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Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

Karine Audouze, Agnieszka Sierakowska Juncker, Francisco J. S. S. A. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak, Olaf G. Wiest
2010 PLoS Computational Biology  
Additionally, the network can be used to identify unexpected potential associations between chemicals and proteins.  ...  Examples are shown for chemicals associated with breast cancer, lung cancer and necrosis, and potential protein targets for di-ethylhexyl-phthalate, 2,3,7,8-tetrachlorodibenzo-p-dioxin, pirinixic acid  ...  Acknowledgments The authors would like to thank Daniel Edsgä rd for his technical help and Ramneek Gupta for critical reading of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000788 pmid:20502671 pmcid:PMC2873901 fatcat:kmspfh4hubdzhjdovcj26fqn5m

In Silico Systems Pharmacology to Assess Drug's Therapeutic and Toxic Effects

Alejandro Aguayo-Orozco, Karine Audouze, Soren Brunak, Olivier Taboureau
2017 Current pharmaceutical design  
For many years, the "one target, one drug" paradigm has been the driving force behind developments in pharmaceutical research.  ...  The integration of large and diverse amount of data from chemistry and biology coupled with the development and the application of network-based approaches to cope with these data is the next paradigm  ...  ACKNOWLEDGEMENTS We would like to acknowledge EU-ToxRisk, a project funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 681002.  ... 
doi:10.2174/1381612822666160907093215 pmid:27604605 fatcat:ivd7ucersbbqtlnnxtf5rhe7ta

Approaches and perspectives to toxicogenetics and toxicogenomics

Ana Lucia Castiblanco Rodriguez
2015 Revista de la Facultad de Medicina  
The latter is the discipline that studies<br />the genomic response of organisms exposed to chemical<br />agents, including drugs, environmental pollutants, food<br />additives, and other commonly used  ...  The application<br />of this knowledge in toxicology is known as toxicogenetics<br />and toxicogenomics.  ...  Acknowledgments To the Pharmacogenetics Group of the Department of Pharmacy (Faculty of Science), to the Environmental and Occupational Toxicology Group of the Department of Toxicology (Faculty of Medicine  ... 
doi:10.15446/revfacmed.v62n4.45218 fatcat:qxsk3qxjufgaxjlywd5ikiyhgq

Computational systems biology as an animal-free approach to characterize toxicological effects of persistent organic pollutants_suppl

Qier Wu
2020 ALTEX: Alternatives to Animal Experimentation  
This work was also supported by the Université de Paris and INSERM.  ...  Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks.  ...  Using the POP-PPAN model for chemical toxicity prediction Besides revealing POP-AOP linkages, the network can be used to predict potential MoA for environmental chemicals.  ... 
doi:10.14573/altex.1910161s fatcat:55xgavru6rdp7o4iffpmlp6pkq

Human Environmental Disease Network: Deciphering disease-disease and chemicaldisease associations using chemical contaminants information_suppl

Olivier Taboureau
2016 ALTEX: Alternatives to Animal Experimentation  
Acknowledgments We would like to acknowledge EU-ToxRisk, a project funded by the European Union's Horizon 2020 research and innovation program under grant agreement No 681002.  ...  chemicals and biological targets .  ...  Deciphering possible links between novel chemicals and disease Besides revealing connections between diseases, the EDN can be used to assess the risk of a chemical to induce diseases.  ... 
doi:10.14573/altex.1607201s fatcat:igh22c2sb5hwnphsiacqby4xni

Application of Computational Systems Biology to Explore Environmental Toxicity Hazards

Karine Audouze, Philippe Grandjean
2011 Environmental Health Perspectives  
Methods: We extracted chemical-protein association networks for each DDT isomer and its metabolites using ChemProt, a disease chemical biology database that includes both binding and gene expression data  ...  As a complement to these databases, ChemProt, a new disease chemical biology database (Center for Biological Sequence Analysis 2011), provides information on chemical links to proteins along with chemical  ...  Because of these developments, advanced computational systems chemical biology models have been developed to decipher the association between environmental chemicals and diseases (Audouze et al. 2010)  ... 
doi:10.1289/ehp.1103533 pmid:21846611 pmcid:PMC3261980 fatcat:lvzjy5xdhnebxcmbi3ywnlncyi

Systems-level differential gene expression analysis reveals new genetic variants of oral cancer

Syeda Zahra Abbas, Muhammad Imran Qadir, Syed Aun Muhammad
2020 Scientific Reports  
We used human proteomic data for post-translational modifications to interpret disease mutations and inter-individual genetic variations.  ...  The MiRNA target prediction showed functional molecular annotation including specific miRNA-targets hsa-miR-4282, hsa-miR-2052, hsa-miR-216a-3p, for CYP1B1, C7, and ADCY2 respectively associated with oral  ...  The integration of chemical-gene interaction revealed different environmental chemical exposure to disease progression 52, 53 .  ... 
doi:10.1038/s41598-020-71346-7 pmid:32887903 fatcat:pnuz5xhgkjcurajjxjn4paapym

Computational systems biology as an animal-free approach to characterize toxicological effects of persistent organic pollutants

Qier Wu
2020 ALTEX: Alternatives to Animal Experimentation  
This study highlights that computational systems toxicology approach may help to decipher putative biological mechanisms of poorly studied chemicals, and to link them to possible adverse effects with the  ...  This model was used to predict protein complexes for several candidate POPs, including dicofol, methoxychlor and perfluorooctanoic acid (PFOA), that are listed or proposed to be listed as POPs in the Stockholm  ...  This work was also supported by the Université de Paris and INSERM.  ... 
doi:10.14573/altex.1910161 pmid:31960936 fatcat:ume6qamuzfa7pacuvxsg2j52tu

Toxicogenomics Investigation Under the eTOX Project

Olivier Taboureau, Anne Hersey
2012 Journal of Pharmacogenomics & Pharmacoproteomics  
Acknowledgement The authors would like to acknowledge the Innovative Medicines Initiative Joint Undertaking (eTOX) for supporting the work.  ...  In addition, Low Y. et al. showed that hybrid models combining both chemical descriptors and gene expression profiles could be useful for the interpretation of druginduced hepatotoxicity [25] .  ...  For example, a tool like GenMAPP integrates several biological pathways relevant for rat and human toxicicty [19] .  ... 
doi:10.4172/2153-0645.s7-001 fatcat:p3zasutmibc7xckgrzb2dcy5kq

The use of systems biology in chemical risk assessment

Alejandro Aguayo-Orozco, Olivier Taboureau, Søren Brunak
2019 Current Opinion in Toxicology  
Although all omics technologies may contribute to better understanding of the toxicological impact of chemicals, their application in chemical risk assessment has not yet been recommended for regulatory  ...  In this review, we discuss the advantages of the use of systems biology tools in chemical risk assessment, as well as the challenges they present, such as model over-parametrisation in quantitative modelling  ...  The author would like to thank Catherine Collin Bjerre for proof reading of the manuscript.  ... 
doi:10.1016/j.cotox.2019.03.003 fatcat:3u6hxjdygbfstlnbwhtzlj7wzq

Human environmental disease network: A computational model to assess toxicology of contaminants

Olivier Taboureau
2017 ALTEX: Alternatives to Animal Experimentation  
We developed a human environmental disease network (EDN) to explore and suggest novel disease-disease and chemical-disease relationships.  ...  During the past decades, many epidemiological, toxicological and biological studies have been performed to assess the role of environmental chemicals as potential toxicants for diverse human disorders.  ...  Acknowledgments We would like to acknowledge EU-ToxRisk, a project funded by the European Union's Horizon 2020 research and innovation program under grant agreement No 681002.  ... 
doi:10.14573/altex.1607201 pmid:27768803 fatcat:abwcetsju5cnjeovp7tkfmnc2q

Metabolomics as a powerful tool to decipher the biological effects of environmental contaminants in humans

Nathalie Bonvallot, Arthur David, Frédéric Chalmel, Cécile Chevrier, Sylvaine Cordier, Jean-Pierre Cravedi, Daniel Zalko
2018 Current Opinion in Toxicology  
An innovative work is carrying out in order to integrate 265 massive toxicogenomics data for classification of chemicals and prediction of toxicity.  ...  Such an integrative approach provides 263 global biological signatures to better categorize groups of chemicals both for environmental 264 epidemiology and risk assessment.  ... 
doi:10.1016/j.cotox.2017.12.007 fatcat:yekpvtjlxrhwnkno4w75cmqs2q

Toxicogenomics: A 2020 Vision

Zhichao Liu, Ruili Huang, Ruth Roberts, Weida Tong
2019 TIPS - Trends in Pharmacological Sciences  
) to study the adverse effects of environmental and pharmaceutical chemicals on human health and the environment.  ...  KEGG: Kyoto Encyclopedia of Genes and Genomes database, a collection of data resources that takes account of the complex relationship among biological pathways, diseases, and chemical substances/drugs.  ... 
doi:10.1016/ fatcat:bzqazo7oenhavkon7u6qn4zh4e

The EDCMET Project: Metabolic Effects of Endocrine Disruptors

Jenni Küblbeck, Taina Vuorio, Jonna Niskanen, Vittorio Fortino, Albert Braeuning, Khaled Abass, Arja Rautio, Jukka Hakkola, Paavo Honkakoski, Anna-Liisa Levonen
2020 International Journal of Molecular Sciences  
understanding of the molecular mechanisms of metabolic disease and comprehensive in vitro and in vivo methodological skills; and, ultimately, epidemiologists linking environmental exposure to adverse  ...  The concept of endocrine disruption has recently been extended to metabolic alterations that may result in diseases, such as obesity, diabetes, and fatty liver disease, and constitute an increasing health  ...  Gene expression data, biological annotations, and manually-curated associations between chemicals, genes, phenotypes, and diseases will be fed into data-mining and machine-learning algorithms to characterize  ... 
doi:10.3390/ijms21083021 pmid:32344727 fatcat:65jyzqhwiffidkyualtrezhrlm

Pluripotent Stem Cells in Toxicity Testing: An Omics Approach [chapter]

Smita Jagtap, Kesavan Meganathan, Vilas Wagh
2016 Pluripotent Stem Cells - From the Bench to the Clinic  
In order to provide cost-efficient and high-throughput methods, various in vitro test systems have been proposed to access toxicity for environmental toxicants and many drugs.  ...  Although effective, these platforms are based on in vitro cell cultures and ex vivo models using embryo cultures and often do not accurately interpret results for human safety because of interspecies difference  ...  Omics technologies have been used to decipher the networks of signaling events and perturb molecular signaling to identify the new therapeutic targets [6] .  ... 
doi:10.5772/63929 fatcat:rcgseuh5wzgkrpa6wdrlzlz7ie
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