Ecological and evolutionary functional genomics - How can it contribute to the risk assessment of chemicals?

Ecological and evolutionary functional genomics has progressed enormously over the last 10 years. One of the developments most relevant for environmental science is genome-wide gene expression profiling, using microarrays and RNAseq, of organisms exposed to toxic chemicals. In this way, the action spectrum of chemicals can be characterized on the basis of an extremely large number of endpoints. In this paper we identify a number of formidable problems for the use of transcription profiling in risk assessment. We raise four issues (1) Is it possible at all to assess environmental quality based on transcriptomes (mRNA abundance)? (2) Does gene expression classify treatments according to exposure or effect? (3) Do gene expressions allow identification of chemicals in mixtures? (4) Is it possible to discriminate fitness-neutral gene expressions from those associated with adverse outcomes? We call for the generation of more background data under normal, clean conditions. A close connection between traditional ecotoxicology and genomics seems to be particularly fruitful. Only in this way can transcriptome data be connected to endpoints accepted in risk assessment schemes. © 2011 American Chemical Society.