Frontiers in Predictive Toxicology Thomas Hartung · Classification Kilobases Percentage of genome...
Transcript of Frontiers in Predictive Toxicology Thomas Hartung · Classification Kilobases Percentage of genome...
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Thomas Hartung
Frontiers in Predictive Toxicology
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“Away-from-here that is
my destination”
Franz Kafka
You only bother about frontiers, if you need to travel
1st frontier
Agreement
that animal tests
are not good enough
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Genotoxic: sugar Genotoxic: salt
Protected against
TCDD in eggs
Same calculation
for alcohol:
One glass per
345 years
Protected
against minute
amounts of
pesticides
23 of 31
tested coffee
ingredients
carcinogenic
Natural
pesticides
10,000x more,
35 of 63
carcinogenic
Enjoy!!!
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Age 0 -100 years Mostly 3 months,
max 2 years
Different ethnics,
both gender
Mostly twins,
one gender
Diverse food,
environment
Standardized
chow and cage
2-200 kg 20-500 g
Disease history,
Comorbidities,
Multiple treatments
Healthy,
Artificial diseases,
Mono-treatments
We are not 70kg rats !!!
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Interspecies prediction of cancer
Concordance 57%
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Prediction of noncancer toxicologic outcomes in rodent bioassays of 37 chemicals from the National Toxicology Program was evaluated. … Overall, there is considerable uncertainty in predicting the site of toxic lesions in different species exposed to the same chemical and from short-term to long-term tests of the same chemical.
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37 chemicals
tested by US
National
Toxicology
Program
Earlier repeat-dose
studies
Cancer studies in
mice and rats of
both gender
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The test solution:
The uterotrophic assay
on ovarectomized rats + estrogenic
chemical
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Part of peer-
review
The uterotrophic assays
OECD-”validated” test
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OECD “Validated” Uterotrophic Assay
• “Of chemicals with >1 guideline-like
study, 26% had contradictory results
with at least one positive and one
negative study”
• “24 guideline- like uterotrophic assays
conducted for bisphenol A (BPA)
delivered by subcutaneous injection to
the immature rat, discordant results
ranged over 3 orders of magnitude”
500x more
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Bayer, 2011: 20-25% in-house studies reproduce publications
Amgen, 2012: 6% of cancer hallmark papers reproducible
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Systematic reviews
- Stroke
- Colon cancer
- head injury,
antifibrinolytics,
stroke, neonatal
resp. distress,
osteoporosis
- Emergency med.
- 25 other SR
- stroke
- diverse
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Consumer are little
aware of animal
testing for food
Strong
discrepancies for
e.g. food additives
vs. pesticides Evident data gaps
(PEW report 2013), but
traditional approaches
not suitable
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2nd frontier
Understanding that misleading animal
tests make a problem
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FDA-approved drugs per billion $ R&D
(inflation corrected) “Eroom’s Law”
Scannel et al., Nature Rev. Drug Disc. 2012
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Research Drug development Clinical trials
92% fail:
- 20% tox not
predicted
- 40% no efficacy
Average cost
$1,4 billion
1 in 100 patients
in hospitals dies
from adverse
drug reactions
$4-11 billion
Forbes 2012
95% fail
(Arrowsmith
2012)
47 drugs
withdrawn
since 1990
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3rd frontier
Understanding and overcoming
shortcomings of current in vitro tests
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Limitations of in vitro models
Mycoplasma
Dedifferentiation favored by
growth conditions and cell
selection
Cells are bored to death
Lack of oxygen
Lack of metabolism and
defense
Unknown fate of test
compounds in culture
Tumor origin of many cells
Cell identity
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Mapping the Human Toxome by Systems Toxicology
Hewitt et al., 2005. Science, 307:1572-1573
Endocrine disruption
• Use “omics” to map PoT for
endocrine disruption
• Develop software tools
• Identify PoT
• Develop a process for PoT
annotation, validation
• Establish public database on
PoT.
www.humantoxome.com
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negative controls, 4h, gene level, n = 3 / group
Same batch from ATCC
Method transfer
Transcriptomics
Comparison of MCF-7 in two laboratories
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QA of cell system is of critical importance
Good Cell Culture Practice (Coecke et al. 2005)
Karyotyping
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Extent of deviations from normal genome
Classification Kilobases Percentage of genome
Losses 4587603 51.2%
Deletions 667374 7.5%
Amplifications 26904 0.3%
Gains 2587093 28.9%
Normal 871166 9.7%
Centromeres 217339 2.4%
Total Abberations 7868974 87.8%
All Entries 8957479
SurePrint G3 ISCA CGH+SNP Microarray Kit, 4x180K
115234 CGH features.2440 CGH replicate probes, 59647 SNP features
reference mapping: caucasian female human reference DNA
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Workshops
Jun, Baltimore
Dec, Konstanz
Good Cell Culture Practice Collaboration Coecke et al. (2005), secretariat: David Pamies
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4th frontier
Creating organo-typic cell cultures
& organs on chip
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http://en.wikipedia.org/wiki/Organ-on-a-chip Stem cells &
Organo-typic
culture & High-
content
21st century
toxicology starts
with 21st century
cell culture
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Our mini-brain project
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Summary
Human “mini-brain”
• All cell types but micro-glia
• 350um diameter
• 800 per batch
• Reproducible
• Electrophysiological active
• From patient cells:
gene/environment
interactions
developing from iPSC
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Opportunities for human mini-
brain research
• Map the neurotoxic
chemical universe
• Characterization of medical
countermeasures
• Neurotoxic and DNToxic side effects
• Brain trauma, infectious disease and
neurodegenerative disease research
• Individual susceptibility using patient
iPSC – genetic risk factors
• Long-term culture and co-culture with
other organs
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5th frontier
Embracing other new technologies
and approaches
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Cell Culture (one cell type,
few parameters)
Structure / Activity-
Relationships (Correlations)
Early Alternatives
Organo-typic
Cell Culture (Coculture, Organ function,
often Perfusion)
Today
Automated Cell
Culture (high-
throughput Screening)
Systems Toxicology (“Virtual Patient”)
Human-on-chip (Multi-Organ Models
With Microfluidics)
Future
Toxicity Mechanisms (“Adverse Outcome Pathways”,
“Human Toxome”)
Modeling (Receptor binding,
Virtual Organs, Kinetics)
Cell Culture
+ Omics or Image
Analysis (high-content)
Integrated
Test Strategies (combined tests)
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Many PoT = many tests
Need for data integration
Use of multiple information,
not stand-alone replacement
OECD: Integrated Approaches to
Testing and Assessment (IATA)
= ITS + kinetics + exposure + RA
Integrated Testing Strategies
Toxicology will make more use of
Integrated Testing Strategies
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• ITS development sensitization &
eye irritation
• Commissioned whitepaper
Jaworska & Hoffmann
• WORKSHOP 2013
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Chemical similarity map (Tanimoto index)
• Structure alone does not suffice
• Feature elimination as good or
better than QSAR
• Supervised machine learning
optimizes ITS for skin sensitization
potency
• Hidden Markov Chain reduces
extreme misclassification
• Accuracy 60-70%, off-by-one-class
>90% standing cross-validation
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Mapping the Human
Toxome by Systems
Toxicology
In vitro
model
omics data
generation
Pathways
of Toxicity Software
tools
Validation
tools
Human
Toxome
Database
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ALTEX 2013
30, 209-225
METABOLOMICS
3 WORKSHOPS
2 INFODAYS
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International expansion?
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6th frontier
Big data & bioinformatics
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‘Omics’ Image analysis
High content High through-put
Information rich
Bioinformatics &
Data-mining
Knowledge on
pathways
Systems Toxicology
Robotised / automated
testing
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Big Data
Big Sense?
Big Problem!
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You don’t need perfect resolution to recognize
something important
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7th frontier
Handling evidence differently
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2006-7: Publication / 1st conference
Mar 2011: US EBTC
Oct 2011: Secretariat at CAAT
www.ebtox.com
Jan 2012: First conference hosted by EPA
Jun 2012: EU EBTC
Diverse working groups
Jul 2013: IUTOX, Seoul, Korea
Sep 2013: EuroTox, Interlaken, Switzerland
Systematic reviews increasingly embraced
by EPA/IRIS, NTP and EFSA
Nov 2014: Forum Systematic Reviews
Feb 2015: FDA Training
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New organization in progress:
• Board of directors
• Scientific Advisory Council
• Secretariat / administration
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• Jack Fowle, retired, EPA (Pres)
• Jim Freeman, ExxonMobil
• Ian Kimber, U. of Manchester
• Rob de Vries, SYRCLE (VP)
New BoD Members
• Nancy Beck, ACC
• Thomas Hartung, Hopkins
• Thomas Singer, Hoffmann-LaR.
• Andrew Rooney, NTP/OHAT
Ex officio, non-voting: Katya Tsaouin (director), Sebastian Hoffmann & Martin Stephens
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Systematic review & related approaches: Gaining acceptance in toxicology
Feb. ‘15 Workshop
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8th frontier
Pragmatism - Getting the rubber on the
ground
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Frontloading of toxicology / Green Toxicology
“fail early, fail cheap”
Anticipate human or
regulatory problems?
“test early, develop clean”
Green Toxicology
Green Toxicology
Collaboration
• Connecticut, Dec
2012
• Baltimore, Nov 2013
• Zurich, Switzerland
23 Oct 2014
• Frankfurt, Mar 2014
• SoT 2015, San Diego
• EUROTOX Sep 2016,
Istanbul
• TRAINING !!!
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ALTEX 2014, 31:387-396
Read-across Collaboration
International Steering Group & Whitepaper
Workshop in Baltimore Oct 8-9, 2015
“Good Read-across Practice”
Stakeholder Fora Brussels & Washington early 2016
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Top-down development
of new toxicological tools
Tox-21c
3Rs
Bottom-up support to
alternative methods and
legislative pressure
9th frontier
Managing the trans-Atlantic divide
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• Better science
• Less animals
• Human relevance
• Faster and cheaper results
• Refinement
• Information, Grants
• Think tank
• New tools, quality control
• EU branch, policy program
• Stakeholder consensus
Scientific American 2005
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The Bernice Barbour
Foundation
Funding from industry, philanthropy and research funding agencies
…and individuals
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CAAT-Europe 2010
transatlantic cooperation
Daneshian et al. (2010) Altex, 27, 63 – 69.
US Policy program 2006
EU center of excellence EU Policy program 2012
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Challenge and
opportunity of TTIP for
harmonization of
regulation
53
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10th frontier
In a global market, no new method will
be used until the last important region
accepts it.
…
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Russell and Burch
In vitro testing
Validation
Tox-21c
Toward humane
science
CAAT
ECVAM
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“There is a destination
but no way:
what we call ‘The Way’,
is our hesitation.”
Franz Kafka
Yes, we
can!
Let’s do
it!