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In Vitro Data and In Silico Models for
Predictive Toxicology
The SEURAT project
Elisabet Berggren
European Commission, Joint Research Centre / COACH
2
• Cluster of seven collaborative projects
• 50 million Euro investment
• Co-financed by EC and Cosmetics Europe
• Over 70 research partners
• 16 countries plus EC
• 6 year programme
Seurat-1: towards replacement of in vivo
repeated dose systemic toxicity testing
http://www.seurat-1.eu/
210 3 4 5 6 years
2nd PoC ,
1st PoC updated
SEURAT-1
case study
descriptions
2nd PoC
Kick-off
Kick-Off
Meeting Final Report
COACH
SEURAT-1 MAIN SEURAT-2
    
GC WG
DA WG JRC

SA WG
MoA WG
BKWG
Data
Ware-
house
T&M Cat.
3rd PoC
1st PoC
The SEURAT-1 Roadmap
SEURAT-1
Annual Meeting
 SEURAT-1
Annual Report
SCWG
WE ARE HERE
http://www.seurat-1.eu/
The SEURAT strategy is to adopt a toxicological
mode-of-action framework to describe how
any substance may adversely affect human health,
and to use this knowledge to develop
complementary theoretical, computational and
experimental (in vitro) models that predict
quantitative points of departure needed for safety
assessment.
SEURAT - The Strategy
www.seurat-1.eu
Scientific Tools
Chemical
Cells exchange
… development underpinned by mode-of-action rationale
Bioreactors for
engineering tissues
Models to link in vitro
to in vivo biokinetics
Database on cosmetics
ingredients and properties
Genetically engineered
reporter-gene cell lines
Multi-scale models of
organ toxicity
Protocols for stably
differentiated iPSC
Project data and
protocol warehouse
6
Adverse Outcome Pathway:
Structure the information in order to be able
to PREDICT adverse health effects
Molecular
Initiating Events
Key Events
Adverse
Outcomes
7
Level 1, KNOWLEDGE:
Adverse Outcome Pathway (AOP) constructs
Level 3, APPLICATION:
Predictive systems to support regulatory safety assessment
SEURAT-1 Proof of Concept on three levels:
Level 2, PREDICTION: Integrated systems including in
vitro and computational methods to predict toxicity
8
Visit AOP Wiki (https://aopkb.org) to
explore currently mapped AOPs,
improve them or add new ones.
Structure the AOP information in
collaboration with the rest of the world
http://wiki.toxbank.net/wiki
ToxBank Wiki
10
For the first time ever hiPS-
derived hepatocytes was used
for repeated dose toxicity
studies (Holmgren et al. (2014)
in Drug Metab. Disp., 42(9):
1401-1406
Development of an in vitro drug‐induced
liver fibrosis model
Differentiation of stem cell-derived
hepatocytes
A flavor of highlights from the SEURAT-1
projects
(MTX = Methotrexate)
Spheroids with co-cultured HepaRG
and Hepatic Stellate Cells
showing accumulation of collagen
1
11
Liver cell toxicity reporters to identify
hepatotoxicant-induced cellular stress responses
A flavor of highlights from the SEURAT-1
projects
2
A toxicity reporter platform based on BAC (Bacterial Artificial
Chromosome) engineering of the human HepG2 cells (Wink et al
(2014) in Chem.Res. Toxicol., 27: 338-355.)
Prediction of steatosis through repeated dose
exposure to 3D HepaRG system combined with
Biokinetic modelling
In vitro data and in silico models for predictive toxicology
COSMOS database
o Open-access
o High-quality toxicity data (quality
controlled, curated structures)
o User-friendly query builder (chemical
name, structure, toxicity data)
o 44,765 unique chemical structures
o 12,538 toxicity studies for 1,660
compounds across 27 endpoints
Webinar and tutorial:
http://www.cosmostox.eu/what/COSMOSdb/
http://cosmosdb.cosmostox.eu/
13
Models are Freely Available Through
COSMOS KNIME WebPortal and Space
Documentation,
user guidance,
web tutorials
JRC, Ispra, June 2013
Scientific Tools
Chemical
Cells exchange
… how to translate
them into solutions for
safety assessment?
Safety Assessment Working Group
TTC
One conceptual framework - three case studies:
Pieces of evidence and initial considerations
· Purpose of the assessment
· Exposure context
· Expert knowledge and judgement based on existing evidence / data
General adversities Organ specific adversities
Toxicodynamics
· Target organ: full assessment based on
Adverse Outcome Pathway (AOP)1
· Non-target organ: limited assessment
Toxicokinetics
Assessment of ADME properties
Overall Assessment (including uncertainties and knowledge gaps)
Use of prediction for pre-defined
purpose (with consideration of
acceptable uncertainty)
Improve assessment if necessary
1) The steps in the AOP (molecular initiating event, key events) will be assessed using a
selection of tools including in silico predictions and in vitro tests.
Hypothesis generation
regarding mode of action
Toxicodynamics
· Many biological targets (based on chemi-
cal structure, e.g. alkylating agents)
· Specific targets present in many cells /
tissues / organs (e.g. AhR-pathway)
Type of adversity
Definition of relevant
dose range
Determination of
point of departure
Evaluation
Result
AB INITIO
I. Chemical similarity of compounds that do not require metabolic
transformation to exert a potential adverse human health effect
II. Chemical similarity involving metabolic transformation resulting in
exposure to the same/similar proximal toxicant
III. Chemicals with general low or no toxicity
IV. Distinguishing chemicals in a structurally similar category with variable
toxicities based on Mode of Action hypothesis
Four different scenarios
In vitro data and in silico models for predictive toxicology
coach-arttic@eurtd.com20
Final Reporting
You are all welcome Register at: http://www.seurat-1.eu/
Horizon 2020 project: EUToxRisk21
Starting this autumn will continue what
SEURAT-1 started.
Thanks for the attention!

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In vitro data and in silico models for predictive toxicology

  • 1. In Vitro Data and In Silico Models for Predictive Toxicology The SEURAT project Elisabet Berggren European Commission, Joint Research Centre / COACH
  • 2. 2 • Cluster of seven collaborative projects • 50 million Euro investment • Co-financed by EC and Cosmetics Europe • Over 70 research partners • 16 countries plus EC • 6 year programme Seurat-1: towards replacement of in vivo repeated dose systemic toxicity testing http://www.seurat-1.eu/
  • 3. 210 3 4 5 6 years 2nd PoC , 1st PoC updated SEURAT-1 case study descriptions 2nd PoC Kick-off Kick-Off Meeting Final Report COACH SEURAT-1 MAIN SEURAT-2      GC WG DA WG JRC  SA WG MoA WG BKWG Data Ware- house T&M Cat. 3rd PoC 1st PoC The SEURAT-1 Roadmap SEURAT-1 Annual Meeting  SEURAT-1 Annual Report SCWG WE ARE HERE http://www.seurat-1.eu/
  • 4. The SEURAT strategy is to adopt a toxicological mode-of-action framework to describe how any substance may adversely affect human health, and to use this knowledge to develop complementary theoretical, computational and experimental (in vitro) models that predict quantitative points of departure needed for safety assessment. SEURAT - The Strategy www.seurat-1.eu
  • 5. Scientific Tools Chemical Cells exchange … development underpinned by mode-of-action rationale Bioreactors for engineering tissues Models to link in vitro to in vivo biokinetics Database on cosmetics ingredients and properties Genetically engineered reporter-gene cell lines Multi-scale models of organ toxicity Protocols for stably differentiated iPSC Project data and protocol warehouse
  • 6. 6 Adverse Outcome Pathway: Structure the information in order to be able to PREDICT adverse health effects Molecular Initiating Events Key Events Adverse Outcomes
  • 7. 7 Level 1, KNOWLEDGE: Adverse Outcome Pathway (AOP) constructs Level 3, APPLICATION: Predictive systems to support regulatory safety assessment SEURAT-1 Proof of Concept on three levels: Level 2, PREDICTION: Integrated systems including in vitro and computational methods to predict toxicity
  • 8. 8 Visit AOP Wiki (https://aopkb.org) to explore currently mapped AOPs, improve them or add new ones. Structure the AOP information in collaboration with the rest of the world
  • 10. 10 For the first time ever hiPS- derived hepatocytes was used for repeated dose toxicity studies (Holmgren et al. (2014) in Drug Metab. Disp., 42(9): 1401-1406 Development of an in vitro drug‐induced liver fibrosis model Differentiation of stem cell-derived hepatocytes A flavor of highlights from the SEURAT-1 projects (MTX = Methotrexate) Spheroids with co-cultured HepaRG and Hepatic Stellate Cells showing accumulation of collagen 1
  • 11. 11 Liver cell toxicity reporters to identify hepatotoxicant-induced cellular stress responses A flavor of highlights from the SEURAT-1 projects 2 A toxicity reporter platform based on BAC (Bacterial Artificial Chromosome) engineering of the human HepG2 cells (Wink et al (2014) in Chem.Res. Toxicol., 27: 338-355.) Prediction of steatosis through repeated dose exposure to 3D HepaRG system combined with Biokinetic modelling
  • 13. COSMOS database o Open-access o High-quality toxicity data (quality controlled, curated structures) o User-friendly query builder (chemical name, structure, toxicity data) o 44,765 unique chemical structures o 12,538 toxicity studies for 1,660 compounds across 27 endpoints Webinar and tutorial: http://www.cosmostox.eu/what/COSMOSdb/ http://cosmosdb.cosmostox.eu/ 13
  • 14. Models are Freely Available Through COSMOS KNIME WebPortal and Space Documentation, user guidance, web tutorials
  • 16. Scientific Tools Chemical Cells exchange … how to translate them into solutions for safety assessment?
  • 17. Safety Assessment Working Group TTC One conceptual framework - three case studies: Pieces of evidence and initial considerations · Purpose of the assessment · Exposure context · Expert knowledge and judgement based on existing evidence / data General adversities Organ specific adversities Toxicodynamics · Target organ: full assessment based on Adverse Outcome Pathway (AOP)1 · Non-target organ: limited assessment Toxicokinetics Assessment of ADME properties Overall Assessment (including uncertainties and knowledge gaps) Use of prediction for pre-defined purpose (with consideration of acceptable uncertainty) Improve assessment if necessary 1) The steps in the AOP (molecular initiating event, key events) will be assessed using a selection of tools including in silico predictions and in vitro tests. Hypothesis generation regarding mode of action Toxicodynamics · Many biological targets (based on chemi- cal structure, e.g. alkylating agents) · Specific targets present in many cells / tissues / organs (e.g. AhR-pathway) Type of adversity Definition of relevant dose range Determination of point of departure Evaluation Result AB INITIO
  • 18. I. Chemical similarity of compounds that do not require metabolic transformation to exert a potential adverse human health effect II. Chemical similarity involving metabolic transformation resulting in exposure to the same/similar proximal toxicant III. Chemicals with general low or no toxicity IV. Distinguishing chemicals in a structurally similar category with variable toxicities based on Mode of Action hypothesis Four different scenarios
  • 21. Final Reporting You are all welcome Register at: http://www.seurat-1.eu/ Horizon 2020 project: EUToxRisk21 Starting this autumn will continue what SEURAT-1 started.
  • 22. Thanks for the attention!