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New Approach for Efficiently Isolating Differentially Expressed Genes

Lead Researcher: Paul B. Fisher

Changes in gene expression are important determinants of normal cellular physiology, including cell cycle regulation, differentiation, and development, and they directly contribute to abnormal cellular physiology, including developmental abnormalities, aberrant programs of differentiation, and cancer. Dr. Paul B. Fisher’s research has focused on improving methodologies for identifying and cloning differentially expressed genes. A novel strategy, reciprocal subtraction differential RNA display (RSDD), described in the October 1998 issue of the Proceedings of the National Academy of Sciences, provides researchers with an approach that will accelerate the ability to define genes that determine important cellular processes such as growth, development, aging, differentiation, and cancer.

The techniques of subtraction hybridization and differential RNA display have been widely used for gene discovery. However, both of these methods can be problematic. RSDD comprises and refines these two approaches, involving reciprocal subtraction of cDNA libraries followed by differential RNA display. Dr. Fisher has used this method to identify and clone differentially expressed genes that are not apparent using either approach alone. In this context, RSDD will assist researchers in defining a larger proportion of genes of potential interest that are expressed at different levels between complex genomes or resulting from changes in cellular physiology.

The RSDD approach has been used by Dr. Fisher, professor of clinical pathology and Michael and Stella Chernow Urological Cancer Research Scientist, to define genes associated with cancer progression as cells acquire new or display a further elaboration of pre-existing transformation-related properties. Sixteen differentially expressed genes, including five novel genes elevated during cancer progression (progression-elevated gene) and six novel genes suppressed during cancer progression (progression-suppressed gene) have been identified. Intensive studies are now in progress in Dr. Fisher’s laboratory to define the roles of these novel genes in the cancer process.

A defining element in the cancer paradigm is the conversion of a benign, slow-growing, non-lethal cancer into an aggressive, rapid-growing, fatal cancer. The RSDD approach and the novel genes identified using this approach will provide important insights into this critical component of cancer development. With this knowledge, it may be possible to develop improved methods for detecting and ultimately treating aggressive cancers.

Dr. Fisher’s research is supported by grants from the NIH, the National Cancer Institute, the Samuel Waxman Cancer Foundation, and the Chernow Endowment. Other members of the research team involved in this study were Dr. Dong-chul Kang, Dr. Zao-zhong Su, and Raphael LaFrance.

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