Identification of new candidate breast cancer genes

Institution: University of California, San Francisco
Investigator(s): Donna Albertson, Ph.D. - Donna Albertson, Ph.D. -
Award Cycle: 1996 (Cycle II) Grant #: 2RB-0225A Award: $186,755
Award Type: Research Project Awards
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease

This is a collaboration with: 2RB-0225 -

Initial Award Abstract (1996)
The nature of a cancerous or pre-cancerous cell differs from that of a normal cell in ways that allow the cell to escape from normal growth controls and grow without restriction. Often it is possible to associate changes in the genetic material of the cell with this change in behavior; in some cases the cell acquires extra copies of genes, and in others good copies of the genes are lost. These altered regions of the genetic material, or genome, can be recognized and the search for new cancer genes begins with the isolation of the changed region of DNA. The region, many times larger than a single gene, may contain tens to hundreds of genes, and scientists face the challenge of trying to find which of these genes has changed, leading to the development of a particular type of cancer. In order to do this, it is first necessary to identify which of the genes no longer function properly in the tumor cells. Currently, the best method to accomplish this task is not clear, and new approaches are needed to facilitate gene discovery. Therefore, in this proposal we will use a technique called "Fluorescent In Situ Hybridization" (FISH) to investigate whether or not a particular gene product is being produced in a normal or abnormal way in the tumor cells. Using FISH we will be able to see what is being produced within each cell. To use this technique, a "probe" is made that corresponds to the gene product. If the cell is making this gene product, then the probe sticks to the cell and the cell, now labeled with a fluorescent color, becomes visible in the microscope. By comparing how normal and tumor cells become labeled by the gene probe, we will be able to determine if the gene is turned on incorrectly in the tumor cells.

We will use FISH to look at the genes from a region on human chromosome 20 that is present in many extra copies in 30% of breast tumors. Studies have shown that in patients with tumors of this type, there is a greater likelihood of metastasis, and the patients have shorter disease-free survival times. Thus, the activity of extra copies of a gene or genes from this region appears to play a role in promoting metastasis and is an indicator of probable poorer outcome. Work in identifying the breast cancer gene(s) in this region has resulted in the isolation of DNA which spans this region of the genome and the identification of a number of candidate genes by biochemical methods. Identification of these breast cancer genes will be important in understanding the pathology of breast cancer and for devising strategies for patient treatment. The FISH technique we will use in the research laboratory may itself form the basis of future tests to classify breast tumors with respect to the activity of these and other genes and so aid in earlier detection and clinical management of disease progression.

Final Report (2002)
Notes: The PI relocated to the University of California, San Francisco in 1998. The grant was extended 1-yr to complete the project aims and expenditures.

Specifically, work in this project, is focused on identifying genes, whose expression is altered in breast tumor cells carrying extra copies of genetic material from chromosome 20. The protein products from the genes that play a role in contributing to breast cancer are expected to be present at higher levels compared to normal cells. We are using a technique called fluorescent in situ hybridization (FISH) in order to "see" whether or not a particular gene from this region of chromosome 20 is being turned on abnormally in tumor tissue. To use FISH, a "probe" or tag is made that corresponds to the gene. If the gene is being expressed in a cell, then the probe sticks to the cell and the cell, now labeled with a fluorescent color, becomes visible under the microscope.

The gene, ZNF217 (formerly called ZABCI) has been identified by us as one gene from this region that is likely to be an important oncogene (i.e., tumor promoting) in breast cancer, because it is frequently present in extra chromosomal copies in breast tumors and is expressed as protein at high levels in tumors. A further indication of the importance of ZNF217 in breast cancer has been obtained by recent, very precise measurements of the number of extra copies of genes from this region of Chromosome 20. In some tumors, only a small portion of the region was at high copy number and this included ZNF217, which was present at the highest copy number. However, these studies also revealed that an adjacent region could be at the highest copy number. This information focused our attention on CYP24, which mapped to this additional region.

In order to continue to evaluate ZNF217 and CYP24 as putative oncogenes, the expression patterns of these genes in tumor and normal tissue was determined using mRNA FISH, quantitative PCR and gene expression microarrays. In summary, the BCRP funding and future research will focus on how chromosomal changes in cancer cells and the genes present in these chromosomal duplications represent important causes of tumor initiation and progression.

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
Periodical:Nature Genetics
Index Medicus: Nat Genet
Authors: Pinkel D, Seagraves R, Sudar D, Alberston DG, et al.
Yr: 1998 Vol: 20 Nbr: Abs: Pg:207-211

Positional cloning of ZNF217 and NABC1: genes amplified at 20q13.2 and overexpressed in breast tumors
Periodical:Proceedings of the National Academy of Sciences of the United States of America
Index Medicus: Proc Nat Acad Sci, U S A
Authors: Collins C, Rommens JM, Kowbel D, Godfrey T, Tanner M, Albertson D, et al.
Yr: 1998 Vol: 95 Nbr: 15 Abs: Pg:8703-8708

Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene
Periodical:Nature Genetics
Index Medicus: Nat Genet
Authors: Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, et al
Yr: 2000 Vol: 25 Nbr: Abs: Pg:144-146