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The Living Genome
Summary: Patrick Brown uses DNA microarrays—microscope slides onto which tens of thousands of genes are printed in a tiny array—to watch genomes in action. He and his colleagues are systematically characterizing the genetic script that controls the expression of our genes, in healthy cells acting out their roles in normal development and physiology and in diseases such as cancer.
The genome project has revitalized exploration in biological research. Seeing the complete repertoire of genes in a genome confronts us with the fact that we know the biochemical activities and the biological functions of only a tiny fraction of the genes and proteins that make up a living organism. The discovery of this genetic "terra incognita" has reminded us how much of the living world is beyond the frontier and challenged us to explore this new world.
DNA Microarrays
The torrent of DNA sequences has not only made a new era of exploration imperative but also made it possible: nucleic acid hybridization provides a simple, direct way to use the DNA sequence of a gene as a specific assay reagent to detect and monitor that gene and its activity. We have therefore developed a convenient tool, a "DNA microarray," that uses nucleic acid hybridization to monitor thousands of genes at once. DNA microarrays are physical arrays of thousands of tiny spots of DNA, each spot representing a specific gene, attached to a glass microscope slide. In the past few years, we have constructed DNA microarrays representing essentially every known gene of Saccharomyces cerevisiae (baker's yeast) and Escherichia coli, as well as microarrays representing more than 30,000 different human genes.
Each cell in our bodies expresses a specific set of genes according to a precisely controlled program that gives that cell its distinctive design and functional capabilities. The gene expression program of a genome defines the role and behavior of each cell in the body. The expression program that unfolds during a developmental or physiological or pathological process can be read as a kind of script for that process. Cells use RNA transcripts—chemical copies of the information in a gene—to carry the blueprint for the protein that a gene specifies to the cell's protein synthesis machinery. The genetic script for each cell controls which proteins are made, and in what amounts, by precisely controlling the expression of RNA transcripts from each gene.
A DNA microarray can be used as a new kind of microscope that allows us to observe a genome's gene expression program. To survey expression of every gene, all the RNA transcripts are isolated from a sample of cells or a tissue, labeled with a fluorescent dye, and hybridized to a DNA microarray. The fluorescent signal at the spot in the array representing each individual gene provides a quantitative readout of the level of expression of that gene in the sample. This simple procedure offers a systematic way to monitor expression of tens of thousands of genes simultaneously, in thousands of samples per year.
One important kind of information we can get from these studies is a detailed picture of the rules that govern expression of each gene. Because the expression pattern of a gene is closely tied to its biological role, systematic studies of global gene expression provide clues to the functions of thousands of genes. In fact, DNA microarrays can allow a systematic approach to be used to study diverse functional properties of genes. We are using DNA microarrays to explore gene transcription, translation of messenger RNAs into proteins, subcellular localization of the proteins, changes in a cell or organism caused by mutations in each of its genes, and interactions of specific proteins with the genes that they regulate.
Surveying and Mapping Gene Expression Programs
We have launched a systematic effort to survey and map the gene expression script of the yeast genome—how it reacts to the diverse challenges yeast encounter in nature. We are developing new genetic and biochemical approaches to map systematically the regulatory circuitry and the metabolic machinery that control synthesis, processing, trafficking, translation, and degradation of each gene's transcripts. Because we suspect that inherited variation in gene expression scripts is an important source of the diversity of forms and lifestyles among yeast in nature, we are systematically mapping the genes that control differences in the gene expression script in yeast strains found in different natural environments.
We have also used DNA microarrays containing up to 30,000 different genes to survey the gene expression patterns in thousands of samples of human cells and tissues under diverse conditions. The results are providing detailed molecular pictures of the programmed responses of the human genome to diverse physiological and pathological conditions, and they are yielding clues to the mechanisms by which these processes are deranged in cancer and other disease processes.
To build useful maps representing the global program of gene expression, it has been necessary to develop new approaches to finding and displaying the systematic features inherent in large sets of global gene expression data. Our current approach to making a map of the expression program of a genome involves two steps. First, we use multidimensional clustering algorithms or profiling methods to find inherent orderly features in the data from hundreds to thousands of observations on each of thousands of genes. Second, we use "naturalistic" displays to view the systematically ordered data in a way that allows biologists to assimilate the patterns of gene expression both on a broad scale (overview of the choreography) and fine scale (gene by gene). We are pursuing the development of diverse methods for finding and displaying the intrinsic order in large systematic bodies of gene expression data and for recognizing correlations between specific gene expression patterns and specific biological phenomena.
Gene Expression Patterns as Molecular Portraits of Cancer
It has been known for a long time that faults in the gene expression program of cancer cells are a fundamental part of the pathogenesis of cancer. We therefore hypothesized that differences in the gene expression programs could be found in tumors destined to follow different clinical courses. By using cDNA microarrays to examine gene expression patterns in each of more than 500 human tumors, we have found that there is enormous variation among gene expression patterns in these tumors, even between tumors that would classically be considered to be the same type. The gene expression patterns, which we now can readily observe, provide distinctive molecular portraits of each patient's tumor and even paint a picture of the biological differences that distinguish one tumor from another.
Current systems for classification of cancer group together tumors with important differences in clinical behavior. Our results strongly suggest that a systematic molecular taxonomy may underlie the apparent heterogeneity among cancers that we currently call by the same name. We are systematically characterizing the gene expression programs in thousands of human cancers and using multivariate clustering methods to search for new ways to classify cancers based on their gene expression programs.
Just as DNA microarrays have allowed us to measure the transcripts of thousands of genes at once, we have recently found that we can use microarrays of specific antibodies to measure the abundance of thousands of different proteins in samples from cells or in biological fluids, such as serum or urine. We are exploring the possible application of protein microarrays in monitoring health and in detecting and diagnosing disease. (This work was also supported in part by grants from the National Institutes of Health.)
Last updated: November 12, 2007
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