Cancer Research - Europa

CARCINOGENOMICS
Development of a high throughput
genomics-based test for assessing
genotoxic and carcinogenic properties
of chemical compounds in vitro
Summary
The major aim of CARCINOGENOMICS is to develop in vitro
methods for assessing the carcinogenic potential of compounds,
as an alternative to current rodent bioassays for
genotoxicity and carcinogenicity. The major goal is to develop
a battery of mechanism-based in vitro tests accounting
for various modes of carcinogenic action. These tests will be
designed to cover major target organs for carcinogenic
action e.g. the liver, the lung, and the kidney. The novel assays
will be based on the application of ‘omics’ technologies
(i.e. genome-wide transcriptomics as well as metabonomics)
to robust in vitro systems (rat/human), thereby also exploring
stem cell technology, to generate ‘omic’ responses from
a well-defi ned set of model compounds causing genotoxicity
and carcinogenicity. Phenotypic markers for genotoxic and
carcinogenic events will be assessed for the purpose of
anchoring gene expression modulations, metabolic profi les
and mechanism pathways. Through extensive biostatistics,
literature mining, and analysis of molecular-expression datasets,
diff erential genetic pathways will be identifi ed capable
of predicting mechanisms of chemical carcinogenesis in vivo.
Furthermore, generated transcriptomic and metabonomic
data will be integrated into a holistic understanding of systems
biology, and applied to build an iterative in silico model
of chemical carcinogenesis. Subsequently, predictive genetic
pathways will be used as the scientifi c basis to develop high
throughput technology for accelerating analysis of genomics
responses in vitro, indicative for human carcinogenic risk, by
a factor of 100. It is expected that the outcome of this project
will generate a platform enabling the investigation of large
numbers of compounds for their genotoxic and carcinogenic
potential, as envisaged under the REACH initiative.
This will contribute to speeding the identifi cation of potential
harmful substances to man, while lowering costs and
reducing animal tests.
Problem
The evaluation of the carcinogenic potential of a compound
is currently completely depending on chronic
rodent bioassays administering chemicals at maximally
tolerated doses. Chemical carcinogens are classifi ed as
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Keywords | Life Sciences, Genomics and Biotechnology for Health |
either genotoxic or non-genotoxic. For the important class
of non-genotoxic carcinogens, no suitable test model is
available at all. The available mechanistic information is
relatively more clear-cut for genotoxic carcinogens, and
genotoxicity testing of chemicals is mandated by regulatory
agencies worldwide. A four-test battery is required
comprising bacterial mutagenesis, in vitro mammalian
mutagenesis, in vitro chromosome aberration analysis and
in vivo chromosome stability analysis. However, for pharmaceuticals,
it has been assessed that these assays in
combination predict rodent carcinogenicity correctly by
not more than 38 % while simultaneously producing high
percentages of false positives; the correctness of prediction
by the in vivo assay appears only 11,5 % while the
percentage of false positives is 15 %. A survey of over
700 chemicals demonstrates that even 75–95 % of noncarcinogens
gave positive (i.e. false positive) results in at
least one test in the in vitro test battery. False positive
results in in vitro/in vivo assays for genotoxicity obviously
overrate the necessity of rodent carcinogenicity studies.
But also rodent cancer bioassays provide inadequate data
to estimate human cancer risk: this creates a signifi cant
problem for interpreting the results of animal experiments
with carcinogens in relation to humans.
Aim
This project concedes to a crucial area within the LifeSci-
Health Priority, namely “the Development of new in vitro tests
to replace animal experimentation”. With reference to the
Three R Principle (Replace, Reduce, Refi ne) as highlighted in
the LifeSciHealth Priority, the CARCINOGENOMICS project is
directed towards replacing chronic rodent bioassays for
assessing chemical genotoxicity and carcinogenicity.
For this purpose, CARCINOGENOMICS will produce innovative
genomics-based in vitro screens for assessing
carcinogenic properties of chemicals, with high throughput
features which upon proper validation by ECVAM will
bring technology applicable to REACH Combining pathway-associated
gene expression with metabolic profi les
generated in vitro, as is foreseen in the CARCINOGENOM-
ICS represents a highly innovative approach possibly
leading to in silico models that may be used to predict the
carcinogenic potential of a compound in vivo.
With the aim to develop in vitro methods for testing the carcinogenic
properties of compounds as an alternative to the
chronic rodent bioassays for assessing chemical genotoxicity
and carcinogenicity, the CARCINOGENOMICS project will
address the following S&T objectives to:
• develop predictive mechanistic models based on transcriptome
and metabonome profi ling in rat and human
primary cells from prioritized target organs, in order to
discriminate genotoxic from non-genotoxic carcinogens;
CANCER RESEARCH PROJECTS FUNDED UNDER THE SIXTH FRAMEWORK PROGRAMME