DNA Microarray Technology
One of the most powerful new techniques in modern biology, called DNA microarrays, or DNA chip arrays, emerged from recent studies on yeast at Stanford University. During the past year, we have been working to merge this method with techniques developed at the Laboratory that were designed to identify mutations in human cancers. Mike Wigler has entered into a collaboration with Larry Norton, M.D., of Memorial Sloan-Kettering Cancer Center in New York City, to use DNA chip technology to look for genes that are mutated in breast cancer.
To use chip technology, researchers place fragments of different DNA samples on a glass microscope slide in a grid of very high density. They expose the slide to labeled DNA, or a complementary DNA (cDNA) copy of mRNA, which hybridizes with the DNA on the glass slide, and then analyze the amount of hybridization in each spot on the slide. The results are color-coded, so that the most active genes (with the greatest degree of hybridization) are colored red, and genes that are repressed (hybridized the least) are colored green. Alternatively, the experiment can be set up so that genes that are overrepresented in cancer cells are labeled red and genes that are missing in the tumor cells are labeled green. Mike and his associates are using the method to compare the genes in healthy versus cancerous breast tissue and at various stages of breast cancer progression.
This year, thanks to a $300,000 grant from the Lillian Goldman Charitable Trust through The Breast Cancer Research Foundation in New York City, Mike installed state-of-the-art microarray equipment in his Demerec Laboratory. His lab will now be able to analyze tremendous numbers of DNA samples from breast cancer tissue. The emerging DNA chip technology should make possible the development of better methods for the diagnosis and treatment of breast cancer, because it will allow researchers to design treatment aimed at the specific mutations present in each patient.
Just as Mike uses the microarray technology to study gene activity at various points in disease progression, Bruce Futcher is using it to locate and characterize genes whose activity is determined by the stages of the cell division cycle in yeast.
Bruce is collaborating with David Botstein and Patrick Brown of the Stanford University School of Medicine. In 1998, they used DNA microarray technology to find, characterize, and analyze yeast genes whose activity is regulated by the cell division cycle. In just four months, the two labs located and characterized about 800 yeast cell-cycle-regulated genes. During the past 15 years, many scientists had identified and characterized only 103 cell cycle-regulated genes in yeast, revealing the power of the new technology.
Microarray technology has yielded an unprecedented increase in the rate of accumulation of data. The microarrays used in Bruce's cell cycle experiments contained 6000 discrete DNA fragments, each of which represents one of the approximately 6000 genes in yeast. Michael Zhang, one of our bioinformatics experts, is using the power of computational analysis to sift through the enormous amounts of data.
Knowing the set of 800 yeast genes that are regulated by the cell cycle has provided a wealth of information that is contributing to a more complete understanding of cell division. For example, researchers now have an overview of the different kinds of biochemical processes that change with cell division. They can study the clusters of dozens or hundreds of coregulated genes that cooperate in these processes and probe the molecular mechanisms that allow the different clusters of genes to be turned on one after another in an orderly way. Researchers can begin to identify the functions of uncharacterized genes by analyzing the known functions of genes in the same coregulated cluster. The combination of biochemical studies and microarray analysis is destined to lead to an ever-greater understanding of the vital cell process of cell division in yeast--and in higher organisms.
Through the acquisition of a small campus in nearby Woodbury--a building of 60,000 square feet located on 12 acres--the Laboratory has positioned itself to further exploit and develop microarray technology. The property was previously owned by the American Institute of Physics and will provide the Laboratory with much-needed space for expansion of high-technology research, such as genome sequencing and microarray research.