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Integrated Analysis of Toxicology Data supported by ToxBank

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The SEURAT-1 (Safety Evaluation Ultimately Replacing Animal Testing-1) research cluster is comprised of seven EU FP7 Health projects and is co-financed by Cosmetics Europe. The aim is to generate a proof-of-concept to show how the latest in vitro and in silico technologies, systems toxicology and toxicogenomics can be combined to deliver a test replacement for repeated dose systemic toxicity testing on animals. The SEURAT-1 strategy is to adopt a mode-of-action framework to describe repeated dose toxicity to derive predictions of in vivo toxicity responses. ToxBank is the cross-cluster infrastructure project whose activities include the development of a data warehouse to provide a web-accessible shared repository of research data and protocols. Experiments are generating dose response data over multiple timepoints using different omics platforms including transcriptomics, proteomics, metabolomics, epigenetics over a variety of different cell lines and a common set of reference compounds. Experimental data is also being generated from functional assays and bioreactors, and supplemented with in silico approaches including kinetic information. This complex and heterogeneous data is being consolidated and harmonized through the ToxBank data warehouse. It is being organized in order to perform an integrated data analysis and ultimately predict repeated dose systemic toxicity. Core technologies used include the ISA-Tab universal data exchange format, Representational State Transfer (REST) web services, the W3C Resource Description Framework (RDF) and the OpenTox standards. We describe the design of the data warehouse based on cluster requirements and the implementation based on open standards.

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Integrated Analysis of Toxicology Data supported by ToxBank

  1. 1. Integrated Analysis of Toxicology Data supported by ToxBank OpenTox Euro 2013 Meeting Mainz, Germany October 1, 2013 Barry.Hardy@douglasconnect.com This project is jointly funded by Cosmetics Europe and the European Commission. Any opinions expressed in these slides are those of the author. Cosmetics Europe is not liable for any use that may be made of the information contained therein.
  2. 2. 18M
  3. 3. Islands Source: Baily Ed, U.S. Fish and Wildlife Service
  4. 4. Goal for next year for OpenTox - Accelerating Knowledge Flow of Industry Application and Regulatory Acceptance of New Predictive Toxicology Methods & Testing Strategies based upon an evolving OpenTox framework based on Open Specifications
  5. 5. Knowledge-Oriented Framework Based on Nonaka & Takeuchi, The Knowledge Creating Company, 1995 Socialisation Externalisation Internalisation Combination Tacit Tacit Tacit Tacit Explicit Explicit Explicit Explicit Knowledge Sharing: Discussions Knowledge Creation from R&D: Data, Codes Learning: Apply Models Knowledege Combination: Predictive Models Acceptance
  6. 6. Knowledge Sharing
  7. 7. OpenTox We are an Open Knowledge Community! We collaborate, solve problems and create the best solutions we can together. We learn from each other. We accelerate knowledge flow and innovation.
  8. 8. OpenTox standards Feature GET POST PUT DELETE Compound GET POST PUT DELETE Dataset GET POST PUT DELETE Ontology GET POST PUT DELETE Algorithm GET POST PUT DELETE Model GET POST PUT DELETE AppDomain GET POST PUT DELETE Validation GET POST PUT DELETE Report GET POST PUT DELETE www.opentox.org/dev/apis/api-1.2 Working Group formed to update for end of March 2014. You are invited to join and participate.
  9. 9. Plug In Components that solve Problems Adaptor Solution in Jeddah, 2008
  10. 10. The Building Blocks of SEURAT-1 ~ 70 research groups from European Universities, Public Research Institutes and Companies (more than 30% SMEs) www.seurat-1.eu This project is jointly funded by Cosmetics Europe and the EC. Any opinions expressed in this slide are those of the author. Cosmetics Europe is not liable for any use that may be made of the information contained therein.
  11. 11. Building block 1: Scr&Tox Stem cell differentiation for providing human-based organ specific target cells Coordinator: Marc Peschanski INSERM/i-STEM France website: www.scrtox.eu The cell factory
  12. 12. Building block 2: HeMiBio Development of a hepatic microfluidic bioreactor Coordinator: Catherine Verfaillie KU LEUVEN, Belgium website: www.hemibio.eu The in vitro liver
  13. 13. Building block 3: DETECTIVE Identification of biomarkers for prediction of toxicity in humans Coordinator: Jürgen Hescheler Klinikum der Universität Köln, Germany website: Biomarkers and functional assays PC 1 #15.3 % PC2# 12.4% Day 0 Day 7- EBs Day 7- Thalidomide Td Day 7- Cytarabine Td Day 14 - EBs Day 14- Thalidomide Td Day 14- Cytarabine Td
  14. 14. Building block 4: COSMOS Delivery of computational tools to predict the effects of chemicals based on in silico calculations and estimation techniques Coordinator: Mark Cronin Liverpool John Moores University, UK website: www.cosmos-tox.eu In silico toxicology
  15. 15. Building block 5: NOTOX Coordinator: Elmar Heinzle Universität des Saarlandes, Germany website: www. notox-sb.eu Development of systems biological tools for organotypic human cell cultures Bioreactor Thinking in systems
  16. 16. ToxBank Infrastructure Project (started Jan 2011) Establishment of a … … dedicated web-based data warehouse … database of reference test compounds … repository for the selected test compounds … cell and tissue banking information resource This project is jointly funded by Cosmetics Europe and the EC. Any opinions expressed in this slide are those of the author. Cosmetics Europe is not liable for any use that may be made of the information contained therein. www.toxbank.net
  17. 17. Warehouse Gold Compounds Database Biobank Users access compounds, biological materials, data and models for experimental planning and integrated analysis of experimental results Data Models SOPs Compounds SOPs Biological Materials Our Infrastructure Vision for ToxBank supporting all steps of Predictive Toxicology Research based on Alternative Testing methods This project is jointly funded by Cosmetics Europe and the EC. Any opinions expressed in this slide are those of the author. Cosmetics Europe is not liable for any use that may be made of the information contained therein. Data Models RES www.toxbank.net
  18. 18. Compound Selection  Compound Assessment Team: Dave Bower, Matthew Clark, Matthew Dent, Marina Goumenou, Gabrielle Hawksworth, Nina Jeliazkova, Brigitte Landesmann, Silvia Maggioni, Andrew White, Egon Willighagen, Jeffrey Wiseman  Gold Compound Working Group: Roman Affentranger, Gordana Apic, Emilio Benfenati, Ian Cotgreave, Barry Hardy, Jan Hengstler, Susanne Bremer-Hoffmann, Paul Jennings, Giovanna Lazzari, Inge Mangelsdorf, Filomain Nguemo, Foozia Noor, Agapios Sachinidis, Michael Schwarz, Leo van Grunsven, Mathieu Vinken, Manfred Watzele, Jose-Manuel Zaldivar
  19. 19. Background Assumptions: Assay Readout Examples  Hepatocellular necrosis: release of alanine aminotransferase and propidium iodide uptake without apoptosis  Apoptosis: NF-κB/p53, caspase-3 activation , and Hoechst/annexin staining  Inhibition of transporters, e.g. members of the ABC cassette transporter class  Intra-hepatic cholestatis  Steatosis and phospholipidosis: staining  Hepatocyte function: urea synthesis, glycogen storage, albumin secretion, fibrinogen secretion, P450 transformation capacity  Mitochondrial function: adenosine triphosphate (ATP) and membrane potential  Oxidative stress: glutathione (GSH) levels & lipid peroxidation
  20. 20. Consider adverse events relevant to cosmetics Identify drugs demonstrated to exhibit these adverse events in humans Add Mode of Action (MoA) standards with simpler profiles mapped against key events within Adverse Outcome Pathways (AOPs) Add non-reactive analogues where needed Mapping Mechanism to Pathway
  21. 21. Adverse outcome pathway (AOP) : drug-induced cholestasis Vinken M., Landesmann B., Goumenou M., Vinken S., Shah I., Jaeschke H., Willett C., Whelan M., Rogiers V. (2013) Development of an adverse outcome pathway from drug-mediated bile salt export pump inhibition to cholestatic liver injury. Archives of Toxicology: submitted .
  22. 22. Compound Selection: Reference Toxicities to Biological Pathways Energy Metabolism Lipid Metabolism Inflammatory Response Steatosis Cholestasis Necrosis / Apoptosis Fibrosis Regeneration (Phospho- lipidosis)
  23. 23. Compound Selection and Mechanistic Testing
  24. 24. ToxBank Gold Compound - Doxorubicin
  25. 25. ToxBank Gold Compound - Doxorubicin
  26. 26. ToxBank Gold Compound - Doxorubicin
  27. 27. ToxBank Wiki Development wiki.toxbank.net
  28. 28. Information resources • Gold compound wiki* – Information on selection criteria – In vivo, PB-PK data, ‘omics/IC50, physical data and sources – Discussion forum • Biomaterials wiki – Information on cells (stem cells, hES/iPS-derived cells, primary cells), reagents (e.g. antibodies, growth factors) and suppliers – Discussion forum * See published Open Access materials at wiki.toxbank.net
  29. 29. Requirements
  30. 30. Investigator Principal Investigator Use templates or define new templates Generate and enter data Generate and write protocol Review protocol Upload/update and assign: - summary info - access level - keywords Send email alert Investigator Register interest Investigator Investigator Search for information Access protocols and data Request access to confidential information Bilateral agreement Phase 2: Integrated data analysis Other sources Phase 1: Unified data access Review data Comment Outline of the ToxBank Data Warehouse
  31. 31. ToxBank – Initial Release & Testing Main screen Browse search results Upload protocols and data Download protocols and data Preparing data
  32. 32. Use of SEURAT-configured ISAcreator to prepare datasets SEURAT-1 information Investigation information Publications Templates for different assays Specify experimental factors Materials and results, with links to files containing the raw or processed data Each step linked to a SEURAT-1 protocol Terms mapped to ontologies
  33. 33. Security Use Open Standards on Resources but with extensive Authorisation and Authentication facilities accompanied by confidential data policies. e.g. Validation against Confidential Data Case implemented Spring 2011
  34. 34. ToxBank System for Data and Protocol Management Searching Uploading protocols and data
  35. 35. Uploading a protocol 35
  36. 36. Research Protocol vs. Standard Operating Procedure 36
  37. 37. Guidelines provides suggestions on protocol outline and content 37
  38. 38. Protocol review 38
  39. 39. Protocols are indexed using a keyword hierarchy 39 Set keywords to support searching, browsing and linking
  40. 40. Use of SEURAT-configured ISAcreator to prepare datasets Templates are available for different experiments SEURAT-1 information Investigation information Publications
  41. 41. Use of SEURAT-configured ISAcreator to prepare datasets Templates for different assays Specify experimental factors
  42. 42. Use of SEURAT-configured ISAcreator to prepare datasets Results, with links to files containing the raw or processed data Results, with each step linked to a SEURAT-1 protocol
  43. 43. Use of SEURAT-configured ISAcreator to prepare datasets Mapped to terms in ontologies
  44. 44. Create an ISATAB zip archive for each investigation Test results (a… files) with links to data table or native file (e.g. CEL files) Overall investigation design and information (i… files) Study description (s… files)
  45. 45. Publishing a protocol Unique ID and version number
  46. 46. Viewing the investigation record
  47. 47. Linking to wikis 47 wiki.toxbank.net
  48. 48. ToxBank Wiki Development wiki.toxbank.net
  49. 49. ToxBank integrates systems biology concepts into toxicological assessment Pekka Kohonen,[a] Emilio Benfenati,[b] David Bower,[c] Rebecca Ceder,[a] Michael Crump,[c] Kevin Cross,[c] Roland C. Grafstrçm,[a] Lyn Healy,[d] Christoph Helma,[e] Nina Jeliazkova,[f] Vedrin Jeliazkov,[f] Silvia Maggioni,[b] Scott Miller,[c] Glenn Myatt,[c] Michael Rautenberg,[e] Glyn Stacey,[d] Egon Willighagen,[a] Jeff Wiseman,[g] and Barry Hardy*[h]; [a]Karolinska Institutet, Institute for Environmental Medicine, Molecular Toxicology,Stockholm, Sweden; [b], Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy; [c] Leadscope, Columbus, USA; [d] National Institute for Biological Standards and Control, Potters Bar, UK; [e]In silico toxicology, Basel, Switzerland; [f]Ideaconsult, Sofia, Bulgaria; [g]Pharmatrope,Wayne, USA; [h]Douglas Connect, Zeiningen, Switzerland. Figure 1. Multiple tools will be, step by step, implemented into an innovative toxicity testing strategy based on mode-of-action. Figure 2. Clustering of ToxBank Gold Compounds by biological similarity using chemical-genome links from Comparative Toxicogenomics Database (CTD). Compounds with similar Mode-of-Action cluster together. Systems toxicology - principles Understanding the toxicological interactions in biological systems under compound challenges Based on developments in high-throughput biology  ‘Omics profiling: gene expression, proteins, metabolites and others  cell-based screening: High-Throughput and High-Content analyses Risk assessment carried out primarily using  in vitro  In silico methods Conclusions - great potential to contribute to toxicity evaluation based on Mode-of-Action decreased need for animal experiments ToxBank builds databases and data management solutions to aid in systems toxicology-based risk assessment Clustering by Gene Clustering by Gene Ontology BA Figure 3. A) Enriched gene ontology (GO) categories of genes associated with the oxidizing agent mode-of-action (MOA) B) Protein-protein association network around the Asah1 protein Associated with phospholipid binding MOA. Kohonen P. et al. The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. 17 JAN 2013, DOI: 10.1002/minf.201200114.
  50. 50. Public Data Analysis Molecular function Binding 19 genes adjP=6.61e-01 Catalytic activity 9 genes adjP=6.75e-01 Electron carrier activity 3 genes adjP=1.75e-02 Transporter activity Nucleoside binding 3 genes adjP=6.75e-01 Nucleotide binding Protein binding 12 genes adjP=6.75e-01 Oxidoreductase activity 5 genes adjP=1.75e-02 Transmembrane transporter activity 3 genes adjP=6.61e-01 Phospholipid Binding Oxidative Agent Clustering by Gene Ontology associations from CTD* *CTD = Comparative Toxicogenomics Database (www.ctd.org) Kohonen P. et al. The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Mol. Inf.17 JAN 2013.
  51. 51. onlinelibrary.wiley.com/doi/10.1002/minf.201200114/full Web Resources - Open Access
  52. 52. SAM ICT Architecture CERF Enterprise Service Bus Consensus Rule Editor CEPS Complex Event Pattern Service Collaboration Pattern Assistant Data, Protocols, Results Data Data Events Consensus Rule Outcome Collaboration Pattern Suggestions • There is a data conflict. • Method A is not providing accurate predictions. • New information is available. • etc. • Hold a meeting! • Discuss a new strategy! • Contact partner Y! Data is exchanged as ontology-based messages SAM partners generate data/protocols using external tools and platforms (e.g. OpenTox) Data Hardy and Affentranger, Drug Discovery Today. 2013 Jul;18(13-14):681-6.
  53. 53. Model1 Model2 Model3 1 0 1 Model1 Model2 Model3 1 0 1 Assay1 Assay2 Assay3 - - - Assay1 Assay2 Assay3 - - - Recommendation Rules: 0 0 1 0 1 1 1 0 0 1 0 1 1 1 0 0 1 0 Hit, high confidence Not a hit, high confidence Inconclusive results, further study needed Synergy OpenTox 1 1 1 0 0 0 Event Driven Weight of Evidence Consensus Rule Editor
  54. 54. Event-driven Weight of Evidence Hardy and Affentranger, Drug Discovery Today. 2013 Jul;18(13-14):681-6.
  55. 55. ToxBank Acknowledgements UK Stem Cell Bank, NIBSC-HPA Ideaconsult Ltd

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