Breast cancer 1000

The April 24, 2006 edition of Newsweek includes an article titled, "Leading the Hunt for Cancer Genes", which reports the work of Joan Brugge (chair of the Harvard Medical School Department of Cell Biology, and co-principal investigator) and other scientists responsible for the new Breast Cancer 1000 genetic database. This "library" of genes associated with breast cancer is somewhat misnamed:  there are at least 1300 genes identified in the database.

According to an article in Bio-IT World.com (http://www.bio-itworld.com/issues/2006/april/breast-cancer/) there was a dual approach to selecting the cDNAs for the BC1000 library. The first 200 genes were selected by breast cancer experts, along with another 50 genes known to be over-expressed in breast cancer. The remainder was identified using MedGene, a text-mining program developed by the Harvard Institute of Proteomics that searches content in the Medline database to pick out genes co-cited with a particular disease. The program ranks the significance of those gene-disease relationships based on citation frequency.

The National Library of Medicine Medline database is a compendium of articles indexed and searchable in a program known as PubMed. It includes journal articles since about 1969, but does not include books, reports of meetings, or a number of other publications. Generally, searching is possible by standard keywords, such as those used in a typical Boolean search where combinations of words (eg, statin + medication -intravenous) or partial words (gen* to represent gene, genetic, genetics, etc.) can be searched for, and by using key terms arranged in a hierarchy of headings.  

The Breast Cancer 1000 may include some acronyms or keywords that are not actually related to breast cancer, since other words may match those used to search.

Two of the genes mentioned in the Newsweek article are the BRCA1 gene, which in its nonmutated form acts as a brake stopping cells from replicating out of control, and the HER2 gene, in which many copies of the gene can be found in a tumor cell--like hitting the gas.

Why is this library important? According to the article,

The library allows investigators to set up screens in the lab to see which genes on the list are important. We now have the ability to specifically, in a stealth way, knock out a gene very quickly, in cell cultures or even in animals. Also, drug companies can use it to design new treatments.

The library also allows researchers to begin examining the interaction of tumor cells with the environment. According to Brugge, we have to start thinking about these cells as organs that act in an organized manner rather than as individual cells that function on their own. For example, a tumor stimulates blood vessels to grow and bring it nutrients.

If you want to know more about the details of this work--and the 14 publications recently derived from it--please add a comment to this blog with your request.

Marie Godfrey, PhD

 

 

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