1. Hartung and Le Lab Joining Forces for the Joohns Hopkins Metabolomics Program
Thomas Hartung, Andre Kleensang & team
Center for Alternatives to Animal Testing

2. 2010 1981 2012 Transatlantic Hub CAAT EU Policy Program
Stakeholder Platform

3. Funding from industry, philanthropy and research funding agencies
The Bernice Barbour
Foundation
…and individuals

4. The changing approach in Toxicology
Curated Legacy Data
e.g. REACH, ToxRefDB, PubChem
High-Throughput Screening
e.g. ToxCast, Tox21
Omics techologies
e.g. transcriptomics, metabolomics,
exposomics
High-Content
Imaging
e.g. EuToxRisk

5. Why metabolomics? miRNomics (2,042 miRNAs) Metabolomics
Mammalian Species
Genotype
DNA
Genomics
(25,000 genes)
RNA
Transcriptomics
(100,000 mRNAs)
miRNAs
miRNomics
(2,042 miRNAs)
Proteins
Proteomics
(1,000,000 proteins)
Phenotype
Metabolites
Metabolomics
(5,000-7,000 metabolites)

6. METABOLOMICS 3 WORKSHOPS 2 INFODAYS ALTEX 2015 32, 319-326 ALTEX 2013
30,

7. Mapping the Human Toxome by Systems Toxicology
Pathways of toxicology from multi-omics
In vitro model
omics data generation
Pathways of Toxicity
Software tools
Validation tools
Human Toxome Database
Mapping the Human Toxome by Systems Toxicology
NIH Transformative Research Grant
15 publications, 2 under review

8. Untargeted Metabolomics – pros and cons
Sensitive
Inexpensive
Close to phenotype
Little species differences
Only thousands of parameters
Biochemical pathways
Small effect strengths
Flux more important
Fast changes
Incomplete extractions and measurements
Metabolite identification difficult
QA incomplete

9. Understanding Pathways of Toxicity with –Omics Technologies
Use a weighted correlation approach that clusters metabolites by network topology
The resulting clusters can be used for further analysis with text-mining and other sources of high throughput data
This approach is then compared to other pathway analysis results.

10. Toxome Collaboratorium
A set of connected servers for all Toxome analysis, LIMS and data sharing needs
Hosted in the Amazon cloud, accessible by all members
Commercial and open source software
Compendium of consortium-generated and relevant public domain datasets
Portable, reusable, reference infrastructure
Supported, easy to re-deploy, can be used by future efforts
Amazon Cloud
Integrated Biology
Hamner Ontology Map
GeneSpring PA
OpenLAB ELN
Metadata
Microarrays
Feature Extractor
GeneSpring GX
BioConductor
NGS
Avadis NGS
Aligners
GeneSpring MPP
LC/MS
MassHunter
METLIN PCDL
Commercial, Custom
Open Source Software
Scalable Computing
Consortium Data
Public Data
CONFIDENTIAL

11. Agilent Customized Software for Human Toxome Mapping
GeneSpring Workgroup Plus – server-based collaborative bioinformatics environment in Amazon cloud accessible to all members of the consortium
Agilent BridgeDB – enhanced mapping metabolites onto biological pathways
MassHunter ProFinder – new recursive batch extraction for metabolomics
Correlation Analysis in GeneSpring for transcriptomics & metabolomics
Methods Automation in MPP
KEGG content in Pathway Architect
Pathways-to-PCDL
Feature Finding
MassHunter Qual
Identify
ID Browser
Alignment & Statistics
MPP
Pathways
Pathway Architect

12. The Human Toxome project
Muti-omics, karyotyping and competitive genome hybridization show for the first time the full extent of instability of a tumor cell line.
QA for metabolomics
Tailoring and integration of tools for PoT mapping
Dedicated software tools, some already commercially available
Workflow for pathway mapping established - first examples - scalable process
Ongoing: PoT Annotation and Validation

13. What this project is not….
…an endocrine disruptor screening project
…a test development project
…an academic publish or perish project
…a five year project

14. Nature blog at start
2 hour event in European Parliament
Science coverage
Nature coverage
Lay press like LeMonde, La Recherche, Sueddeutsche Zeitung, BBC, RAI-1, Laboratorio 2000
NIEHS

15. International expansion?

16. Collaborations within JHU and beyond
Examples

17. Goal: Make this experience and instrumentation available

18. But some problems are
– that’s were metabolomics come in!