ABSTRACT
The state of a cell is regulated by the activity as well as the complement and abundance of proteins. Therefore, it is common to have immediate changes in cellular function without any change in the expression of proteins. It is this immediate early response that allows for quick adaptation and compensation to environmental conditions. The presence of phosphate on proteins that alter their specificity or enzymatic rates, is a prime example of changes of state that lead to rapid cellular responses, as is subcellular localization. To use genomic techniques for the characterization of novel drugs that are designed to influence these sort of immediate early responses it is necessary to identify changes in protein activity. This is classically performed through the addition of radioactive phosphate that identifies proteins that have incorporated or lost these molecular markers. The purpose of this experimental approach is to ascertain if a regulatory pathway has been altered. Since genomic approaches rely on the measurement of mRNA and only approximate protein abundance, immediate early responses are not easily recognized. Nevertheless, the induction of early response mechanisms can lead to secondary effects on the abundance of proteins through transcriptional modulation. Transcription factors that regulate their own expression have been observed, and it is this autoregulation that
allows inference of changes in regulatory pathways by levels of protein expression [14]. It is the change in gene expression observed at times later than the initial treatment of cells that can be used to better understand the way in which a drug has influenced the cells’ state. Functional genomics is a tool, and all of the limitations must be recognized when inferring functions onto proteins, cells, and drugs based on changes in gene expression. Nevertheless, the power of large-scale experimentation may provide the information necessary for the informed selection of efficacious drugs.
