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