Hartung and Le Lab Joining Forces for the
Hartung and Le Lab Joining Forces for the Joohns Hopkins Metabolomics Program Thomas Hartung, Andre Kleensang & team Center for Alternatives to Animal Testing
1981 Stakeholder Platform 2010 Transatlantic Hub 2012 CAAT EU Policy Program
Funding from industry, philanthropy and research funding agencies The Bernice Barbour Foundation …and individuals
The changing approach in Toxicology Curated Legacy Data e. g. REACH, Tox. Ref. DB, Pub. Chem High-Throughput Screening e. g. Tox. Cast, Tox 21 Omics techologies e. g. transcriptomics, metabolomics, exposomics High-Content Imaging e. g. Eu. Tox. Risk 4
Why metabolomics? Mammalian Species Genotype DNA Genomics (25, 000 genes) RNA Transcriptomics (100, 000 m. RNAs) mi. RNAs Proteins Phenotype Metabolites mi. RNomics (2, 042 mi. RNAs) Proteomics (1, 000 proteins) Metabolomics (5, 000 -7, 000 metabolites)
ALTEX 2015 32, 319 -326 METABOLOMICS 3 WORKSHOPS 2 INFODAYS ALTEX 2013 30, 209 -225 6
Pathways of toxicology from multi-omics In vitro model omics data generation Software tools Pathways of Toxicity Mapping the Human Toxome by Systems Toxicology NIH Transformative Research Grant 15 publications, 2 under review http: //humantoxome. com Validation tools Human Toxome Database
Untargeted Metabolomics – pros and cons • Small effect strengths • Flux more important • Fast changes • Incomplete extractions and measurements • Metabolite identification difficult • QA incomplete • Sensitive • Inexpensive • Close to phenotype • Little species differences • Only thousands of parameters • Biochemical pathways 8
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.
Toxome Collaboratorium • • • Amazon Cloud Metadata Commercial, Custom Open Source Software Open. LAB ELN 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 Microarrays NGS Feature Extractor Gene. Spring GX Bio. Conductor Avadis NGS Aligners Scalable Computing Consortium Data Public Data CONFIDENTIAL 10 LC/MS Integrated Biology METLIN PCDL Hamner Ontology Map Mass. Hunter Gene. Spring MPP Gene. Spring PA
Agilent Customized Software for Human Toxome Mapping Ø Gene. Spring Workgroup Plus – server-based collaborative bioinformatics environment in Amazon cloud accessible to all members of the consortium Ø Agilent Bridge. DB – enhanced mapping metabolites onto biological pathways Ø Mass. Hunter Pro. Finder – new recursive batch extraction for metabolomics Ø Correlation Analysis in Gene. Spring for transcriptomics & metabolomics Ø Methods Automation in MPP Feature Finding Alignment & Statistics Identify Pathways Mass. Hunter Qual MPP ID Browser Pathway Architect Ø KEGG content in Pathway Architect Ø Pathways-to-PCDL
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 Po. T mapping Dedicated software tools, some already commercially available Workflow for pathway mapping established - first examples - scalable process Ongoing: Po. T Annotation and Validation 12
What this project is not…. …an endocrine disruptor screening project …a test development project …an academic publish or perish project …a five year project 13
• Nature blog at start • 2 hour event in European Parliament • Science coverage • Nature coverage • Lay press like Le. Monde, La Recherche, Sueddeutsche Zeitung, BBC, RAI-1, Laboratorio 2000 • NIEHS
International expansion? 15
Collaborations within JHU and beyond Examples
Goal: Make this experience and instrumentation available http: //ictr. johnshopkins. edu/consulting-services/translational-laboratory -core/metabolomics-program/
But some problems are – that’s were metabolomics come in!
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