DNA Microarrays and Expression Profiling in Drug Abuse Research

It has been a dream of many scientists to gain detailed snapshots of the quantities of all gene transcripts (and all proteins), simultaneously, in a given tissue or cell type at certain times or under specific conditions. This would immediately allow the identification of transcripts upor down-regulated in response to a treatment or to environmental influences, e.g. to familial high-risk conditions or to drug abuse. It is evident that with such knowledge at hand, within the twinkling of an eye, diagnosis of a disease would be child’s play. Many people have worked on that issue to make the dream come true—and have made considerable progress. The first question arising in this context is how many transcripts are to be screened at all? After the full sequencing of the human genome, it is assumed that we are talking about approximately 40 000 – 60 000 genes in total. From those, approximately 15 000 are expressed in specialized tissues, but we do not know which ones, for example, are expressed in a hippocampal neuron. Therefore, we should eventually be able to screen all genes of a genome in any given tissue, in that way sorting out those that are silent. This strategy is even more important because one does not know if any of the suppressed genes in one condition is also not expressed in another condition. Basically, however, the strategy should reveal expression changes of genes that are already expressed. For obvious reasons, expression profiling techniques have been developed first in easily accessible biological systems such as in cell cultures or in the flower Arabidopsis thaliana (Schena et al., 1995), where starting material is not a limiting factor and experimental conditions can be maintained under strict control. With regard to looking into disturbances of higher brain functions in mental illnesses or in behavioral disorders, studies in whole organisms are mandatory. However, the huge gain of complexity in such conditions endows expression profiling with a lot more unpredictable hurdles. The compartmentation of the brain, individual differences, strain and species differences in animal studies as well as pertinence of those results to human disorders immediately come into consideration. These may have been major reasons why people have been reluctant for some time to use expression profiling in drug abuse research. Nevertheless, there are a number of investigations that have appeared in high-ranked journals during the last 5 years (Fig. 1). One of the more recent highlights, e.g. in alcohol dependence research has been a group of presentations displayed at the last joint RSA/ISBRA conference in San Francisco summarized under the title: Gene expression in brain: a window on ethanol dependence, neuroadaptation, and preference (Hoffman et al., 2003). As in all other expression profiling studies, these studies reveal three major thrusts. General screening to identify candidate genes. The resultant gene lists are used to help improve our understanding of molecular interactions and acquire an idea of tentative aberrations in disease. Once candidate genes in disease have been identified they have to be confirmed by an independent method, preferably by quantitative real-time (QRT) polymerase chain reaction (PCR). Following confirmation of candidate genes, a functional validation has to be performed. Drug development: The next step would be to search for corresponding changes of human gene homologues. As soon as changes comparable to results from animal studies are obtained, development of specific drugs becomes feasible. Diagnosis: Target gene patterns may turn out to be specific for a disease. This has been shown for a number of tumor tissues of various malignancies (Schmidt and Begley, 2003). These patterns are becoming increasingly more valuable for the correct diagnosis of tumor type and prognosis of the course of the disease (Yeatman, 2003). They may also help to classify brain tumors more reliably than with standard histological evaluations (Nutt et al., 2003). Diagnosis of psychiatric disorders by specific expression patterns will probably be restrained to analyses of peripheral tissues in patients. Research on drug abuse using methods of expression profiling still rests on the first level. A number of methods that have been developed to perform expression profiling have