Functional Genomics Research

Monica Justice shows mutant beige mice, which are models for the human disease Chediak-Higashi Syndrome human disease, to U.S. Representative Jimmy Duncan of Tennessee’s 2nd District (right) and Rick Woychik, then director of ORNL’s Functional Genomics Program, who briefed the congressman on ORNL’s capabilities in relating genes to function. Photograph by Curtis Boles.

Human genome research worldwide is now shifting into its next phase of completing the sequence of chemical bases in the entire human genome. Within the next decade, the Department of Energy’s Joint Genome Institute and the other genome centers will have discovered, mapped, and sequenced all of the genes that define humanity. This knowledge will undoubtedly change the nature of biological research in the “post-genome era.” Using the sequence gene mapping information from the genome program, molecular geneticists will be able to begin tackling problems in biological research that were previously impossible to define or solve. For the first time in human history, scientists will have the tools that will help them begin to understand, at the molecular level, how complex networks of genes are involved in human disorders, ranging from birth defects to physical and mental illnesses in the adult.

ORNL scientists are preparing to
investigate, at the molecular
level, how complex networks
of genes are involved in
human disorders.

An important focus of research in the post-genome era will be a study of how genes function within the body. Biologists have been studying gene function for many years, but most of their research has been slow, very costly, and directed at single genes. Access to the powerful reagents from the genome program will change all of this. In the post-genome era, among other things, it will be possible to (1) perform gene function experiments on a genome-wide scale, hence the name functional genomics; (2) study large numbers of genes, perhaps all of them, at the same time; and (3) begin to study the large numbers of functional partnerships that genes establish with other genes. The understanding of these genetic relationships will provide an enormous insight into how genes participate in human health and well-being.

Many different approaches can be taken to studying gene function. One of the most useful ways to gain insight into the function of a gene is to turn the gene off or change its normal pattern of expression through genetic mutagenesis. For example, when a gene is not functioning normally and an individual carrying that mutant gene develops a certain form of cancer, the cancerous function can be assigned to that gene. In fact, this approach has enabled scientists to identify the genes associated with major diseases in humans, such as Huntington’s disease, cystic fibrosis, and breast cancer.

Because gene mutagenesis is such a useful way of studying gene function, it would be useful to generate new gene mutations on a genome-wide scale. For obvious reasons this cannot be done in humans. Therefore, genome researchers are turning to model organisms like the mouse. The mouse is anatomically and physiologically similar to humans in many important ways. Mice, for example, develop a kind of obesity and adult-onset diabetes that are very similar to conditions in humans. Mice can be afflicted with many other “human” diseases such as polycystic kidney disease, which is one of the major causes of kidney problems in the human population. The most compelling reason to use the mouse as a model organism is that, in many instances, a mutation in a mouse gene that is the counterpart of a major human disease gene can cause essentially the same disease in mice as that observed in humans. In these instances, the mutant mice are exceptionally appropriate models of human disease. Also, unlike other model organisms, mice have a relatively short generation time. Considering that the gestational period for the mouse is about three weeks, the time to sexual maturity is another three weeks, and each pregnant mouse has about ten offspring, one breeding pair of mice can give rise to tens of thousands of mice in just a matter of months. Mice can also be bred in such a way that all the offspring are essentially twins of each other, which is an important consideration for many genetic experiments.

ORNL’s unique heritage in radiation biology puts it in a strong position to conduct large-scale mutagenesis experiments in the mouse. Based on the extensive work in mouse genetics research by Liane and Bill Russell over the last several decades, the Mammalian Genetics Section in the Life Sciences Division has the knowledge, resources, and experience to perform mouse mutagenesis on a scale that is unparalleled at most other institutions. ORNL operates one of the world’s largest experimental colonies of mice for research purposes. In the facility dubbed the “mouse house,” hundreds of mutant lines of mice are being maintained by trained geneticists. Many of these mutants develop specific forms of disease that model conditions in humans. For example, several different mutations have been identified that give mice a genetic predisposition to becoming fat. One of these “fat” genes has been identified at the molecular level at ORNL (for more details, see “ORNL Closing In on Obesity Genes” ). The human counterpart for this gene has also been identified, and, as is true for most genes in humans and mice, the human gene encodes a protein that is remarkably similar to that encoded by the mouse gene. By cloning the mouse gene and analyzing a mouse mutant line, it was possible to assign an obesity function to a gene on the human DNA.

A comparison of the types and order of DNA bases in human and mouse genes shows a striking similarity.

In FY 1997, through its Laboratory Directed Research and Development Program, ORNL launched a focus area in functional genomics that will be supported by internal funding for the next three years. This new initiative will enhance the Laboratory’s capabilities in support of the DOE mission in determining gene functions. The functional genomics initiative will build on our expertise in mouse mutagenesis and will incorporate many other capabilities at ORNL, including protein chemistry, structural biology, instrumentation, robotics, automation, and computer science. The interdisciplinary nature of this new program will allow the mouse mutagenesis capabilities to be expanded to genome-wide proportions.

Through this exploratory research funding, ORNL is positioning itself ultimately to form a core functional genomics effort dedicated to the large-scale generation, characterization, molecular analysis, and distribution of new mutations in the mouse. To reach this goal, it will be necessary to achieve a major increase in the rate at which new heritable mutations can be generated and screened for disease traits that are caused by single and/or multigenic mutations. To map and quickly identify these new mutations, researchers will need to develop new strategies for high-throughput analyses of DNA fragments that are markers for specific sites on the genome. New approaches in molecular biology and instrumentation must be generated for the purpose of differentiating wild-type from mutagenized genes and to detect changes in gene expression in mutant lines of mice. Innovative approaches must be developed for cataloging this new information, and new user-friendly tools must be generated for disseminating this information to the rest of the world.

Over this past year, this new program began to take shape. Our researchers worked on a variety of projects, such as the development of (1) innovative approaches for conducting mouse mutagenesis experiments that have the potential to be applied on a genome-wide scale; (2) novel, high-throughput techniques using mass spectrometry to detect specific kinds of new mutations in mouse chromosomes; and (3) new functional genomics applications for ORNL’s award-winning “lab on a chip” for detecting genome-wide molecular markers that are generated by the polymerase chain reaction. They also worked on expanding research on new miniaturized devices, called genosensors, that can be applied to the simultaneous analysis of hundreds and even thousands of genes from mutant mice. ORNL’s microfluidics and imaging capabilities are crucial to the success of this research.

We are also working to build a robotics capability for the functional genomics infrastructure at ORNL. To keep all of the data that are being generated from this collective effort organized and to help bring about a new user-friendly interface for this research to the outside world, ORNL investigators are developing innovative bioinformatics capabilities that use the Laboratory’s unique computing capabilities.

Collectively the programs that were funded in FY 1997 are allowing the functional genomics effort to take the shape of a program that is highly compatible with the established goals. Projects that will be funded in the next three-year program will build on the accomplishments of the first year will incorporate more of our capabilities in molecular biology, biochemistry, instrumentation, and automation. The willingness and ability of ORNL researchers to conduct interdisciplinary research increase the likelihood that our functional genomics program will be successful.

Knowledge of gene function may lead
to new therapeutic drugs.

Research in functional genomics will help us continue our tradition of success in the biological sciences, thereby serving the needs of DOE and our society. It will also facilitate expanded outreach and partnerships with industry and academia. In the past, the multidisciplinary achievements at ORNL, which bridge basic and applied research, have been honored by two Enrico Fermi Awards from DOE and more than a dozen memberships in the National Academy of Sciences. The new functional genomics effort should help provide ORNL with improved opportunities for making exciting new discoveries in the post-genome era that will greatly expand our knowledge of how genes function. Using this information, scientists will be able to develop drugs and other therapies to improve human health.—Rick Woychik, former director of ORNL’s Functional Genomics Program.

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