological pathway analysis revealed that nitrosamides had little effect on gene expression after 24 h of exposure, whereas nitrosamines had a strong impact on the transcriptomic profile. Analyses showed modifications of cell cycle regulation and apoptosis pathways for nitrosamines which was supported by flow cytometric analysis. We found additional modifications in gene groups and pathways of oxidative stress and inflammation, which suggest an increase in oxidative stress and proinflammatory immune response upon nitrosamine exposure, although less distinct for NDMA. Furthermore, NDEA, NPIP, and NPYR most strongly affected several developmental motif gene groups and pathways, which may influence developmental processes. Many of these pathways and gene groups are implicated in the carcinogenic process and their modulation by nitrosamine exposure may therefore influence the development of colon cancer. In summary, our study has identified pathway modifications in human colon cells which may be associated with cancer risk of nitrosamine exposure in the human colon.
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Affiliation(s)
- Dennie G A J Hebels
- Department of Health Risk Analysis and Toxicology, Maastricht University, 6200 MD Maastricht, The Netherlands.
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van Breda SGJ, de Kok TMCM, van Delft JHM. Mechanisms of colorectal and lung cancer prevention by vegetables: a genomic approach. J Nutr Biochem 2008; 19:139-57. [PMID: 17651960 DOI: 10.1016/j.jnutbio.2007.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/12/2007] [Accepted: 04/03/2007] [Indexed: 11/15/2022]
Abstract
Colorectal cancer (CRC) and lung cancer (LC) occur at high incidence, and both can be effectively prevented by dietary vegetable consumption. This makes these two types of cancer highly suitable for elucidating the underlying molecular mechanisms of cancer chemoprevention. Numerous studies have shown that vegetables exert their beneficial effects through various different mechanisms, but effects on the genome level remain mostly unclear. This review evaluates current knowledge on the mechanisms of CRC and LC prevention by vegetables, thereby focusing on the modulation of gene and protein expressions. The majority of the effects found in the colon are changes in the expression of genes and proteins involved in apoptosis, cell cycle, cell proliferation and intracellular defense, in favor of reduced CRC risk. Furthermore, vegetables and vegetable components changed the expression of many more genes and proteins involved in other pathways for which biologic meaning is less clear. The number of studies investigating gene and protein expression changes in the lungs is limited to only a few in vitro and animal studies. Data from these studies show that mostly genes involved in biotransformation, apoptosis and cell cycle regulation are affected. In both colon and lungs, genomewide analyses of gene and protein expression changes by new genomics and proteomics technologies, as well as the investigation of whole vegetables, are few in number. Further studies applying these 'omics' approaches are needed to provide more insights on affected genetic/biologic pathways and, thus, in molecular mechanisms by which different chemopreventive compounds can protect against carcinogenesis. Particularly studies with combinations of phytochemicals and whole vegetables are needed to establish gene expression changes in the colon, but especially in the lungs.
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Affiliation(s)
- Simone G J van Breda
- Department of Health Risk Analysis and Toxicology, Nutrition and Toxicology Research Institute, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
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de Waard PWJ, de Kok TMCM, Maas LM, Peijnenburg AACM, Hoogenboom RLAP, Aarts JMMJG, van Schooten FJ. Influence of TCDD and natural Ah receptor agonists on benzo[a]pyrene-DNA adduct formation in the Caco-2 human colon cell line. Mutagenesis 2007; 23:67-73. [PMID: 18065724 DOI: 10.1093/mutage/gem046] [Citation(s) in RCA: 20] [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] [Indexed: 11/13/2022] Open
Abstract
Several compounds originating from cruciferous vegetables and citrus fruits bind to and activate the aryl hydrocarbon receptor (AhR). This receptor plays an important role in the toxicity of the known tumour promoter and potent AhR-agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, vegetables and fruits are generally considered as healthy. Therefore, besides the AhR activation, the natural AhR agonists (NAhRAs) are assumed to show other health-concerning effects. AhR activation induces several cytochrome P450 phase I enzymes involved, e.g. in the bioactivation of carcinogenic polycyclic aromatic hydrocarbons, like benzo[a]pyrene (BaP), and may as such stimulate DNA adduct formation of those compounds. Therefore, the influence of TCDD, indolo[3,2-b]carbazole (ICZ, an NAhRA originating from cruciferous vegetables) and an NAhRA-containing extract of grapefruit juice (GJE) on BaP-DNA adduct formation in the human Caco-2 cell line was studied. Also, we investigated if different effects of TCDD, ICZ and GJE on adduct formation could be related to the modulation of transcription of biotransformation- and DNA-repair enzymes. Co-exposure to high AhR-activating concentrations of both TCDD and ICZ significantly reduced the amount of BaP-DNA adducts at 0.1 microM BaP, while at higher concentrations of BaP no influence was observed. In contrast, exposure to 0.1 microM BaP combined with GJE showed a significant increase in BaP-DNA adducts, and a significant decrease at 0.3 and 1 microM BaP. These differences could not be related to transcription of the phase I and II enzymes CYP1A1, CYP1B1, NQO1, GSTP1 and UGT1A6 or to transcription of the nucleotide excision repair enzymes ERCC1, XPA, XPC, XPF and XPG. We conclude that ICZ showed a similar effect on BaP-DNA adduct formation than TCDD, while GJE influenced the adduct formation in a different way. The difference in the influence on adduct formation may be due to effects at the level of enzyme activity, rather than gene expression.
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Affiliation(s)
- Pim W J de Waard
- Department of Health Risk Analysis and Toxicology, Maastricht University, PO box 616, 6200 MD Maastricht, The Netherlands
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Wilms LC, Claughton TA, de Kok TMCM, Kleinjans JCS. GSTM1 and GSTT1 polymorphism influences protection against induced oxidative DNA damage by quercetin and ascorbic acid in human lymphocytes in vitro. Food Chem Toxicol 2007; 45:2592-6. [PMID: 17706336 DOI: 10.1016/j.fct.2007.06.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 01/26/2007] [Accepted: 06/25/2007] [Indexed: 11/28/2022]
Abstract
UNLABELLED Antioxidants are of major importance in the protection against cellular oxidative damage caused by endogenous as well as exogenous free radicals. This study aims to establish the impact of genetic polymorphisms in GSTM1 and GSTT1, which encode for enzymatic antioxidative defence, on H(2)O(2)-induced oxidative DNA damage and on the effectiveness of quercetin and ascorbic acid in preventing this induced damage in human lymphocytes. Lymphocytes from 12 healthy volunteers were pre-incubated either with 10 microM of quercetin or with 10 microM of ascorbic acid, and exposed to 25 microM H(2)O(2) for 1h. The induction of oxidative DNA damage was quantified using the Comet assay. Genotyping of these 12 subjects showed that six individuals were GSTM1+ and six were GSTM1-; eight were GSTT1+ and four GSTT1-. RESULTS Baseline levels of oxidative DNA damage did not differ between GSTM1 or GSTT1 variants and their respective wild types. Also with respect to ex vivo induced levels of oxidative DNA damage, no significant difference was seen between variants and wild types of both genotypes. The protection against H(2)O(2)-induced oxidative DNA damage by quercetin was significantly higher in GSTT1 wild types than in GSTT1 variants (57% and 9% decrease, respectively; p=0.01); furthermore, GSTT1 wild types were protected against induced oxidative DNA damage by ascorbic acid pre-incubation while GSTT1 variants showed an increase of damage (16% decrease vs. 91% increase; p=0.01). For GSTM1 variants and wild types, observed differences in protective effects of quercetin or ascorbic acid were not statistically significant. Overall, quercetin proves to be better in protecting human lymphocytes in vitro against oxidative DNA damage upon H(2)O(2) challenge than ascorbic acid.
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Affiliation(s)
- Lonneke C Wilms
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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de Kok TMCM, Driece HAL, Hogervorst JGF, Briedé JJ. Toxicological assessment of ambient and traffic-related particulate matter: a review of recent studies. Mutat Res 2006; 613:103-22. [PMID: 16949858 DOI: 10.1016/j.mrrev.2006.07.001] [Citation(s) in RCA: 242] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 07/17/2006] [Accepted: 07/17/2006] [Indexed: 11/24/2022]
Abstract
Particulate air pollution (PM) is an important environmental health risk factor for many different diseases. This is indicated by numerous epidemiological studies on associations between PM exposure and occurrence of acute respiratory infections, lung cancer and chronic respiratory and cardiovascular diseases. The biological mechanisms behind these associations are not fully understood, but the results of in vitro toxicological research have shown that PM induces several types of adverse cellular effects, including cytotoxicity, mutagenicity, DNA damage and stimulation of proinflammatory cytokine production. Because traffic is an important source of PM emission, it seems obvious that traffic intensity has an important impact on both quantitative and qualitative aspects of ambient PM, including its chemical, physical and toxicological characteristics. In this review, the results are summarized of the most recent studies investigating physical and chemical characteristics of ambient and traffic-related PM in relation to its toxicological activity. This evaluation shows that, in general, the smaller PM size fractions (<PM(10)) have the highest toxicity, contain higher concentrations of extractable organic matter (comprising a wide spectrum of chemical substances), and possess a relatively high radical-generating capacity. Also, associations between chemical characteristics and PM toxicity tend to be stronger for the smaller PM size fractions. Most importantly, traffic intensity does not always explain local differences in PM toxicity, and these differences are not necessarily related to PM mass concentrations. This implies that PM regulatory strategies should take PM-size fractions smaller than PM(10) into account. Therefore, future research should aim at establishing the relationship between toxicity of these smaller fractions in relation to their specific sources.
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Affiliation(s)
- Theo M C M de Kok
- Department of Health Risk Analysis and Toxicology, Maastricht University, P.O. Box 616, Maastricht, The Netherlands.
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Abstract
The aqueous phase of feces (fecal water) has been suggested to mediate the effects of diet on colon carcinogenesis. We determined whether human fecal water samples, of varying genotoxic potential, had the capacity to alter adhesion of intestinal bacteria to intestinal (Caco-2) cells. Genotoxicity of fecal water samples was measured using the single-cell gel electrophoresis assay ("comet" assay), and bacterial adhesion was measured using a well-established model system. Fecal water genotoxicity was found to correlate positively with inhibition of adhesion of Escherichia coli strains, Salmonella species, and Enterococcus faecium to Caco-2 cells. The presence of fecal water samples did not interfere with adhesion of Bacteroides and Lactobacillus species. Inhibition of adhesion by fecal water was not due to cytotoxicity to Caco-2 cells as cytotoxicities of most fecal water samples were similar, nor was the inhibitory effect due to bacteriotoxicity as toxicity of fecal waters in the 10 strains of bacteria studied was not detected. Results indicate that components in fecal water may alter adhesion of intestinal bacteria to intestinal cell surfaces and that this effect may be correlated to the genotoxic potential of fecal water. This may have consequences for dietary effects on colon carcinogenesis.
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Affiliation(s)
- Yuan-Kun Lee
- Department of Microbiology, Faculty of Medicine, National University of Singapore
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Hogervorst JGF, de Kok TMCM, Briedé JJ, Wesseling G, Kleinjans JCS, van Schayck CP. Relationship between radical generation by urban ambient particulate matter and pulmonary function of school children. J Toxicol Environ Health A 2006; 69:245-62. [PMID: 16263695 DOI: 10.1080/15287390500227431] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The mechanisms by which particulate matter (PM) produces adverse effects on the respiratory system, such as pulmonary dysfunction in children, are largely unknown. However, oxidative stress is thought to play an important role. Various chemical compounds in ambient particulate matter, including transition metals and aromatic organic compounds, may contribute to adverse effects through intrinsic generation of reactive oxygen species (ROS). It was hypothesized that ROS generation by PM, as determined through electron spin resonance (ESR) spectroscopy, may be negatively associated with pulmonary function in school children. PM(2.5), PM(10), and total suspended particulates (TSP) were sampled at the playgrounds of six elementary schools in the city of Maastricht, the Netherlands. All children (8-13 yr) from the six schools were asked to undergo spirometry. Multivariate linear regression models were constructed to evaluate associations between oxygen radical formation by PM and lung function. The radical-generating capacity per microgram PM correlated negatively to forced expiratory volume in 1 s (FEV(1)) and forced expiratory flow at 50% (FEF(50%)) of forced vital capacity (FVC). The data indicate that chemical features that contribute to intrinsic generation of ROS may be relevant for PM risk assessment.
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Moonen HJJ, Moonen EJC, Maas L, Dallinga JW, Kleinjans JCS, de Kok TMCM. CYP1A2 and NAT2 genotype/phenotype relations and urinary excretion of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in a human dietary intervention study. Food Chem Toxicol 2004; 42:869-78. [PMID: 15110095 DOI: 10.1016/j.fct.2004.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 01/23/2004] [Indexed: 11/24/2022]
Abstract
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a mutagenic and carcinogenic heterocyclic amine formed during ordinary cooking, and is subsequently metabolically activated by cytochrome P4501A2 (CYP1A2) and N-acetyltransferase 2 (NAT2). Respective genes encoding for these enzymes, display polymorphic distribution in the human population and are thus believed to cause interindividual differences in cancer risk susceptibility. The present study investigated the influence of dietary exposure and CYP1A2 and NAT2 genotypes and phenotypes on differential urinary PhIP excretion levels in 71 human volunteers after consumption of either a high (7.4 ng/g) or low (1.7 ng/g) dose of PhIP. Urinary PhIP excretion levels were found to reflect recent dietary exposure levels, with average levels of 174% (high dose group) and 127% (low dose group), as compared to pre-feed levels. Urinary caffeine metabolite ratios were significantly different between the two NAT2 genotypes, whereas for CYP1A2, the apparent difference in metabolic ratios between the genotypes was statistically non-significant. Significant correlations were firstly found between the CYP1A2-164A-->C (CYP1A2*1F) polymorphism and differential urinary PhIP excretion levels. Although the found correlations are driven primarily by a small number of subjects possessing the homozygous variant constellation, the strong influence of this genotype indicates that the CYP1A2*1F polymorphism could play an important role in human cancer risk susceptibility.
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Affiliation(s)
- Harald J J Moonen
- Department of Health Risk Analysis and Toxicology, University of Maastricht, PO Box 616, 6200 MD Maastricht, The Netherlands.
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Kleinjans JCS, van Herwijnen MHM, van Maanen JMS, Maas LM, de Kok TMCM, Moonen HJJ, Briedé JJ. In vitro investigations into the interaction of -carotene with DNA: evidence for the role of carbon-centered free radicals. Carcinogenesis 2004; 25:1249-56. [PMID: 14988220 DOI: 10.1093/carcin/bgh125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [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: 11/13/2022] Open
Abstract
Supplementation by beta-carotene has unexpectedly appeared to increase lung cancer risk among smokers. In order to explain this it has been suggested that at high serum levels of beta-carotene, prooxidant characteristics of beta-carotene may become manifest, yielding reactive oxygen species (ROS) and inducing oxidative DNA damage. It has further been hypothesized that cigarette smoke carcinogens such as benzo[a]pyrene (B[a]P) and/or B[a]P metabolites, may directly react with beta-carotene. Furthermore, beta-carotene oxidation products may have a role in the bioactivation of B[a]P analogous to the peroxide shunt pathway of cytochrome P450 supported by cumene hydroperoxide. The aim of this study was to assess the effects of beta-carotene on the formation of B[a]P-DNA adducts and oxidative DNA damage in vitro in isolated DNA, applying as metabolizing systems rat liver and lung metabolizing fractions and lung metabolizing fractions from smoking and non-smoking humans. We established that beta-carotene in the presence of various metabolizing systems was unable to induce oxidative DNA damage (8-oxo-dG), although beta-carotene is capable of generating ROS spontaneously in the absence of metabolizing fractions. We also could not find an effect of beta-carotene on DNA adduct formation induced by B[a]P upon metabolic activation. We could, however, provide evidence of the occurrence of a carbon-centered beta-carotene radical which was found to be able to interact with B[a]P and to intercalate in DNA.
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Affiliation(s)
- Jos C S Kleinjans
- Department of Health Risk Analysis and Toxicology, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands.
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Moonen HJJ, Briedé JJ, van Maanen JMS, Kleinjans JCS, de Kok TMCM. Generation of free radicals and induction of DNA adducts by activation of heterocyclic aromatic amines via different metabolic pathways in vitro. Mol Carcinog 2002; 35:196-203. [PMID: 12489111 DOI: 10.1002/mc.10089] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [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: 11/10/2022]
Abstract
Food-derived heterocyclic aromatic amines (HCAs) have proved to be carcinogenic in both rodents and nonhuman primates. Two different metabolic pathways are suggested for the metabolic activation of HCA. The hepatic pathway proceeds via a two-step process involving N-hydroxylation by cytochrome P4501A2 and subsequent O-acetylation by N-acetyltransferase-2. An alternative pathway may be of particular interest in extrahepatic tissues and proceeds via one-electron oxidation catalyzed by prostaglandin H synthase (PHS), rendering free-radical metabolites. In this study, we investigated the metabolic activation of two HCAs, 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), by two different enzyme systems in vitro, generating different primary and secondary reactive metabolites. Rat liver S9 mix and PHS were used as the activating system and represent the hepatic and extrahepatic pathways, respectively. Electron-spin resonance spectroscopy showed that both IQ and PhIP exerted inhibiting effects on PHS-mediated formation of hydroxyl radicals during the conversion of arachidonic acid to prostaglandins. Evidence for the formation of HCA free radicals was presented in an indirect way by the formation of glutathione-derived thiyl radicals, with purified PHS as the activating system. Activation by S9 mix did not result in the formation of detectable radical metabolites, showing that the two metabolic routes primarily led to the formation of different metabolites. In all electron-spin resonance experiments, IQ appeared to be more effective than PhIP. In contrasts, DNA adduct analysis by means of (32)P-postlabeling showed similar adduct patterns for S9 and PHS in single-stranded and double-stranded salmon testes DNA after incubation with PhIP, indicating the ultimate formation of a common reactive intermediate. For IQ, activation by PHS led to an additional adduct spot that was not present after S9 activation. Furthermore, activation of IQ resulted in higher adduct levels compared with PhIP for both activation pathways. Overall, adduct levels were higher in single-stranded DNA than double-stranded DNA. Our results showed that the hepatic and extrahepatic pathways resulted in different primary metabolites, while the ultimate formation of a similar reactive intermediate for PhIP, possibly an arylnitrenium ion, suggested that both pathways could play an important role in the onset of carcinogenesis.
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Affiliation(s)
- Harald J J Moonen
- Department of Health Risk Analysis and Toxicology, University of Maastricht, The Netherlands
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