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Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, Dave K, Dilger M, Exner T, Geerke DP, Grafström R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Ménager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJ, van Westen GJ, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Županič A, Willighagen EL. ELIXIR and Toxicology: a community in development. F1000Res 2023; 10:ELIXIR-1129. [PMID: 37842337 PMCID: PMC10568213 DOI: 10.12688/f1000research.74502.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
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Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Rob Stierum
- Risk Analysis for Products In Development (RAPID), Netherlands Organisation for applied scientific research TNO, Utrecht, 3584 CB, The Netherlands
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 EN, The Netherlands
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Hristo Aladjov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Kasia Arturi
- Department Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland
| | | | - Pavel Babica
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Palacky University Olomouc, Olomouc, 77146, Czech Republic
| | | | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Dimitrios Ε. Damalas
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Kirtan Dave
- School of Science, GSFC University, Gujarat, 391750, India
| | - Marco Dilger
- Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH, Freiburg im Breisgau, 79106, Germany
| | | | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, 1081 HZ, The Netherlands
| | - Roland Grafström
- Department of Toxicology, Misvik Biology, Turku, 20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Alasdair Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | | | - Henner Hollert
- Department Evolutionary Ecology & Environmental Toxicology (E3T), Goethe-University, Frankfurt, D-60438, Germany
| | | | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Fabien Jourdan
- MetaboHUB, French metabolomics infrastructure in Metabolomics and Fluxomics, Toulouse, France
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Jana Klanova
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Todor Kondic
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Boï Kone
- Faculty of Pharmacy, Malaria Research and Training Center, Bamako, BP:1805, Mali
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, 50411, Estonia
| | | | - Hervé Ménager
- Institut Français de Bioinformatique, Evry, F-91000, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, F-75015, France
| | - Steffen Neumann
- Research group Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, A-6020, Austria
| | - Noelia Ramirez
- Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili, Tarragona, 43007, Spain
| | | | - Philippe Rocca-Serra
- Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Reza M. Salek
- International Agency for Research on Cancer, World Health Organisation, Lyon, 69372, France
| | - Brett Sallach
- Department of Environment and Geography, University of York, UK, York, YO10 5NG, UK
| | | | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | | | | | - Tobias Schulze
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, SE-75124, Sweden
| | - Jonathan Tedds
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Ralf J.M. Weber
- School of Biosciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gerard J.P. van Westen
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, 2333 CC, The Netherlands
| | - Craig E. Wheelock
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm SE-141-86, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Antony J. Williams
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | | | - Barbara Zdrazil
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Anže Županič
- Department Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
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Nguyen N, Jennen D, Kleinjans J. Omics technologies to understand drug toxicity mechanisms. Drug Discov Today 2022; 27:103348. [PMID: 36089240 DOI: 10.1016/j.drudis.2022.103348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/18/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022]
Abstract
Drug side effects are an important study subject in pharmacology. Recent omics technologies provide a range of omics data and help to understand the biological mechanisms involved in drug effects. These modern technologies provide significant support to all biological disciplines, including drug toxicology. In this review, we provide an overview the use of omics applications to understand drug side effects at the molecular level. We discuss by available omics technologies, their possible uses, as well as their advantages and limitations.
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Affiliation(s)
- Nhan Nguyen
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229ER, the Netherlands
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Kleinjans J. PL01-01 Of genes and the environment, two decades of toxicogenomics. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Rodrigues D, van Kampen R, van Bodegraven A, Kleinjans J, de Kok T, Jennen D. P11-25 Unraveling the molecular mechanisms of capecitabine-induced colon toxicity: a case study. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Nguyen N, Lienhard M, Herwig R, Kleinjans J, Jennen D. Epirubicin Alters DNA Methylation Profiles Related to Cardiotoxicity. FRONT BIOSCI-LANDMRK 2022; 27:173. [DOI: 10.31083/j.fbl2706173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/06/2022]
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Hernández RB, de Souza-Pinto NC, Kleinjans J, van Herwijnen M, Piepers J, Moteshareie H, Burnside D, Golshani A. Manganese-Induced Neurotoxicity through Impairment of Cross-Talk Pathways in Human Neuroblastoma Cell Line SH-SY5Y Differentiated with Retinoic Acid. Toxics 2021; 9:toxics9120348. [PMID: 34941782 PMCID: PMC8704659 DOI: 10.3390/toxics9120348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 01/29/2023]
Abstract
Manganese (Mn) is an important element; yet acute and/or chronic exposure to this metal has been linked to neurotoxicity and neurodegenerative illnesses such as Parkinson’s disease and others via an unknown mechanism. To better understand it, we exposed a human neuroblastoma cell model (SH-SY5Y) to two Mn chemical species, MnCl2 and Citrate of Mn(II) (0–2000 µM), followed by a cell viability assay, transcriptomics, and bioinformatics. Even though these cells have been chemically and genetically modified, which may limit the significance of our findings, we discovered that by using RA-differentiated cells instead of undifferentiated SH-SY5Y cell line, both chemical species induce a similar toxicity, potentially governed by disruption of protein metabolism, with some differences. The MnCl2 altered amino acid metabolism, which affects RNA metabolism and protein synthesis. Citrate of Mn(II), however, inhibited the E3 ubiquitin ligases–target protein degradation pathway, which can lead to the buildup of damaged/unfolded proteins, consistent with histone modification. Finally, we discovered that Mn(II)-induced cytotoxicity in RA-SH-SY5Y cells shared 84 percent of the pathways involved in neurodegenerative diseases.
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Affiliation(s)
- Raúl Bonne Hernández
- Laboratory of Bioinorganic and Environmental Toxicology—LABITA, Department of Chemistry, Federal University of São Paulo, Rua Prof. Artur Riedel, 275, Diadema 09972-270, SP, Brazil
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
- Correspondence: ; Tel.: +55-11-3385-4137 (ext. 3522)
| | - Nadja C. de Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes, 748, Butantã, São Paulo 05508-900, SP, Brazil;
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Marcel van Herwijnen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Jolanda Piepers
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Houman Moteshareie
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Daniel Burnside
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Ashkan Golshani
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
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Baier V, Clayton O, Nudischer R, Cordes H, Schneider ARP, Thiel C, Wittenberger T, Moritz W, Blank LM, Neumann UP, Trautwein C, Kelm J, Schrooders Y, Caiment F, Gmuender H, Roth A, Castell JV, Kleinjans J, Kuepfer L. A Model-Based Workflow to Benchmark the Clinical Cholestasis Risk of Drugs. Clin Pharmacol Ther 2021; 110:1293-1301. [PMID: 34462909 DOI: 10.1002/cpt.2406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/15/2021] [Indexed: 12/13/2022]
Abstract
We present a generic workflow combining physiology-based computational modeling and in vitro data to assess the clinical cholestatic risk of different drugs systematically. Changes in expression levels of genes involved in the enterohepatic circulation of bile acids were obtained from an in vitro assay mimicking 14 days of repeated drug administration for 10 marketed drugs. These changes in gene expression over time were contextualized in a physiology-based bile acid model of glycochenodeoxycholic acid. The simulated drug-induced response in bile acid concentrations was then scaled with the applied drug doses to calculate the cholestatic potential for each compound. A ranking of the cholestatic potential correlated very well with the clinical cholestasis risk obtained from medical literature. The proposed workflow allows benchmarking the cholestatic risk of novel drug candidates. We expect the application of our workflow to significantly contribute to the stratification of the cholestatic potential of new drugs and to support animal-free testing in future drug development.
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Affiliation(s)
- Vanessa Baier
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Olivia Clayton
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Ramona Nudischer
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Henrik Cordes
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | | | | | | | | | - Lars M Blank
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Ulf P Neumann
- Department of Surgery, University Hospital Aachen, Aachen, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | | | - Yannick Schrooders
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | | | | | - José V Castell
- Unidad de Hepatología Experimenta, IIS Hospital Universitario La Fe, Valencia, Spain.,Department of Bioquímica, Facultad de Medicina, Universidad de Valencia, CIBEREHD-ISCIII, Valencia, Spain
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Lars Kuepfer
- Institute of Applied Microbiology, RWTH, Aachen, Germany.,Institute of Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
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Nguyen N, Kleinjans J, Jennen D. Epirubicin alters the DNA methylation in cardiac microtissue. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gupta R, Kleinjans J, Caiment F. Identifying novel transcript biomarkers for hepatocellular carcinoma (HCC) using RNA-Seq datasets and machine learning. BMC Cancer 2021; 21:962. [PMID: 34445986 PMCID: PMC8394105 DOI: 10.1186/s12885-021-08704-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/09/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the leading causes of cancer death in the world owing to limitations in its prognosis. The current prognosis approaches include radiological examination and detection of serum biomarkers, however, both have limited efficiency and are ineffective in early prognosis. Due to such limitations, we propose to use RNA-Seq data for evaluating putative higher accuracy biomarkers at the transcript level that could help in early prognosis. METHODS To identify such potential transcript biomarkers, RNA-Seq data for healthy liver and various HCC cell models were subjected to five different machine learning algorithms: random forest, K-nearest neighbor, Naïve Bayes, support vector machine, and neural networks. Various metrics, namely sensitivity, specificity, MCC, informedness, and AUC-ROC (except for support vector machine) were evaluated. The algorithms that produced the highest values for all metrics were chosen to extract the top features that were subjected to recursive feature elimination. Through recursive feature elimination, the least number of features were obtained to differentiate between the healthy and HCC cell models. RESULTS From the metrics used, it is demonstrated that the efficiency of the known protein biomarkers for HCC is comparatively lower than complete transcriptomics data. Among the different machine learning algorithms, random forest and support vector machine demonstrated the best performance. Using recursive feature elimination on top features of random forest and support vector machine three transcripts were selected that had an accuracy of 0.97 and kappa of 0.93. Of the three transcripts, two were protein coding (PARP2-202 and SPON2-203) and one was a non-coding transcript (CYREN-211). Lastly, we demonstrated that these three selected transcripts outperformed randomly taken three transcripts (15,000 combinations), hence were not chance findings, and could then be an interesting candidate for new HCC biomarker development. CONCLUSION Using RNA-Seq data combined with machine learning approaches can aid in finding novel transcript biomarkers. The three biomarkers identified: PARP2-202, SPON2-203, and CYREN-211, presented the highest accuracy among all other transcripts in differentiating the healthy and HCC cell models. The machine learning pipeline developed in this study can be used for any RNA-Seq dataset to find novel transcript biomarkers. Code: www.github.com/rajinder4489/ML_biomarkers.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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Trairatphisan P, de Souza TM, Kleinjans J, Jennen D, Saez-Rodriguez J. Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury. Toxicol Lett 2021; 350:40-51. [PMID: 34229068 DOI: 10.1016/j.toxlet.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/19/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In recent years, network-based methods have become an attractive analytical approach for toxicogenomics studies. They can capture not only the global changes of regulatory gene networks but also the relationships between their components. Among them, a causal reasoning approach depicts the mechanisms of regulation that connect upstream regulators in signaling networks to their downstream gene targets. In this work, we applied CARNIVAL, a causal network contextualisation tool, to infer upstream signaling networks deregulated in drug-induced liver injury (DILI) from gene expression microarray data from the TG-GATEs database. We focussed on six compounds that induce observable histopathologies linked to DILI from repeated dosing experiments in rats. We compared responses in vitro and in vivo to identify potential cross-platform concordances in rats as well as network preservations between rat and human. Our results showed similarities of enriched pathways and network motifs between compounds. These pathways and motifs induced the same pathology in rats but not in humans. In particular, the causal interactions "LCK activates SOCS3, which in turn inhibits TFDP1" was commonly identified as a regulatory path among the fibrosis-inducing compounds. This potential pathology-inducing regulation illustrates the value of our approach to generate hypotheses that can be further validated experimentally.
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Affiliation(s)
- Panuwat Trairatphisan
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120, Heidelberg, Germany.
| | - Terezinha Maria de Souza
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Danyel Jennen
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120, Heidelberg, Germany; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074, Aachen, Germany.
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Nguyen N, Souza T, Verheijen MCT, Gmuender H, Selevsek N, Schlapbach R, Kleinjans J, Jennen D. Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies. Front Genet 2021; 12:695625. [PMID: 34211507 PMCID: PMC8239409 DOI: 10.3389/fgene.2021.695625] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
Anthracyclines, including doxorubicin, idarubicin, and epirubicin, are common antitumor drugs as well as well-known cardiotoxic agents. This study analyzed the proteomics alteration in cardiac tissues caused by these 3 anthracyclines analogs. The in vitro human cardiac microtissues were exposed to drugs in 2 weeks; the proteomic data were measured at 7 time points. The heart biopsy data were collected from heart failure patients, in which some patients underwent anthracycline treatment. The anthracyclines-affected proteins were separately identified in the in vitro and in vivo dataset using the WGCNA method. These proteins engage in different cellular pathways including translation, metabolism, mitochondrial function, muscle contraction, and signaling pathways. From proteins detected in 2 datasets, a protein-protein network was established with 4 hub proteins, and 7 weighted proteins from both cardiac microtissue and human biopsies data. These 11 proteins, which involve in mitochondrial functions and the NF-κB signaling pathway, could provide insights into the anthracycline toxic mechanism. Some of them, such as HSPA5, BAG3, and SH3BGRL, are cardiac therapy targets or cardiotoxicity biomarkers. Other proteins, such as ATP5F1B and EEF1D, showed similar responses in both the in vitro and in vivo data. This suggests that the in vitro outcomes could link to clinical phenomena in proteomic analysis.
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Affiliation(s)
- Nhan Nguyen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Marcha C T Verheijen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | | | | | - Ralph Schlapbach
- Functional Genomics Center, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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Gupta R, Schrooders Y, Verheijen M, Roth A, Kleinjans J, Caiment F. FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. Bioinformatics 2021; 37:375-381. [PMID: 32814975 PMCID: PMC8058771 DOI: 10.1093/bioinformatics/btaa735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 07/13/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022] Open
Abstract
Summary Typical RNA sequencing (RNA-Seq) analyses are performed either at the gene level by summing all reads from the same locus, assuming that all transcripts from a gene make a protein or at the transcript level, assuming that each transcript displays unique function. However, these assumptions are flawed, as a gene can code for different types of transcripts and different transcripts are capable of synthesizing similar, different or no protein. As a consequence, functional changes are not well illustrated by either gene or transcript analyses. We propose to improve RNA-Seq analyses by grouping the transcripts based on their similar functions. We developed FuSe to predict functional similarities using the primary and secondary structure of proteins. To estimate the likelihood of proteins with similar functions, FuSe computes two confidence scores: knowledge (KS) and discovery (DS) for protein pairs. Overlapping protein pairs exhibiting high confidence are grouped to form ‘similar function protein groups’ and expression is calculated for each functional group. The impact of using FuSe is demonstrated on in vitro cells exposed to paracetamol, which highlight genes responsible for cell adhesion and glycogen regulation which were earlier shown to be not differentially expressed with traditional analysis methods. Availability and implementation The source code is available at https://github.com/rajinder4489/FuSe. Data for APAP exposure are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession numbers S-HECA143, S-HECA(158) and S-HECA139. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, 6229ER, The Netherlands
| | - Yannick Schrooders
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, 6229ER, The Netherlands
| | - Marcha Verheijen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, 6229ER, The Netherlands
| | - Adrian Roth
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, CH-4070, Switzerland
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, 6229ER, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, 6229ER, The Netherlands
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13
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Giovagnoni C, Ali M, Eijssen LMT, Maes R, Choe K, Mulder M, Kleinjans J, Del Sol A, Glaab E, Mastroeni D, Delvaux E, Coleman P, Losen M, Pishva E, Martinez-Martinez P, van den Hove DLA. Altered sphingolipid function in Alzheimer's disease; a gene regulatory network approach. Neurobiol Aging 2021; 102:178-187. [PMID: 33773368 DOI: 10.1016/j.neurobiolaging.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/04/2020] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Sphingolipids (SLs) are bioactive lipids involved in various important physiological functions. The SL pathway has been shown to be affected in several brain-related disorders, including Alzheimer's disease (AD). Recent evidence suggests that epigenetic dysregulation plays an important role in the pathogenesis of AD as well. Here, we use an integrative approach to better understand the relationship between epigenetic and transcriptomic processes in regulating SL function in the middle temporal gyrus of AD patients. Transcriptomic analysis of 252 SL-related genes, selected based on GO term annotations, from 46 AD patients and 32 healthy age-matched controls, revealed 103 differentially expressed SL-related genes in AD patients. Additionally, methylomic analysis of the same subjects revealed parallel hydroxymethylation changes in PTGIS, GBA, and ITGB2 in AD. Subsequent gene regulatory network-based analysis identified 3 candidate genes, that is, SELPLG, SPHK1 and CAV1 whose alteration holds the potential to revert the gene expression program from a diseased towards a healthy state. Together, this epigenomic and transcriptomic approach highlights the importance of SL-related genes in AD, and may provide novel biomarkers and therapeutic alternatives to traditionally investigated biological pathways in AD.
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Affiliation(s)
- Caterina Giovagnoni
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands.
| | - Muhammad Ali
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Lars M T Eijssen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Richard Maes
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Monique Mulder
- Department of Internal Medicine, Division of Pharmacology, Vascular and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Diego Mastroeni
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Paul Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Mario Losen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Ehsan Pishva
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Pilar Martinez-Martinez
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
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14
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Gupta R, Schrooders Y, Hauser D, van Herwijnen M, Albrecht W, Ter Braak B, Brecklinghaus T, Castell JV, Elenschneider L, Escher S, Guye P, Hengstler JG, Ghallab A, Hansen T, Leist M, Maclennan R, Moritz W, Tolosa L, Tricot T, Verfaillie C, Walker P, van de Water B, Kleinjans J, Caiment F. Comparing in vitro human liver models to in vivo human liver using RNA-Seq. Arch Toxicol 2020; 95:573-589. [PMID: 33106934 PMCID: PMC7870774 DOI: 10.1007/s00204-020-02937-6] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023]
Abstract
The liver plays an important role in xenobiotic metabolism and represents a primary target for toxic substances. Many different in vitro cell models have been developed in the past decades. In this study, we used RNA-sequencing (RNA-Seq) to analyze the following human in vitro liver cell models in comparison to human liver tissue: cancer-derived cell lines (HepG2, HepaRG 3D), induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-HLCs), cancerous human liver-derived assays (hPCLiS, human precision cut liver slices), non-cancerous human liver-derived assays (PHH, primary human hepatocytes) and 3D liver microtissues. First, using CellNet, we analyzed whether these liver in vitro cell models were indeed classified as liver, based on their baseline expression profile and gene regulatory networks (GRN). More comprehensive analyses using non-differentially expressed genes (non-DEGs) and differential transcript usage (DTU) were applied to assess the coverage for important liver pathways. Through different analyses, we noticed that 3D liver microtissues exhibited a high similarity with in vivo liver, in terms of CellNet (C/T score: 0.98), non-DEGs (10,363) and pathway coverage (highest for 19 out of 20 liver specific pathways shown) at the beginning of the incubation period (0 h) followed by a decrease during long-term incubation for 168 and 336 h. PHH also showed a high degree of similarity with human liver tissue and allowed stable conditions for a short-term cultivation period of 24 h. Using the same metrics, HepG2 cells illustrated the lowest similarity (C/T: 0.51, non-DEGs: 5623, and pathways coverage: least for 7 out of 20) with human liver tissue. The HepG2 are widely used in hepatotoxicity studies, however, due to their lower similarity, they should be used with caution. HepaRG models, iPSC-HLCs, and hPCLiS ranged clearly behind microtissues and PHH but showed higher similarity to human liver tissue than HepG2 cells. In conclusion, this study offers a resource of RNA-Seq data of several biological replicates of human liver cell models in vitro compared to human liver tissue.
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Affiliation(s)
- Rajinder Gupta
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Yannick Schrooders
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Duncan Hauser
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Wiebke Albrecht
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Tim Brecklinghaus
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Jose V Castell
- Instituto de Investigación Sanitaria La Fe, Experimental Hepatology Unit, Valencia, Spain
| | - Leroy Elenschneider
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Sylvia Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Patrick Guye
- InSphero AG, Wagistrasse 27, 8952, Schlieren, Switzerland
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Tanja Hansen
- Fraunhofer Institute for Toxicology and Experimental Medicine Preclinical Pharmacology and In-Vitro Toxicology, Nikolai-Fuchs-Straße 1, 30625, Hannover, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated, Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Richard Maclennan
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | | | - Laia Tolosa
- Instituto de Investigación Sanitaria La Fe, Unidad Hepatología Experimental, Valencia, Spain
| | - Tine Tricot
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Paul Walker
- Cyprotex Discovery, No 24 Mereside, Alderley Park, Cheshire, SK10 4TG, UK
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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15
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Caiment F, Wolters J, Smit E, Schrooders Y, Kleinjans J, van den Beucken T. Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression. Arch Toxicol 2020; 94:3463-3473. [PMID: 32623605 PMCID: PMC7502062 DOI: 10.1007/s00204-020-02835-x] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022]
Abstract
Valproic acid (VPA) is a frequently prescribed anti-epileptic drug which is known to cause liver toxicity and steatosis through mitochondrial dysfunction. Nevertheless the mechanisms underlying these adverse effects are incompletely understood. In this study, we determined the effect of relatively short (3 h) or prolonged (72 h) exposure to VPA on mitochondrial function in primary human hepatocytes (PHHs). While 3 h VPA exposure did not affect oxygen consumption rates (OCRs) in PHHs, prolonged exposure (24–72 h) significantly reduced basal and maximal OCRs. Given that in particular prolonged VPA exposure is required to cause mitochondrial dysfunction, we investigated gene expression data after VPA exposure for 24, 48, 72 h and 72 h VPA followed by a 72 h washout period. We were able to reduce the comprehensive gene expression changes into a more comprehensible set of 18 TFs that were predicted to be persistently activated after 72 h of VPA exposure. Lentiviral knock-down of one of the candidate TFs, C/EBPα, partly rescued VPA-induced mitochondrial dysfunction. Furthermore, RNA-Seq analysis of shC/EBPα and shGFP control PHHs identified 24 genuine C/EBPα target genes that are regulated in response to prolonged VPA exposure in PHHs. Altogether this provides new insights on the involvement of C/EBPα in driving VPA-induced mitochondrial dysfunction in human liver cells. This hub gene, with its downstream regulators involved in this deregulation, thus represent potential new biomarkers for VPA-induced mitochondrial dysfunction.
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Affiliation(s)
- F Caiment
- Maastricht University, Maastricht, The Netherlands
| | - J Wolters
- Maastricht University, Maastricht, The Netherlands
| | - E Smit
- Maastricht University, Maastricht, The Netherlands
| | - Y Schrooders
- Maastricht University, Maastricht, The Netherlands
| | - J Kleinjans
- Maastricht University, Maastricht, The Netherlands
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16
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Sillivan SE, Jamieson S, de Nijs L, Jones M, Snijders C, Klengel T, Joseph NF, Krauskopf J, Kleinjans J, Vinkers CH, Boks MP, Geuze E, Vermetten E, Berretta S, Ressler KJ, Rutten BP, Rumbaugh G, Miller CA. MicroRNA regulation of persistent stress-enhanced memory. Mol Psychiatry 2020; 25:965-976. [PMID: 31142820 PMCID: PMC6883139 DOI: 10.1038/s41380-019-0432-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022]
Abstract
Disruption of persistent, stress-associated memories is relevant for treating posttraumatic stress disorder (PTSD) and related syndromes, which develop in a subset of individuals following a traumatic event. We previously developed a stress-enhanced fear learning (SEFL) paradigm in inbred mice that produces PTSD-like characteristics in a subset of mice, including persistently enhanced memory and heightened cFos in the basolateral amygdala complex (BLC) with retrieval of the remote (30-day-old) stress memory. Here, the contribution of BLC microRNAs (miRNAs) to stress-enhanced memory was investigated because of the molecular complexity they achieve through their ability to regulate multiple targets simultaneously. We performed small-RNA sequencing (smRNA-Seq) and quantitative proteomics on BLC tissue collected from mice 1 month after SEFL and identified persistently changed microRNAs, including mir-135b-5p, and proteins associated with PTSD-like heightened fear expression. Viral-mediated overexpression of mir-135b-5p in the BLC of stress-resilient animals enhanced remote fear memory expression and promoted spontaneous renewal 14 days after extinction. Conversely, inhibition of BLC mir-135b-5p in stress-susceptible animals had the opposite effect, promoting a resilient-like phenotype. mir-135b-5p is highly conserved across mammals and was detected in post mortem human amygdala, as well as human serum samples. The mir-135b passenger strand, mir-135b-3p, was significantly elevated in serum from PTSD military veterans, relative to combat-exposed control subjects. Thus, miR-135b-5p may be an important therapeutic target for dampening persistent, stress-enhanced memory and its passenger strand a potential biomarker for responsivity to a mir-135-based therapeutic.
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Affiliation(s)
- Stephanie E. Sillivan
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL USA,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA
| | - Sarah Jamieson
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL USA,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA
| | - Laurence de Nijs
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Meghan Jones
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL USA,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA
| | - Clara Snijders
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Nadine F. Joseph
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL USA,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA
| | - Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Christiaan H. Vinkers
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, The Netherlands
| | - Marco P.M. Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, The Netherlands
| | - Elbert Geuze
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, The Netherlands.,Research Centre for Military Mental Healthcare, Ministry of Defence, Utrecht, The Netherlands
| | - Eric Vermetten
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, The Netherlands.,Research Centre for Military Mental Healthcare, Ministry of Defence, Utrecht, The Netherlands.,Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Sabina Berretta
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Kerry J. Ressler
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Bart P.F. Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
| | - Gavin Rumbaugh
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA
| | - Courtney A. Miller
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL USA,Department of Neuroscience, The Scripps Research Institute, Jupiter, FL USA.,Correspondence to: Courtney Miller , 130 Scripps Way, Jupiter, FL 33458, Phone 561-228-2958
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17
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Krauskopf J, Gosink MM, Schomaker S, Caiment F, Warner R, Johnson K, Kleinjans J, Aubrecht J. The MicroRNA-based Liquid Biopsy Improves Early Assessment of Lethal Acetaminophen Poisoning: A Case Report. Am J Case Rep 2020; 21:e919289. [PMID: 32086430 PMCID: PMC7049075 DOI: 10.12659/ajcr.919289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/24/2020] [Accepted: 11/04/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Acetaminophen overdose is the most common cause of acute liver failure. Nevertheless, new biomarker approaches enabling early prediction of the outcome of the acetaminophen overdose are needed. Recently, using next-generation sequencing analysis of serum from human study participants we uncovered injury-specific signatures of circulating microRNAs (miRNAs) that represented underlying molecular mechanisms of toxicity. This case study is first to show the application of miRNA profiling to assess prognosis of acetaminophen poisoning. CASE REPORT The patient was admitted to the hospital following supra therapeutic acetaminophen ingestion. The patient showed elevated levels of biomarkers of hepatocellular injury alanine aminotransferase, aspartate transaminase, and glutamate dehydrogenase. Even though treatment with N-acetyl cysteine was initiated 24 hours post-ingestion, levels of alanine-aminotransferase and aspartate transaminase peaked at about 40 hours post ingestion of acetaminophen. We analyzed global circulating miRNA levels from 24 consecutive serum samples from this study participant covering the period from admission to time of death. CONCLUSIONS The resulting global miRNA profiles were compared with profiles from study participants with non-lethal acetaminophen poisoning and healthy controls. At the admission, the miRNA profiles of both lethal and non-lethal acetaminophen poisoning showed induction of cellular stress and oxidative damage. Later, the miRNA profiles of the lethal poisoning featured fibrosis and coagulation pathways while profiles of non-lethal cases resembled those of healthy study participants. Although additional confirmatory studies are needed, our case study is first to indicate that global miRNA profiles to be used as liquid biopsies have potential to facilitate the assessment of acetaminophen poisoning.
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Affiliation(s)
- Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Mark M. Gosink
- Department of Pathology, University of Michigan, Ann Arbor, MI, U.S.A
| | - Shelli Schomaker
- Drug Safety Research and Development, Pfizer, Inc., Groton, CT, U.S.A
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Roscoe Warner
- Department of Pathology, University of Michigan, Ann Arbor, MI, U.S.A
| | - Kent Johnson
- Department of Pathology, University of Michigan, Ann Arbor, MI, U.S.A
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Jiri Aubrecht
- Drug Safety Research and Development, Pfizer, Inc., Groton, CT, U.S.A
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18
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Snijders C, Krauskopf J, Pishva E, Eijssen L, Machiels B, Kleinjans J, Kenis G, van den Hove D, Kim MO, Boks MPM, Vinkers CH, Vermetten E, Geuze E, Rutten BPF, de Nijs L. Circulating Serum MicroRNAs as Potential Diagnostic Biomarkers of Posttraumatic Stress Disorder: A Pilot Study. Front Genet 2019; 10:1042. [PMID: 31824554 PMCID: PMC6883918 DOI: 10.3389/fgene.2019.01042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 07/29/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is a psychiatric disorder that can develop upon exposure to a traumatic event. While most people are able to recover promptly, others are at increased risk of developing PTSD. However, the exact underlying biological mechanisms of differential susceptibility are unknown. Identifying biomarkers of PTSD could assist in its diagnosis and facilitate treatment planning. Here, we identified serum microRNAs (miRNAs) of subjects that underwent a traumatic event and aimed to assess their potential to serve as diagnostic biomarkers of PTSD. Next-generation sequencing was performed to examine circulating miRNA profiles of 24 members belonging to the Dutch military cohort Prospective Research in Stress-Related Military Operations (PRISMO). Three groups were selected: "susceptible" subjects who developed PTSD after combat exposure, "resilient" subjects without PTSD, and nonexposed control subjects (N = 8 per group). Differential expression analysis revealed 22 differentially expressed miRNAs in PTSD subjects compared to controls and 1 in PTSD subjects compared to resilient individuals (after multiple testing correction and a log2 fold-change cutoff of ≥|1|). Weighted Gene Coexpression Network Analysis (WGCNA) identified a module of coexpressed miRNAs which could distinguish between the three groups. In addition, receiver operating characteristic curve analyses suggest that the miRNAs with the highest module memberships could have a strong diagnostic accuracy as reflected by high areas under the curves. Overall, the results of our pilot study suggest that serum miRNAs could potentially serve as diagnostic biomarkers of PTSD, both individually or grouped within a cluster of coexpressed miRNAs. Larger studies are now needed to validate and build upon these preliminary findings.
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Affiliation(s)
- Clara Snijders
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
- College of Medicine and Health, University of Exeter Medical School, Exeter, United Kingdom
| | - Lars Eijssen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
- Department of Bioinformatics (BiGCaT), NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Barbie Machiels
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Gunter Kenis
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Daniel van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Myeong Ok Kim
- Division of Applied Life Science (BK 21), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea
| | - Marco P. M. Boks
- UMC Utrecht Brain Center, Department of Psychiatry, Utrecht, Netherlands
| | - Christiaan H. Vinkers
- Amsterdam UMC (location VUmc), Department of Anatomy and Neurosciences, Amsterdam, Netherlands
- Amsterdam UMC (location VUmc), Department of Psychiatry, Amsterdam, Netherlands
| | - Eric Vermetten
- Arq, Psychotrauma Research Expert Group, Diemen, Netherlands
- Department of Psychiatry, Leiden University Medical Center, Leiden, Netherlands
- Military Mental Healthcare, Netherlands Ministry of Defense, Utrecht, Netherlands
- Department of Psychiatry, New York University School of Medicine, New York, United States
| | - Elbert Geuze
- UMC Utrecht Brain Center, Department of Psychiatry, Utrecht, Netherlands
- Military Mental Healthcare, Netherlands Ministry of Defense, Utrecht, Netherlands
| | - Bart P. F. Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Laurence de Nijs
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
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19
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Dertinger SD, Totsuka Y, Bielas JH, Doherty AT, Kleinjans J, Honma M, Marchetti F, Schuler MJ, Thybaud V, White P, Yauk CL. High information content assays for genetic toxicology testing: A report of the International Workshops on Genotoxicity Testing (IWGT). Mutation Research/Genetic Toxicology and Environmental Mutagenesis 2019; 847:403022. [DOI: 10.1016/j.mrgentox.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 12/21/2022]
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20
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Lewalle A, Land S, Merken JJ, Raafs A, Sepúlveda P, Heymans S, Kleinjans J, Niederer SA. Balance of Active, Passive, and Anatomical Cardiac Properties in Doxorubicin-Induced Heart Failure. Biophys J 2019; 117:2337-2348. [PMID: 31447110 PMCID: PMC6990149 DOI: 10.1016/j.bpj.2019.07.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 01/31/2023] Open
Abstract
Late-onset heart failure (HF) is a known side effect of doxorubicin chemotherapy. Typically, patients are diagnosed when already at an irreversible stage of HF, which allows few or no treatment options. Identifying the causes of compromised cardiac function in this patient group may improve early patient diagnosis and support treatment selection. To link doxorubicin-induced changes in cardiac cellular and tissue mechanical properties to overall cardiac function, we apply a multiscale biophysical biomechanics model of the heart to measure the plausibility of changes in model parameters representing the passive, active, or anatomical properties of the left ventricle for reproducing measured patient phenotypes. We create representative models of healthy controls (N = 10) and patients with HF induced by (N = 22) or unrelated to (N = 25) doxorubicin therapy. The model predicts that HF in the absence of doxorubicin is characterized by a 2- to 3-fold stiffness increase, decreased tension (0–20%), and ventricular dilation (of order 10–30%). HF due to doxorubicin was similar but showed stronger bias toward reduced active contraction (10–30%) and less dilation (0–20%). We find that changes in active, passive, and anatomical properties all play a role in doxorubicin-induced cardiotoxicity phenotypes. Differences in parameter changes between patient groups are consistent with doxorubicin cardiotoxicity having a greater dependence on reduced cellular contraction and less anatomical remodeling than HF not caused by doxorubicin.
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Affiliation(s)
- Alexandre Lewalle
- Department of Biomedical Engineering, St Thomas's Hospital, King's College London, London, United Kingdom
| | - Sander Land
- Department of Biomedical Engineering, St Thomas's Hospital, King's College London, London, United Kingdom
| | - Jort J Merken
- Department of Cardiology, Maastricht University, Maastricht, the Netherlands
| | - Anne Raafs
- Department of Cardiology, Maastricht University, Maastricht, the Netherlands
| | - Pilar Sepúlveda
- Regenerative Medicine and Heart Transplantation Unit, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Stéphane Heymans
- Department of Cardiology, Maastricht University, Maastricht, the Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
| | - Steven A Niederer
- Department of Biomedical Engineering, St Thomas's Hospital, King's College London, London, United Kingdom.
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21
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Bohler S, Krauskopf J, Espín-Pérez A, Gebel S, Palli D, Rantakokko P, Kiviranta H, Kyrtopoulos SA, Balling R, Kleinjans J. Genes associated with Parkinson's disease respond to increasing polychlorinated biphenyl levels in the blood of healthy females. Environ Pollut 2019; 250:107-117. [PMID: 30991279 DOI: 10.1016/j.envpol.2019.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/13/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Polychlorinated biphenyls (PCBs) are a class of widespread environmental pollutants, commonly found in human blood, that have been suggested to be linked to the occurrence of sporadic Parkinson's disease (PD). It has been reported that some non-coplanar PCBs accumulate in the brains of female PD patients. To improve our understanding of the association between PCB exposure and PD risk we have applied whole transcriptome gene expression analysis in blood cells from 594 PCB-exposed subjects (369 female, 225 male). Interestingly, we observe that in females, blood levels of non-coplanar PCBs appear to be associated with expression levels of PD-specific genes. However, no such association was detected in males. Among the 131 PD-specific genes affected, 39 have been shown to display similar changes in expression levels in the substantia nigra of deceased PD patients. Especially among the down-regulated genes, transcripts of genes involved in neurotransmitter vesicle-related functions were predominant.
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Affiliation(s)
- Sacha Bohler
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands, 6229, ER Maastricht, the Netherlands
| | - Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands, 6229, ER Maastricht, the Netherlands.
| | - Almudena Espín-Pérez
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands, 6229, ER Maastricht, the Netherlands
| | - Stephan Gebel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L, 4362, Luxembourg
| | - Domenico Palli
- Istituto per lo Studio e la Prevenzione Oncologica (ISPO Toscana), FVia Cosimo Il Vecchio, 2, 50139, Florence, Italy
| | - Panu Rantakokko
- National Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701, Kuopio, Finland
| | - Hannu Kiviranta
- National Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701, Kuopio, Finland
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Pharmaceutical Chemistry and Biotechnology, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, Esch-sur-Alzette L, 4362, Luxembourg
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands, 6229, ER Maastricht, the Netherlands
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22
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Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D. Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. Front Genet 2018; 9:527. [PMID: 30515189 PMCID: PMC6255978 DOI: 10.3389/fgene.2018.00527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
In toxicogenomics, functional annotation is an important step to gain additional insights into genes with aberrant expression that drive pathophysiological mechanisms. Nevertheless, there exists a gap on annotation of these genes which often hampers the interpretation of results and limits their applicability in translational medicine. In this study, we evaluated the coverage of functional annotations of differentially expressed genes (DEGs) induced by 10 selected compounds from the TG-GATEs database identified as high- or no-risk in causing drug-induced liver injury (most-DILI or no-DILI, respectively) using in vitro human data. Functional roles of DEGs not present in the most common biological annotation databases – termed “dark genes” – were unveiled via literature mining and via the identification of shared regulatory transcription factors or signaling pathways. Our results demonstrated that there were approximately 13% of dark genes induced by these compounds in vitro and we were able to obtain additional relevant information for up to 76% of those. Using interactome data from several sources, we have uncovered genes such as LRBA, and WDR26 as highly connected in the protein network that play roles in drug response. Genes such as MALAT1, H19, and MIR29C – whose links to hepatotoxicity have been confirmed – were identified as markers for the most-DILI group and appeared as top hits across all literature-based mining methods. Furthermore, we investigated the potential impact of dark genes on liver toxicity by identifying their rat orthologs in combination with their correlation to drug-induced liver pathologies observed in vivo following chemical exposure. We identified a set of important regulatory transcription factors of dark genes for all most-DILI compounds including E2F1 and JUND with supporting evidences in literature and we found Magee1 correlated with chemically induced bile duct hyperplasia and adverse responses at 29 days in rats in vivo. In conclusion, in this study we show the potential role of these poorly annotated genes in mechanisms underlying hepatotoxicity and offer a number of computational approaches that may help to minimize current gaps in gene annotation and highlight their values as potential biomarkers in toxicological studies.
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Affiliation(s)
- Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Panuwat Trairatphisan
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Janet Piñero
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura I Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Cambridge, United Kingdom
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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23
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Verheijen M, Schrooders Y, Gmuender H, Nudischer R, Clayton O, Hynes J, Niederer S, Cordes H, Kuepfer L, Kleinjans J, Caiment F. Bringing in vitro analysis closer to in vivo: Studying doxorubicin toxicity and associated mechanisms in 3D human microtissues with PBPK-based dose modelling. Toxicol Lett 2018; 294:184-192. [DOI: 10.1016/j.toxlet.2018.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/08/2018] [Accepted: 05/23/2018] [Indexed: 01/07/2023]
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24
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Corvi R, Madia F, Guyton KZ, Kasper P, Rudel R, Colacci A, Kleinjans J, Jennings P. Moving forward in carcinogenicity assessment: Report of an EURL ECVAM/ESTIV workshop. Toxicol In Vitro 2017; 45:278-286. [PMID: 28911985 PMCID: PMC5735222 DOI: 10.1016/j.tiv.2017.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 10/27/2022]
Abstract
There is an increased need to develop novel alternative approaches to the two-year rodent bioassay for the carcinogenicity assessment of substances where the rodent bioassay is still a basic requirement, as well as for those substances where animal use is banned or limited or where information gaps are identified within legislation. The current progress in this area was addressed in a EURL ECVAM- ESTIV workshop held in October 2016, in Juan les Pins. A number of initiatives were presented and discussed, including data-driven, technology-driven and pathway-driven approaches. Despite a seemingly diverse range of strategic developments, commonalities are emerging. For example, providing insight into carcinogenicity mechanisms is becoming an increasingly appreciated aspect of hazard assessment and is suggested to be the best strategy to drive new developments. Thus, now more than ever, there is a need to combine and focus efforts towards the integration of available information between sectors. Such cross-sectorial harmonisation will aid in building confidence in new approach methods leading to increased implementation and thus a decreased necessity for the two-year rodent bioassay.
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Affiliation(s)
- Raffaella Corvi
- European Commission, Joint Research Centre (JRC), EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Ispra, (VA), Italy.
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), EU Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Ispra, (VA), Italy
| | - Kathryn Z Guyton
- Monographs Programme, International Agency for Research on Cancer, Lyon, France
| | - Peter Kasper
- Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | | | - Annamaria Colacci
- Centre for Environmental Toxicology and Risk Assessment, Environmental Protection and Health Prevention Agency, Emilia Romagna Region, Italy
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, HZ Amsterdam, The Netherlands
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25
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Plusquin M, Guida F, Polidoro S, Vermeulen R, Raaschou-Nielsen O, Campanella G, Hoek G, Kyrtopoulos SA, Georgiadis P, Naccarati A, Sacerdote C, Krogh V, Bas Bueno-de-Mesquita H, Monique Verschuren WM, Sayols-Baixeras S, Panni T, Peters A, Hebels DGAJ, Kleinjans J, Vineis P, Chadeau-Hyam M. DNA methylation and exposure to ambient air pollution in two prospective cohorts. Environ Int 2017; 108:127-136. [PMID: 28843141 PMCID: PMC6139298 DOI: 10.1016/j.envint.2017.08.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [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: 01/30/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 05/17/2023]
Abstract
Long-term exposure to air pollution has been associated with several adverse health effects including cardiovascular, respiratory diseases and cancers. However, underlying molecular alterations remain to be further investigated. The aim of this study is to investigate the effects of long-term exposure to air pollutants on (a) average DNA methylation at functional regions and, (b) individual differentially methylated CpG sites. An assumption is that omic measurements, including the methylome, are more sensitive to low doses than hard health outcomes. This study included blood-derived DNA methylation (Illumina-HM450 methylation) for 454 Italian and 159 Dutch participants from the European Prospective Investigation into Cancer and Nutrition (EPIC). Long-term air pollution exposure levels, including NO2, NOx, PM2.5, PMcoarse, PM10, PM2.5 absorbance (soot) were estimated using models developed within the ESCAPE project, and back-extrapolated to the time of sampling when possible. We meta-analysed the associations between the air pollutants and global DNA methylation, methylation in functional regions and epigenome-wide methylation. CpG sites found differentially methylated with air pollution were further investigated for functional interpretation in an independent population (EnviroGenoMarkers project), where (N=613) participants had both methylation and gene expression data available. Exposure to NO2 was associated with a significant global somatic hypomethylation (p-value=0.014). Hypomethylation of CpG island's shores and shelves and gene bodies was significantly associated with higher exposures to NO2 and NOx. Meta-analysing the epigenome-wide findings of the 2 cohorts did not show genome-wide significant associations at single CpG site level. However, several significant CpG were found if the analyses were separated by countries. By regressing gene expression levels against methylation levels of the exposure-related CpG sites, we identified several significant CpG-transcript pairs and highlighted 5 enriched pathways for NO2 and 9 for NOx mainly related to the immune system and its regulation. Our findings support results on global hypomethylation associated with air pollution, and suggest that the shores and shelves of CpG islands and gene bodies are mostly affected by higher exposure to NO2 and NOx. Functional differences in the immune system were suggested by transcriptome analyses.
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Affiliation(s)
- Michelle Plusquin
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom; Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Florence Guida
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
| | | | - Roel Vermeulen
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom; Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands
| | - Ole Raaschou-Nielsen
- Danish Cancer Society Research Center, Copenhagen, Denmark; Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Gerard Hoek
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | | | - Carlotta Sacerdote
- Unit of Cancer Epidemiology-CERMS, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza Hospital, Turin, Italy
| | - Vittorio Krogh
- Epidemiology Unit, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - H Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Department of Social & Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - W M Monique Verschuren
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands; Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain
| | - Tommaso Panni
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Dennie G A J Hebels
- Department of Toxicogenomics, Maastricht University, The Netherlands; Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute, Maastricht University, Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, The Netherlands
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom; IIGM, Italian Institute for Genomic Medicine, Turin, Italy
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, United Kingdom; Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands.
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26
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Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J. A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity. Arch Toxicol 2017; 92:553-555. [PMID: 28852801 PMCID: PMC5773653 DOI: 10.1007/s00204-017-2041-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/10/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Lars Kuepfer
- Institute of Applied Microbiology, RWTH, Aachen, Germany.
| | - Olivia Clayton
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Henrik Cordes
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Ramona Nudischer
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Vanessa Baier
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Stephane Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands.,Department of Cardiovascular Sciences, Leuven University, Leuven, Belgium
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Adrian Roth
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - José Castell
- Instituto de Investigación Sanitaria. Hospital Universitario La Fe, Valencia, Spain
| | - Nathalie Selevsek
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Hector Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, Cambridge, UK
| | | | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Steven Niederer
- Department of Imaging Sciences and BioMedical Engineering, King's College London, London, UK
| | | | | | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
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27
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Winckelmans E, Nawrot TS, Tsamou M, Den Hond E, Baeyens W, Kleinjans J, Lefebvre W, Van Larebeke N, Peusens M, Plusquin M, Reynders H, Schoeters G, Vanpoucke C, de Kok TM, Vrijens K. Transcriptome-wide analyses indicate mitochondrial responses to particulate air pollution exposure. Environ Health 2017; 16:87. [PMID: 28821289 PMCID: PMC5563023 DOI: 10.1186/s12940-017-0292-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Due to their lack of repair capacity mitochondria are critical targets for environmental toxicants. We studied genes and pathways reflecting mitochondrial responses to short- and medium-term PM10 exposure. METHODS Whole genome gene expression was measured in peripheral blood of 98 adults (49% women). We performed linear regression analyses stratified by sex and adjusted for individual and temporal characteristics to investigate alterations in gene expression induced by short-term (week before blood sampling) and medium-term (month before blood sampling) PM10 exposure. Overrepresentation analyses (ConsensusPathDB) were performed to identify enriched mitochondrial associated pathways and gene ontology sets. Thirteen Human MitoCarta genes were measured by means of quantitative real-time polymerase chain reaction (qPCR) along with mitochondrial DNA (mtDNA) content in an independent validation cohort (n = 169, 55.6% women). RESULTS Overrepresentation analyses revealed significant pathways (p-value <0.05) related to mitochondrial genome maintenance and apoptosis for short-term exposure and to the electron transport chain (ETC) for medium-term exposure in women. For men, medium-term PM10 exposure was associated with the Tri Carbonic Acid cycle. In an independent study population, we validated several ETC genes, including UQCRH and COX7C (q-value <0.05), and some genes crucial for the maintenance of the mitochondrial genome, including LONP1 (q-value: 0.07) and POLG (q-value: 0.04) in women. CONCLUSIONS In this exploratory study, we identified mitochondrial genes and pathways associated with particulate air pollution indicating upregulation of energy producing pathways as a potential mechanism to compensate for PM-induced mitochondrial damage.
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Affiliation(s)
- Ellen Winckelmans
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Maria Tsamou
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | | | - Willy Baeyens
- Department of Analytical and Environmental Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | | | - Nicolas Van Larebeke
- Department of Radiotherapy and Nuclear Medicine, Ghent University, Ghent, Belgium
| | - Martien Peusens
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Hans Reynders
- Environment, Nature and Energy Department, Flemish Government, Brussels, Belgium
| | - Greet Schoeters
- Flemish Institute for Technological Research, Mol, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute of Public Health, Department of Environmental Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Theo M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Karen Vrijens
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
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28
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Winckelmans E, Vrijens K, Tsamou M, Janssen BG, Saenen ND, Roels HA, Kleinjans J, Lefebvre W, Vanpoucke C, de Kok TM, Nawrot TS. Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort. Environ Health 2017; 16:52. [PMID: 28583124 PMCID: PMC5458481 DOI: 10.1186/s12940-017-0264-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 02/20/2017] [Accepted: 05/22/2017] [Indexed: 05/14/2023]
Abstract
BACKGROUND Air pollution exposure during pregnancy has been associated with adverse birth outcomes and health problems later in life. We investigated sex-specific transcriptomic responses to gestational long- and short-term exposure to particulate matter with a diameter < 2.5 μm (PM2.5) in order to elucidate potential underlying mechanisms of action. METHODS Whole genome gene expression was investigated in cord blood of 142 mother-newborn pairs that were enrolled in the ENVIRONAGE birth cohort. Daily PM2.5 exposure levels were calculated for each mother's home address using a spatial-temporal interpolation model in combination with a dispersion model to estimate both long- (annual average before delivery) and short- (last month of pregnancy) term exposure. We explored the association between gene expression levels and PM2.5 exposure, and identified modulated pathways by overrepresentation analysis and gene set enrichment analysis. RESULTS Some processes were altered in both sexes for long- (e.g. DNA damage) or short-term exposure (e.g. olfactory signaling). For long-term exposure in boys neurodevelopment and RhoA pathways were modulated, while in girls defensin expression was down-regulated. For short-term exposure we identified pathways related to synaptic transmission and mitochondrial function (boys) and immune response (girls). CONCLUSIONS This is the first whole genome gene expression study in cord blood to identify sex-specific pathways altered by PM2.5. The identified transcriptome pathways could provide new molecular insights as to the interaction pattern of early life PM2.5 exposure with the biological development of the fetus.
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Affiliation(s)
- Ellen Winckelmans
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Karen Vrijens
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Maria Tsamou
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Bram G. Janssen
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Nelly D. Saenen
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
| | - Harry A. Roels
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
- Louvain Centre for Toxicology and Applied Pharmacology (LTAP), Université catholique de Louvain, Brussels, Belgium
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Wouter Lefebvre
- Environmental Risk and Health, Flemish Institute for Technical Research (VITO), Mol, Belgium
| | | | - Theo M. de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Kapucijnenvoer 35, 3000 Leuven, Belgium
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29
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Vrijens K, Winckelmans E, Tsamou M, Baeyens W, De Boever P, Jennen D, de Kok TM, Den Hond E, Lefebvre W, Plusquin M, Reynders H, Schoeters G, Van Larebeke N, Vanpoucke C, Kleinjans J, Nawrot TS. Sex-Specific Associations between Particulate Matter Exposure and Gene Expression in Independent Discovery and Validation Cohorts of Middle-Aged Men and Women. Environ Health Perspect 2017; 125:660-669. [PMID: 27740511 PMCID: PMC5381989 DOI: 10.1289/ehp370] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 08/12/2016] [Accepted: 08/22/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Particulate matter (PM) exposure leads to premature death, mainly due to respiratory and cardiovascular diseases. OBJECTIVES Identification of transcriptomic biomarkers of air pollution exposure and effect in a healthy adult population. METHODS Microarray analyses were performed in 98 healthy volunteers (48 men, 50 women). The expression of eight sex-specific candidate biomarker genes (significantly associated with PM10 in the discovery cohort and with a reported link to air pollution-related disease) was measured with qPCR in an independent validation cohort (75 men, 94 women). Pathway analysis was performed using Gene Set Enrichment Analysis. Average daily PM2.5 and PM10 exposures over 2-years were estimated for each participant's residential address using spatiotemporal interpolation in combination with a dispersion model. RESULTS Average long-term PM10 was 25.9 (± 5.4) and 23.7 (± 2.3) μg/m3 in the discovery and validation cohorts, respectively. In discovery analysis, associations between PM10 and the expression of individual genes differed by sex. In the validation cohort, long-term PM10 was associated with the expression of DNAJB5 and EAPP in men and ARHGAP4 (p = 0.053) in women. AKAP6 and LIMK1 were significantly associated with PM10 in women, although associations differed in direction between the discovery and validation cohorts. Expression of the eight candidate genes in the discovery cohort differentiated between validation cohort participants with high versus low PM10 exposure (area under the receiver operating curve = 0.92; 95% CI: 0.85, 1.00; p = 0.0002 in men, 0.86; 95% CI: 0.76, 0.96; p = 0.004 in women). CONCLUSIONS Expression of the sex-specific candidate genes identified in the discovery population predicted PM10 exposure in an independent cohort of adults from the same area. Confirmation in other populations may further support this as a new approach for exposure assessment, and may contribute to the discovery of molecular mechanisms for PM-induced health effects.
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Affiliation(s)
- Karen Vrijens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Ellen Winckelmans
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Maria Tsamou
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Willy Baeyens
- Department of Analytical and Environmental Chemistry, Free University of Brussels, Brussels, Belgium
| | - Patrick De Boever
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Theo M. de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Elly Den Hond
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Provincial Institute for Hygiene, Antwerp, Belgium
| | - Wouter Lefebvre
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Hans Reynders
- Environment, Nature and Energy Department, Flemish Government, Brussels, Belgium
| | - Greet Schoeters
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- University of Southern Denmark, Institute of Public Health, Department of Environmental Medicine, Odense, Denmark
| | - Nicolas Van Larebeke
- Department of Radiotherapy and Nuclear Medicine, Ghent University, Ghent, Belgium
| | | | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health and Primary Care, Leuven University, Leuven, Belgium
- Address correspondence to T.S. Nawrot, Centre for Environmental Sciences, Hasselt University, Agoralaan gebouw D, B-3590 Diepenbeek, Belgium. Telephone: 0032/11-26.83.82. E-mail:
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30
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Vineis P, Chadeau-Hyam M, Gmuender H, Gulliver J, Herceg Z, Kleinjans J, Kogevinas M, Kyrtopoulos S, Nieuwenhuijsen M, Phillips DH, Probst-Hensch N, Scalbert A, Vermeulen R, Wild CP. The exposome in practice: Design of the EXPOsOMICS project. Int J Hyg Environ Health 2017; 220:142-151. [PMID: 27576363 PMCID: PMC6192011 DOI: 10.1016/j.ijheh.2016.08.001] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 11/04/2022]
Abstract
EXPOsOMICS is a European Union funded project that aims to develop a novel approach to the assessment of exposure to high priority environmental pollutants, by characterizing the external and the internal components of the exposome. It focuses on air and water contaminants during critical periods of life. To this end, the project centres on 1) exposure assessment at the personal and population levels within existing European short and long-term population studies, exploiting available tools and methods which have been developed for personal exposure monitoring (PEM); and 2) multiple "omic" technologies for the analysis of biological samples (internal markers of external exposures). The search for the relationships between external exposures and global profiles of molecular features in the same individuals constitutes a novel advancement towards the development of "next generation exposure assessment" for environmental chemicals and their mixtures. The linkage with disease risks opens the way to what are defined here as 'exposome-wide association studies' (EWAS).
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Key Words
- pem, personal exposure monitoring
- gis, geographic information system
- ewas, exposome-wide association studies
- sts, experimental short-term studies
- mco, mother-child cohorts
- alts, adult long-term studies
- lur, land-use regression
- dbp, disinfection by-products
- op, oxidative potential
- ufp, ultrafine particles
- pm, particulate matter
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Affiliation(s)
- P Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK.
| | - M Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | | | - J Gulliver
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, UK
| | - Z Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | - J Kleinjans
- Maastricht University, Department of Health Risk Analysis and Toxicology, Maastricht, Netherlands
| | - M Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - S Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Division of Organic and Medicinal Chemistry, Athens, Greece
| | - M Nieuwenhuijsen
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - D H Phillips
- King's College London, Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, London, UK
| | - N Probst-Hensch
- Swiss Tropical School of Public Health, Department of Epidemiology and Public Health, Basel, Switzerland and University of Basel, Basel, Switzerland
| | - A Scalbert
- International Agency for Research on Cancer (IARC), Lyon, France
| | - R Vermeulen
- Utrecht University, Institute for Risk Assessment Sciences, Environmental Epidemiology Division, Utrecht, Netherlands
| | - C P Wild
- International Agency for Research on Cancer (IARC), Lyon, France
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Escher BI, Hackermüller J, Polte T, Scholz S, Aigner A, Altenburger R, Böhme A, Bopp SK, Brack W, Busch W, Chadeau-Hyam M, Covaci A, Eisenträger A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Herberth G, Jahnke A, Kleinjans J, Klüver N, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Müller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schüürmann G, Schwikowski B, Tan YM, Trump S, Walter-Rohde S, Wambaugh JF. From the exposome to mechanistic understanding of chemical-induced adverse effects. Environ Int 2017; 99:97-106. [PMID: 27939949 PMCID: PMC6116522 DOI: 10.1016/j.envint.2016.11.029] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [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: 08/10/2016] [Revised: 10/27/2016] [Accepted: 11/29/2016] [Indexed: 05/17/2023]
Abstract
The exposome encompasses an individual's exposure to exogenous chemicals, as well as endogenous chemicals that are produced or altered in response to external stressors. While the exposome concept has been established for human health, its principles can be extended to include broader ecological issues. The assessment of exposure is tightly interlinked with hazard assessment. Here, we explore if mechanistic understanding of the causal links between exposure and adverse effects on human health and the environment can be improved by integrating the exposome approach with the adverse outcome pathway (AOP) concept that structures and organizes the sequence of biological events from an initial molecular interaction of a chemical with a biological target to an adverse outcome. Complementing exposome research with the AOP concept may facilitate a mechanistic understanding of stress-induced adverse effects, examine the relative contributions from various components of the exposome, determine the primary risk drivers in complex mixtures, and promote an integrative assessment of chemical risks for both human and environmental health.
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Affiliation(s)
- Beate I Escher
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany.
| | - Jörg Hackermüller
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Tobias Polte
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stefan Scholz
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Achim Aigner
- Leipzig University, Rudolf Boehm Institute for Pharmacology & Toxicology, Clinical Pharmacology, Haertelstr. 16-18, 04107 Leipzig, Germany
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Alexander Böhme
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Stephanie K Bopp
- European Commission Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Werner Brack
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marc Chadeau-Hyam
- University London, Imperial College, Department Epidemiology & Biostatistics, School of Public Health, St Marys Campus, Norfolk Place, London W2 1PG, England, United Kingdom
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk-Antwerp, Belgium
| | | | - James J Galligan
- Vanderbilt University, School of Medicine, A.B. Hancock Jr. Memorial Laboratory for Cancer Research, Department Biochemistry, Nashville, TN 37232, USA
| | - Natalia Garcia-Reyero
- US Army Engineer Research & Development Center, Vicksburg, MS, USA; Mississippi State University, Starkville, MS, USA
| | - Thomas Hartung
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA; University of Konstanz, Germany
| | - Michaela Hein
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gunda Herberth
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Annika Jahnke
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Jos Kleinjans
- Maastricht University, Department Toxicogenomics, 6200 MD Maastricht, The Netherlands
| | - Nils Klüver
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Martin Krauss
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marja Lamoree
- Vrije Universiteit, Faculty of Earth & Life Sciences, Institute for Environmental Studies, 1081 HV Amsterdam, The Netherlands
| | - Irina Lehmann
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Till Luckenbach
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gary W Miller
- Dept of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Andrea Müller
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - David H Phillips
- King's College London, MRC-PHE Centre for Environment & Health, Analytical & Environmental Sciences Division, London SE1 9NH, England, United Kingdom
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gerrit Schüürmann
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; Technical University Bergakademie Freiberg, Institute for Organic Chemistry, 09596 Freiberg, Germany
| | | | - Yu-Mei Tan
- US EPA, National Exposure Research Laboratory, Research Triangle Park, NC 27711, USA
| | - Saskia Trump
- Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | | | - John F Wambaugh
- US EPA, National Center for Computational Toxicology, Research Triangle Park, NC 27711, USA
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32
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Castagné R, Kelly-Irving M, Campanella G, Guida F, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Kleinjans J, de Kok T, Kyrtopoulos SA, Lang T, Stringhini S, Vermeulen R, Vineis P, Delpierre C, Chadeau-Hyam M. Biological marks of early-life socioeconomic experience is detected in the adult inflammatory transcriptome. Sci Rep 2016; 6:38705. [PMID: 27934951 PMCID: PMC5146729 DOI: 10.1038/srep38705] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 07/21/2016] [Accepted: 11/10/2016] [Indexed: 12/12/2022] Open
Abstract
Consistent evidence is accumulating to link lower socioeconomic position (SEP) and poorer health, and the inflammatory system stands out as a potential pathway through which socioeconomic environment is biologically embedded. Using bloodderived genome-wide transcriptional profiles from 268 Italian participants of the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, we evaluated the association between early life, young and later adulthood SEP and the expression of 845 genes involved in human inflammatory responses. These were examined individually and jointly using several inflammatory scores. Our results consistently show that participants whose father had a manual (as compared to nonmanual) occupation exhibit, later in life, a higher inflammatory score, hence indicating an overall increased level of expression for the selected inflammatory-related genes. Adopting a life course approach, these associations remained statistically significant upon adjustment for later-in-life socioeconomic experiences. Sensitivity analyses indicated that our findings were not affected by the way the inflammatory score was calculated, and were replicated in an independent study. Our study provides additional evidence that childhood SEP is associated with a sustainable upregulation of the inflammatory transcriptome, independently of subsequent socioeconomic experiences. Our results support the hypothesis that early social inequalities impacts adult physiology.
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Affiliation(s)
- Raphaële Castagné
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
- INSERM, UMR1027, Toulouse F-31000, France
- Université Toulouse III Paul-Sabatier, UMR1027, Toulouse F-31000, France
| | - Michelle Kelly-Irving
- INSERM, UMR1027, Toulouse F-31000, France
- Université Toulouse III Paul-Sabatier, UMR1027, Toulouse F-31000, France
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
| | - Florence Guida
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS- Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Istituto per lo Studio e la Prevenzione Oncologica (ISPO Toscana), Via delle Oblate 2, 50141, Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Viale Settimio Severo nr. 65, 10133 Turin, Italy
| | - Rosario Tumino
- Cancer registry and Histopathology Unit, Azienda Ospedaliera ‘Civile –M.P.Arezzo’, Via Dante N 109, 97100 Ragusa, Italy
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Theo de Kok
- Department of Toxicogenomics, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Soterios A. Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Pharmaceutical Chemistry and Biotechnology, Vas. Constantinou 48, 11635 Athens, Greece
| | - Thierry Lang
- INSERM, UMR1027, Toulouse F-31000, France
- Université Toulouse III Paul-Sabatier, UMR1027, Toulouse F-31000, France
| | - Silvia Stringhini
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Route de la Corniche 10, 1010 Lausanne, Switzerland
| | - Roel Vermeulen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80178, 3508 TD, Utrecht, The Netherlands
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
- HuGeF, Human Genetics Foundation, Via Nizza 52, 10126 Torino, Italy
- MRC-PHE Centre for Environment and Health, Imperial College, Praed Street Wing, St Mary’s Campus, W2 1PG London, UK
| | - Cyrille Delpierre
- INSERM, UMR1027, Toulouse F-31000, France
- Université Toulouse III Paul-Sabatier, UMR1027, Toulouse F-31000, France
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, W2 1PG London, UK
- MRC-PHE Centre for Environment and Health, Imperial College, Praed Street Wing, St Mary’s Campus, W2 1PG London, UK
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Souza TM, Rieswijk L, Beucken TVD, Kleinjans J, Jennen D. Persistent transcriptional responses show the involvement of feed-forward control in a repeated dose toxicity study. Toxicology 2016; 375:58-63. [PMID: 27765683 DOI: 10.1016/j.tox.2016.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 01/17/2023]
Abstract
Chemical carcinogenesis, albeit complex, often relies on modulation of transcription through activation or repression of key transcription factors. While analyzing extensive networks may hinder the biological interpretation, one may focus on dynamic network motifs, among which persistent feed-forward loops (FFLs) are known to chronically influence transcriptional programming. Here, to investigate the relevance a FFL-oriented approach in depth, we have focused on aflatoxin B1-induced transcriptomic alterations during distinct states of exposure (daily administration during 5days followed by a non-exposed period) of human hepatocytes, by exploring known interactions in human transcription. Several TF-coding genes were persistently deregulated after washout of AFB1. Oncogene MYC was identified as the prominent regulator and driver of many FFLs, among which a FFL comprising MYC/HIF1A was the most recurrent. The MYC/HIF1A FFL was also identified and validated in an independent set as the master regulator of metabolic alterations linked to initiation and progression of carcinogenesis, i.e. the Warburg effect, possibly as result of persistent intracellular alterations arising from AFB1 exposure (nuclear and mitochondrial DNA damage, oxidative stress, transcriptional activation by secondary messengers). In summary, our analysis shows the involvement of FFLs as modulators of gene expression suggestive of a carcinogenic potential even after termination of exposure.
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Affiliation(s)
- Terezinha M Souza
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Linda Rieswijk
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Twan van den Beucken
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
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Wolters J, Breda S, Caiment F, Claessen S, Kok T, Kleinjans J. Valproic acid-induced 5-methylcytosine pattern changes in the nuclear and mitochondrial DNA of primary human hepatocytes. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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O'Callaghan-Gordo C, Kogevinas M, Fthenou E, Pedersen M, Espinosa A, Chalkiadaki G, Daraki V, Dermitzaki E, Decordier I, Georgiou V, Merlo DF, Roumeliotaki T, Vande Loock K, Kleinjans J, Kirsch-Volders M, Chatzi L. Vitamin D insufficient levels during pregnancy and micronuclei frequency in peripheral blood T lymphocytes mothers and newborns (Rhea cohort, Crete). Clin Nutr 2016; 36:1029-1035. [PMID: 27396287 DOI: 10.1016/j.clnu.2016.06.016] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/03/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND & AIMS Vitamin D deficiency is common among pregnant women and may be associated with several adverse health outcomes including cancer. Micronuclei frequency is a biomarker of early genetic effects and has been used to examine the association between genotoxic exposures and cancer. We examined maternal vitamin D levels during pregnancy in associations with micronuclei frequency in maternal blood and in cord blood. METHODS 173 mothers and 171 newborns born between 2007 and 2008 in Heraklion (Crete, Greece) were included in the study. Between 14th and 18th weeks of gestation we collected information on maternal diet using food frequency questionnaires (FFQs). We measured maternal serum concentrations of 25-hydroxyvitamin D [25(OH)D] between the first and second trimester of pregnancy. We estimated dietary vitamin D intake using information from FFQ. After delivery we collected cord blood and maternal peripheral blood. We used the cytokinesis-block micronucleus (CBMN) assay to assess the frequencies of micronucleated cells in binucleated T lymphocytes (MNBN). RESULTS Maternal insufficient serum levels of 25(OH)D (<50 nmol/L) during pregnancy were associated with increased MNBN frequency in cord blood [IRR = 1.32 (95%CI: 1.00, 1.72)]. This increase was higher for newborns with birth weight above the third quartile [≥3.500 kg; IRR = 2.21 (1.26, 3.89)]. Similarly, low levels of dietary vitamin D were associated with increased MNBN frequency in cord blood [middle tertile IRR = 1.08 (0.78, 1.47), lower tertile IRR = 1.51 (1.06, 2.14)]. Insufficient levels of vitamin D were not associated with MNBN in mothers. CONCLUSION Our results suggest that vitamin D deficiency during pregnancy increases genotoxic risks in newborns. The prevalence of vitamin D deficiency globally is high and it is important to further investigate whether vitamin D supplementation or similar interventions during pregnancy could prevent DNA damage at early stages of life.
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Affiliation(s)
- Cristina O'Callaghan-Gordo
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 80, 08003 Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain.
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 80, 08003 Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eleni Fthenou
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Marie Pedersen
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 80, 08003 Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; INSERM (National Institute of Health and Medical Research), U823, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Institute Albert Bonniot, Rond-point de la Chantourne, 38706 La Tronche, Grenoble, France
| | - Ana Espinosa
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 80, 08003 Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Georgia Chalkiadaki
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Vasiliki Daraki
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Eirini Dermitzaki
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Ilse Decordier
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Vaggelis Georgiou
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Domenico Franco Merlo
- Epidemiology, Biostatistics, and Clinical Trials, Instituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino - Istituto Nazionale per la Ricerca sul Cancro (IST), Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Theano Roumeliotaki
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
| | - Kim Vande Loock
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Minderbroedersberg 4-6, 6211 LK Maastricht, The Netherlands
| | - Micheline Kirsch-Volders
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Leda Chatzi
- Faculty of Medicine, University of Crete, Voutes Campus, Heraklion, Crete GR-71003, Greece
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Souza T, Jennen D, van Delft J, van Herwijnen M, Kyrtoupolos S, Kleinjans J. New insights into BaP-induced toxicity: role of major metabolites in transcriptomics and contribution to hepatocarcinogenesis. Arch Toxicol 2016; 90:1449-58. [PMID: 26238291 PMCID: PMC4873527 DOI: 10.1007/s00204-015-1572-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]
Abstract
Benzo(a)pyrene (BaP) is a ubiquitous carcinogen resulting from incomplete combustion of organic compounds and also present at high levels in cigarette smoke. A wide range of biological effects has been attributed to BaP and its genotoxic metabolite BPDE, but the contribution to BaP toxicity of intermediary metabolites generated along the detoxification path remains unknown. Here, we report for the first time how 3-OH-BaP, 9,10-diol and BPDE, three major BaP metabolites, temporally relate to BaP-induced transcriptomic alterations in HepG2 cells. Since BaP is also known to induce AhR activation, we additionally evaluated TCDD to source the expression of non-genotoxic AhR-mediated patterns. 9,10-Diol was shown to activate several transcription factor networks related to BaP metabolism (AhR), oxidative stress (Nrf2) and cell proliferation (HIF-1α, AP-1) in particular at early time points, while BPDE influenced expression of genes involved in cell energetics, DNA repair and apoptotic pathways. Also, in order to grasp the role of BaP and its metabolites in chemical hepatocarcinogenesis, we compared expression patterns from BaP(-metabolites) and TCDD to a signature set of approximately nine thousand gene expressions derived from hepatocellular carcinoma (HCC) patients. While transcriptome modulation by TCDD appeared not significantly related to HCC, BaP and BPDE were shown to deregulate metastatic markers via non-genotoxic and genotoxic mechanisms and activate inflammatory pathways (NF-κβ signaling, cytokine-cytokine receptor interaction). BaP also showed strong repression of genes involved in cholesterol and fatty acid biosynthesis. Altogether, this study provides new insights into BaP-induced toxicity and sheds new light onto its mechanism of action as a hepatocarcinogen.
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Affiliation(s)
- Terezinha Souza
- Department of Toxicogenomics, Maastricht University, 6229 ER, Maastricht, The Netherlands.
- Department of Toxicogenomics, Maastricht University, Universiteitsingel 50, 6200 MD, Maastricht, The Netherlands.
| | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Joost van Delft
- Department of Toxicogenomics, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Soterios Kyrtoupolos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, 6229 ER, Maastricht, The Netherlands
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Herwig R, Gmuender H, Corvi R, Bloch KM, Brandenburg A, Castell J, Ceelen L, Chesne C, Doktorova TY, Jennen D, Jennings P, Limonciel A, Lock EA, McMorrow T, Phrakonkham P, Radford R, Slattery C, Stierum R, Vilardell M, Wittenberger T, Yildirimman R, Ryan M, Rogiers V, Kleinjans J. Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective. Arch Toxicol 2015; 90:2215-2229. [PMID: 26525393 DOI: 10.1007/s00204-015-1617-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 01/29/2023]
Abstract
The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored the gene expression responses of such systems, reports on robustness and reproducibility, when testing them independently in different laboratories, are still uncommon. Furthermore, there is limited knowledge about variability induced by the data analysis protocols. We have conducted an inter-laboratory study for testing chemical carcinogenicity evaluating two human in vitro assays: hepatoma-derived cells and hTERT-immortalized renal proximal tubule epithelial cells, representing liver and kidney as major target organs. Cellular systems were initially challenged with thirty compounds, genome-wide gene expression was measured with microarrays, and hazard classifiers were built from this training set. Subsequently, each system was independently established in three different laboratories, and gene expression measurements were conducted using anonymized compounds. Data analysis was performed independently by two separate groups applying different protocols for the assessment of inter-laboratory reproducibility and for the prediction of carcinogenic hazard. As a result, both workflows came to very similar conclusions with respect to (1) identification of experimental outliers, (2) overall assessment of robustness and inter-laboratory reproducibility and (3) re-classification of the unknown compounds to the respective toxicity classes. In summary, the developed bioinformatics workflows deliver accurate measures for inter-laboratory comparison studies, and the study can be used as guidance for validation of future carcinogenicity assays in order to implement testing of human in vitro alternatives to animal testing.
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Affiliation(s)
- R Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany.
| | - H Gmuender
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Corvi
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - K M Bloch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - A Brandenburg
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - J Castell
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Valencia, Av. Blasco Ibanez 15, 46010, Valencia, Spain
| | - L Ceelen
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - C Chesne
- Biopredic International, Parc d'affaires de la Bretèche, Bldg. A4, 35760, St Gregoire, France
| | - T Y Doktorova
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - D Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - P Jennings
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - A Limonciel
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - E A Lock
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - T McMorrow
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - P Phrakonkham
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - R Radford
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - C Slattery
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Stierum
- Department of Risk Analysis for Products in Development, Netherlands Organisation for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE, Zeist, The Netherlands
| | - M Vilardell
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - T Wittenberger
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Yildirimman
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - M Ryan
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - V Rogiers
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - J Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
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O'Callaghan-Gordo C, Fthenou E, Pedersen M, Espinosa A, Chatzi L, Beelen R, Chalkiadaki G, Decordier I, Hoek G, Merlo DF, Nieuwenhuijsen M, Roumeliotaki T, Vafeiadi M, Vande Loock K, Kleinjans J, Stephanou E, Kirsch-Volders M, Kogevinas M. Outdoor air pollution exposures and micronuclei frequencies in lymphocytes from pregnant women and newborns in Crete, Greece (Rhea cohort). Environ Res 2015; 143:170-176. [PMID: 26496153 DOI: 10.1016/j.envres.2015.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 06/22/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Micronuclei (MN) are biomarkers of early genetic effects that have been used to investigate the association between environmental exposures and cancer. However, few studies have examined the association between environmental exposures during pregnancy and MN in mothers and newborns. OBJECTIVES We examined MN frequency in maternal blood and in cord blood, in relation to maternal air pollution exposure, and the potential interaction with maternal vitamin C intake and maternal smoking. METHODS We used the cytokinesis-block micronucleus assay to assess MN frequency per 1000 bi-nucleated T-lymphocytes from 181 mothers and 183 newborns born in 2007-2008 in Heraklion (Crete, Greece). The ESCAPE land-use regression methods were used to estimate annual mean exposure to outdoor air pollution [particulate matter (PM), black carbon, nitrogen dioxide (NO2) and nitrogen oxides (NOx)] at maternal home addresses. Food frequency questionnaires were used to estimate maternal dietary vitamin C intake during pregnancy. Smoking habits were self-reported using questionnaires which were checked by measuring maternal urinary cotinine levels. RESULTS Exposure to PM2.5 was associated with increased MN frequencies in pregnant women [rate ratio [RR (95%CI)] per 5 µg/m(3)=1.53 (1.02, 2.29)]. This increase was considerably higher among women who did not fulfill the recommended vitamin C dietary allowances [RR=9.35 (2.77, 31.61); n=20]. Exposure to PM2.5-10, PM10, NO2 and NOx were also associated with a higher incidence of MN frequencies in smoker women (n=56). No associations were found for newborns. CONCLUSIONS We found an association between air pollution, particularly PM2.5, and MN frequency in mothers but not in newborns. This association was more pronounced among women with a lower dietary intake of vitamin C during pregnancy and among women who smoked during pregnancy. While results are clear in mothers, the association between maternal carcinogenic exposures during pregnancy and biomarkers of early biologic effect in the newborn remains poorly understood.
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Affiliation(s)
- Cristina O'Callaghan-Gordo
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
| | - Eleni Fthenou
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Marie Pedersen
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; INSERM (National Institute of Health and Medical Research), U823, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Institute Albert Bonniot, Grenoble, France
| | - Ana Espinosa
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Leda Chatzi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Rob Beelen
- Institute for Risk Assessment Sciences (IRAS), Division Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands
| | - Georgia Chalkiadaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Ilse Decordier
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universitei Brussel, Brussels, Belgium
| | - Gerard Hoek
- Institute for Risk Assessment Sciences (IRAS), Division Environmental Epidemiology, Utrecht University, Utrecht, The Netherlands
| | - Domenico Franco Merlo
- Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino - Istituto Nazionale per la Ricerca sul Cancro (IST), Genoa, Italy
| | - Mark Nieuwenhuijsen
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Theano Roumeliotaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Kim Vande Loock
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universitei Brussel, Brussels, Belgium
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Euripides Stephanou
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Heraklion, Greece
| | - Micheline Kirsch-Volders
- Laboratory of Cell Genetics, Faculty of Science and Bio-engineering, Vrije Universitei Brussel, Brussels, Belgium
| | - Manolis Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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Abstract
Many studies now produce parallel data sets from different omics technologies; however, the task of interpreting the acquired data in an integrated fashion is not trivial. This review covers those methods that have been used over the past decade to statistically integrate and interpret metabolomics and transcriptomic data sets. It defines four categories of approaches, correlation-based integration, concatenation-based integration, multivariate-based integration and pathway-based integration, into which all existing statistical methods fit. It also explores the choices in study design for generating samples for analysis by these omics technologies and the impact that these technical decisions have on the subsequent data analysis options.
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Affiliation(s)
- Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Maria Botsivali
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Manolis Kogevinas
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Domenico Franco Merlo
- IRCCS AOU San Martino-IST- Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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Deferme L, Wolters J, Claessen S, Briedé J, Kleinjans J. Oxidative Stress Mechanisms Do Not Discriminate between Genotoxic and Nongenotoxic Liver Carcinogens. Chem Res Toxicol 2015. [DOI: 10.1021/acs.chemrestox.5b00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lize Deferme
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jarno Wolters
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Sandra Claessen
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jacco Briedé
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
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Caiment F, Gaj S, Claessen S, Kleinjans J. High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity. Nucleic Acids Res 2015; 43:2525-34. [PMID: 25690898 PMCID: PMC4357716 DOI: 10.1093/nar/gkv115] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [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: 01/06/2023] Open
Abstract
The chain of events leading from a toxic compound exposure to carcinogenicity is still barely understood. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using two different RNA libraries, we sequenced the complete transcriptome of human HepG2 liver cells exposed to benzo[a]pyrene, a potent human carcinogen, across six time points. Data were integrated in order to reveal novel complex chemical–gene interactions. Notably, we hypothesized that the inhibition of MGMT, a DNA damage response enzyme, by the over-expressed miR-181a-1_3p induced by BaP, may lead to liver cancer over time.
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Affiliation(s)
- Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht 6200, The Netherlands
| | - Stan Gaj
- Department of Toxicogenomics, Maastricht University, Maastricht 6200, The Netherlands
| | - Sandra Claessen
- Department of Toxicogenomics, Maastricht University, Maastricht 6200, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht 6200, The Netherlands
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43
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Jennen D, Polman J, Bessem M, Coonen M, van Delft J, Kleinjans J. Drug-induced liver injury classification model based on in vitro human transcriptomics and in vivo rat clinical chemistry data. ACTA ACUST UNITED AC 2014. [DOI: 10.4161/sysb.29400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Vande Loock K, Botsivali M, Zangogianni M, Anderson D, Baumgartner A, Fthenou E, Chatzi L, Marcos R, Agramunt S, Namork E, Granum B, Knudsen LE, Nielssen JKS, Meltzer HM, Haugen M, Kyrtopoulos SA, Decordier I, Plas G, Roelants M, Merlo F, Kleinjans J, Kogevinas M, Kirsch-Volders M. The effect of dietary estimates calculated using food frequency questionnaires on micronuclei formation in European pregnant women: a NewGeneris study. Mutagenesis 2014; 29:393-400. [DOI: 10.1093/mutage/geu052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stierum R, Aarts J, Boorsma A, Bosgra S, Caiment F, Ezendam J, Greupink R, Hendriksen P, Soeteman-Hernandez LG, Jennen D, Kleinjans J, Kroese D, Kuper F, van Loveren H, Monshouwer M, Russel F, van Someren E, Tsamou M, Groothuis G. Assuring safety without animal testing concept (ASAT). Integration of human disease data with in vitro data to improve toxicology testing. Toxicol Lett 2014. [DOI: 10.1016/j.toxlet.2014.06.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kleinjans J, van Ravenzwaay B. Epigenetics and chemical safety - concluding remarks. Mutat Res Genet Toxicol Environ Mutagen 2014; 764-765:72-73. [PMID: 24674849 DOI: 10.1016/j.mrgentox.2014.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, The Netherlands
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47
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van Ravenzwaay B, Kleinjans J, Vrijhof H. Editorial - epigenetics and chemical safety. Mutat Res Genet Toxicol Environ Mutagen 2014; 764-765:1-2. [PMID: 24472829 DOI: 10.1016/j.mrgentox.2014.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 11/27/2022]
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Nymark P, Jensen KA, Suhonen S, Kembouche Y, Vippola M, Kleinjans J, Catalán J, Norppa H, van Delft J, Briedé JJ. Free radical scavenging and formation by multi-walled carbon nanotubes in cell free conditions and in human bronchial epithelial cells. Part Fibre Toxicol 2014; 11:4. [PMID: 24438343 PMCID: PMC3933237 DOI: 10.1186/1743-8977-11-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/09/2014] [Indexed: 01/22/2023] Open
Abstract
Background Certain multi-walled carbon nanotubes (MWCNTs) have been shown to elicit asbestos-like toxicological effects. To reduce needs for risk assessment it has been suggested that the physicochemical characteristics or reactivity of nanomaterials could be used to predict their hazard. Fibre-shape and ability to generate reactive oxygen species (ROS) are important indicators of high hazard materials. Asbestos is a known ROS generator, while MWCNTs may either produce or scavenge ROS. However, certain biomolecules, such as albumin – used as dispersants in nanomaterial preparation for toxicological testing in vivo and in vitro - may reduce the surface reactivity of nanomaterials. Methods Here, we investigated the effect of bovine serum albumin (BSA) and cell culture medium with and without BEAS 2B cells on radical formation/scavenging by five MWCNTs, Printex 90 carbon black, crocidolite asbestos, and glass wool, using electron spin resonance (ESR) spectroscopy and linked this to cytotoxic effects measured by trypan blue exclusion assay. In addition, the materials were characterized in the exposure medium (e.g. for hydrodynamic size-distribution and sedimentation rate). Results The test materials induced highly variable cytotoxic effects which could generally be related to the abundance and characteristics of agglomerates/aggregates and to the rate of sedimentation. All carbon nanomaterials were found to scavenge hydroxyl radicals (•OH) in at least one of the solutions tested. The effect of BSA was different among the materials. Two types of long, needle-like MWCNTs (average diameter >74 and 64.2 nm, average length 5.7 and 4.0 μm, respectively) induced, in addition to a scavenging effect, a dose-dependent formation of a unique, yet unidentified radical in both absence and presence of cells, which also coincided with cytotoxicity. Conclusions Culture medium and BSA affects scavenging/production of •OH by MWCNTs, Printex 90 carbon black, asbestos and glass-wool. An unidentified radical is generated by two long, needle-like MWCNTs and these two CNTs were more cytotoxic than the other CNTs tested, suggesting that this radical could be related to the adverse effects of MWCNTs.
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Affiliation(s)
- Penny Nymark
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands.
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De Boever P, Wens B, Forcheh AC, Reynders H, Nelen V, Kleinjans J, Van Larebeke N, Verbeke G, Valkenborg D, Schoeters G. Characterization of the peripheral blood transcriptome in a repeated measures design using a panel of healthy individuals. Genomics 2013; 103:31-9. [PMID: 24321174 DOI: 10.1016/j.ygeno.2013.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 06/14/2013] [Accepted: 11/29/2013] [Indexed: 01/01/2023]
Abstract
A repeated measures microarray design with 22 healthy, non-smoking volunteers (aging 32±5years) was set up to study transcriptome profiles in whole blood samples. The results indicate that repeatable data can be obtained with high within-subject correlation. Probes that could discriminate between individuals are associated with immune and inflammatory functions. When investigating possible time trends in the microarray data, we have found no differential expression within a sampling period (within-season effect). Differential expression was observed between sampling seasons and the data suggest a weak response of genes related to immune system functioning. Finally, a high number of probes showed significant season-specific expression variability within subjects. Expression variability increased in springtime and there was an association of the probe list with immune system functioning. Our study suggests that the blood transcriptome of healthy individuals is reproducible over a time period of several months.
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Affiliation(s)
- Patrick De Boever
- Flemish Institute for Technological Research, Unit Environmental Risk and Health, Belgium; Hasselt University, Centre for Environmental Sciences, Belgium.
| | - Britt Wens
- Flemish Institute for Technological Research, Unit Environmental Risk and Health, Belgium
| | - Anyiawung Chiara Forcheh
- Catholic University of Leuven, Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Belgium
| | - Hans Reynders
- Flemish Government, Environment, Nature and Energy Department, Belgium
| | - Vera Nelen
- Provincial Institute for Hygiene, Belgium
| | - Jos Kleinjans
- Maastricht University, Department of Toxicogenomics, The Netherlands
| | - Nicolas Van Larebeke
- Ghent University, Study Centre for Carcinogenesis and Primary Prevention of Cancer, Belgium
| | - Geert Verbeke
- Catholic University of Leuven, Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research, Unit Environmental Risk and Health, Belgium; Hasselt University, Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Belgium
| | - Greet Schoeters
- Flemish Institute for Technological Research, Unit Environmental Risk and Health, Belgium; University of Antwerp, Department of Biomedical Sciences, Belgium; University of Southern Denmark, Department of Environmental Medicine, Denmark
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Fucic A, Katic J, Fthenou E, Kogevinas M, Plavec D, Koppe J, Batinic D, Chalkiadaki G, Chatzi L, Lasan R, Kleinjans J, Kirsch-Volders M. Increased frequency of micronuclei in mononucleated lymphocytes and cytome analysis in healthy newborns as an early warning biomarkers of possible future health risks. Reprod Toxicol 2013; 42:110-5. [DOI: 10.1016/j.reprotox.2013.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/06/2013] [Accepted: 08/16/2013] [Indexed: 11/17/2022]
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