Federal funds boost UF’s gene analysis efforts

Aided by a new $1.5 million federal grant, College of Medicine researchers are stepping up their efforts to comb through billions of bits of genetic data that may hold important clues about diabetes, appetite control, and kidney, liver and gastrointestinal diseases.

UF is one of ten institutions to win a grant from the National Institute of Diabetes and Digestive and Kidney Diseases to establish sophisticated gene expression analysis laboratories, each to be known as an NIDDK Biotechnology Center. The funds will enable UF, Harvard, Yale, Duke and several other universities to capitalize on recently developed technology that gives scientists the power to simultaneously analyze the activity of tens of thousands of genes rather than one at a time.

At the new center in the College of Medicine’s department of pathology, immunology and laboratory medicine, scientists will seek to understand patterns of gene expression in a variety of disorders; that is, they want to learn the combination of genes that are switched “on” or “off” at a particular moment and place in the body. Those patterns govern which proteins the body makes, determining the functioning of various tissues and the course of diseases.

Experts say gene expression profiling may someday help them predict who will get certain diseases. It also could lead to the development of new diagnostic tools, improved methods of preventing or treating illness and even novel laboratory techniques for growing tissues for transplantation. Researchers also hope it will help them design strategies for evaluating the effectiveness of disease prevention efforts.

“The new DNA chip technology speeds up by tens of thousands of times the process of analyzing gene expression,” said the center’s director and principal investigator, Jin-Xiong She, a professor of pathology, immunology and laboratory medicine. “In the past we were only able to examine the potential roles of a small number of genes. Now we have powerful technologies to systematically and simultaneously examine all genes that are expressed in a given tissue to identify the important ones involved in diseases.”

A critical element of the center will be the development of software and statistical tools for analyzing and managing the enormous amount of data to be produced. This effort will be headed by the center’s director for bioinformatics and co-principal investigator, Richard A. McIndoe, an assistant professor of pathology, immunology and laboratory medicine.

The center will support 10 scientific projects. Five of the projects involve efforts to predict, prevent or treat type 1 diabetes, the insulin-dependent form of the disease.

Scientists have identified some of the genes that can contribute to susceptibility to the disorder, but they are seeking others among the more than 100,000 human genes. At the same time, researchers also plan to analyze changes in gene expression over time in an effort to discover the environmental factors, which may include diet or viral infections, that trigger the disease in people genetically at risk. In the process, they also may find new targets for drug treatment – delivered conventionally or through gene therapy.

In the effort to treat diabetes, Ammon B. Peck, a professor of pathology, immunology and laboratory medicine, is trying to identify genes that guide the development of pancreatic islet cells, the insulin-producing cells destroyed by the disease. That knowledge could be useful in Peck’s effort to grow islet cells in the laboratory, which eventually may be used as transplant tissue to try to reverse diabetes.

Other projects supported by the center grant include an examination of gene expression profiles in hepatitis C, cirrhosis of the liver, kidney stones and inflammatory bowel diseases.

Scientists also plan to analyze the role genes play in the progression of Prader-Willi syndrome, an inherited disorder that typically leads to severe obesity beginning in early childhood. People with the disorder have an insatiable appetite and lack the sensation of feeling full after a large meal. The researchers will compare gene expression profiles among people with Prader-Willi, severely obese people without the disorder and people who are not overweight.

The new NIDDK Biotechnology Center at UF will be a resource for about 40 scientists; they include UF researchers conducting projects funded by the NIDDK, a branch of the National Institutes of Health, and their research collaborators at the University of Miami, Case Western Reserve University and the University of Colorado.