DNA MICROARRAYS AND GENOME SCANS IN NUTRITION RESEARCH Application of Genomic Technologies: DNA Microarrays and Metabolic Profiling of Obesity in the Hypothalamus and in Subcutaneous Fat

Now that the sequences of several mammalian genomes (and the identities of the genes present in them) are known, the challenge facing modern medical researchers is how to understand this information and determine its biological relevance. Expression profiling of the human genome and various laboratory animal genomes under different conditions and in different disease states is now a routine method that can provide numerous biological answers in a cost-effective and timely manner. At the heart of expression profiling technology are devices developed over the past decade that make it possible to simultaneously quantify and compare the levels of thousands of different messages present in two different samples of cells and to screen for patterns of sequence abnormalities in the DNA of these samples. These devices, termed gene chips or microarrays, contain tens or hundreds of thousands of tiny probes for the different messages.1 To quantify the relative levels of different messages in different samples, the RNA is purified from these samples and labeled with a detectable marker. The labeled samples are then added to a special buffer and placed on the microarray. If the message for a given gene is present in the sample, it will bind to its matching probe sequence and emit a signal that is proportional to its abundance in that sample. By using high-resolution scanners and sophisticated software, the levels of expression of each of the tens of thousands of probes for different messages can be calculated and compared. One of the benefits of analyzing the expression patterns of tens of thousands of messages at the same time is the ability to carry out a very detailed analysis of a disease or biological state without having to rely on preconceived ideas about which genes to study. Thus, microarrays provide the opportunity to discover abnormalities in the expression or sequence of genes that were never thought to be involved in a disease. In addition, it is possible to analyze entire groups of genes that perform similar functions in a cell, to determine the most affected gene groups in a disease, or to analyze entire groups of genes present in close proximity (at the same cytogenetic locus) to rapidly determine the most affected functional or genetic regions. In this paper, in the context of the application of microarray technology to studies of nutritional or metabolic science, we present the results of our recent study regarding DNA microarrays and obesity. We discuss issues of experimental design, quality control, and basic and advanced data analyses, with a particular emphasis on the use of the Affymetrix GeneChip (Affymetrix, Santa Clara, CA) platform in nutrition research. MICROARRAY PLATFORMS