Locating Novel Breast Cancer Genes using DNA Microarrays

Institution: Stanford University
Investigator(s): Jonathan Pollack, M.D., Ph.D. -
Award Cycle: 2002 (Cycle VIII) Grant #: 8KB-0135 Award: $477,295
Award Type: New Investigator Awards
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease



Initial Award Abstract (2002)
Cancer results from the deregulated control of normal cell growth, and is caused by alterations in the cell's DNA sequence- its genetic code. These alterations can take the form of DNA sequence mutations, which are subtle alterations in the genetic code (e.g. Sickle cell anemia). But in cancer, especially advanced disease, these genetic alterations often take the form of duplicated (or triplicated, etc.) and deleted DNA sequences. The result is that too much or too little of a given gene is present, leading to the dramatic cellular changes seen in tumor cells. Cataloguing these gene copy number alterations, and identifying the specific genes involved, might lead to an improved understanding of cancer and point us towards developing improved therapeutic agents. For example, Herceptin is a therapeutic now used to treat breast cancers with excess Her-2/neu growth oncogene on the tumor cell surface. But, the use of Heceptin became most effective only after patients were directly evaluated for multiple copies of the gene using a microscopic assay, called FISH (fluorescence in situ hybridization).

Our hypothesis is that chromosome regions (genes) of "extra" DNA sequence copy number are, (1) undiscovered by conventional, lower-resolution techniques, and (2) contain possible breast cancer genes that might be used as "markers" or therapy targets in treatment. We aim to test and develop this hypothesis by using a new technique, based on DNA microarrays. A DNA microarray consists of a glass microscope slide onto which thousands of different DNA sequences (genes) are placed in an ordered array of rows and columns. DNA microarrays were first used to measure the expression of genes, and this has proven to be a powerful method for classifying breast cancer into molecular subtypes. In this project we plan to extend this approach to map DNA sequence copy number. The advantage is that thousands of genes can be assayed simultaneously, and any identified gene can be immediately located using data from the Human Genome Project. We plan to use 25 human breast cancer cell lines and >100 primary human tumor samples to obtain a database of genetic changes. We will "map" the genetic changes in these samples versus a standard human genome. While the data are accumulating we anticipate finding genes where amplifications or deletions are recurrent, and we will be able to differentiate these from non-informative DNA alterations (i.e., not associated with breast cancer). Finally, we plan to combine this novel approach of molecular genetics analysis with our growing database of gene expression. Taken together we will have a list of potential oncogenes (i.e., genes increased in cancer) and tumor suppressors (i.e., genes lost in cancer progression) for further study.

In the past, gene copy number alterations have been mapped by examining chromosomes through a microscope. Such methods have provided comparatively low mapping resolution, which has slowed efforts to locate actual cancer genes. The proposed study takes advantage of an innovate DNA microarray technique to map DNA at unprecedented resolution, thereby speeding the process and making sense of the complex problem of cancer genetics.


Final Report (2005)
Breast cancer results from the alteration of genes that control normal cell growth. Tumor suppressor genes (TSGs), which normally function to put the brakes on cell growth, are frequently deleted in breast cancer. The goal of this study has been to identify novel TSGs in breast cancer by first discovering sites of DNA deletion. To accomplish this goal, we have applied a new technique we developed, based on DNA microarray technology, to map chromosome regions of DNA deletion at unprecedented resolution in breast cancer, thereby pinpointing the location and speeding the identification of previously uncharacterized TSGs.

In our study, we have used this method to characterize DNA deletions in 50 different breast cancer cell lines and 144 primary breast tumors. We have discovered numerous chromosome regions of recurrent DNA deletion, including 15 sites of highly-localized deletion, implicating new TSGs. A subset of DNA deletions was associated with unfavorable patient prognosis, underscoring the clinical relevance of our findings. Future efforts will be directed towards characterizing key TSGs within sites of DNA deletion, which will both improve our understanding of breast cancer, and provide new targets for cancer therapies.


Symposium Abstract (2003)
Cancer results from the deregulated control of normal cell growth, and is caused by alterations in the cellís DNA sequence, its genetic code. These alterations can take the form of DNA sequence mutations, that is, subtle alterations in the sequence of the genetic code. Equally common, these alterations can take the form of duplicated and deleted DNA sequences. These so-called DNA sequence copy number alterations result in changes in the dosage of expressed genes, too much or too little of which can lead to the development or progression of cancer. Locating these DNA sequence copy number alterations, and identifying those genes whose expression is altered, can lead not only to an improved understanding of cancer, but also can be the first step towards developing improved therapeutic agents.

We hypothesize that chromosomal regions of recurrent DNA sequence copy number alteration harbor breast cancer genes that remain largely undiscovered by conventional, lower-resolution techniques. We aim to test this hypothesis by using a new technique, based on DNA microarrays, to map at unprecedented resolution the boundaries and structure of DNA sequence copy number alterations in human breast cancer cell lines and tumors, thereby pinpointing previously concealed novel candidate breast cancer genes.

Using this DNA microarray-based technique, we have so far profiled DNA copy number alterations in a set of 20 breast cancer cell lines and 30 primary breast tumors, using DNA microarrays containing 26,000 mapped human genes. Here we report chromosomal regions of recurrent DNA duplication and deletion, pinpointing the location of novel breast cancer genes.

Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer.
Periodical:Genes Chromosomes Cancer
Index Medicus:
Authors: Bergamaschi A, et al., and Pollack JR
Yr: 2006 Vol: E-pub Nbr: August Abs: Pg: