Cloning of the X Chromosome's Putative Tumor Suppressor Gene

Institution: The Burnham Institute for Medical Research
Investigator(s): Sergei Malkhosyan, Ph.D. -
Award Cycle: 2002 (Cycle VIII) Grant #: 8WB-0086 Award: $284,375
Award Type: STEP Award
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease



Initial Award Abstract (2002)
Determining the genetic changes that occur in breast tumors should help to understand the mechanism of breast cancer, which in turn should elucidate novel approaches for cancer treatment. Nonrandom recurrent losses and gains of chromosomal segments in tumors are a consequence of mutational selection during the development and progression of abnormal cell growth.

Chromosomal deletions play a role in the loss of tumor suppressor gene function and are generally thought to reflect the existence of a tumor suppressor gene within the lost region. In our previous studies, we observed losses of the q25 region of the X chromosome, which occurred in as many as 50% of breast tumors (the project was sponsored by the CA BCRP). The major part of one of the two X chromosomes is silent in females. Interestingly, the chromosomal segment losses we found occurred preferentially on the inactive X chromosome. The loss of the Xq25 region was significantly associated with the larger tumor size, higher histologic grade (the higher the "grade" the more abnormal the cell is) and axillary lymph node metastasis.

Our observation that the q25 region of the X chromosome is so frequently deleted in tumors means that this event provides the tumor cells with growth advantage necessary for cancer development. This indicates that the region contains a negative cell growth regulator, a so-called tumor suppressor gene, whose inactivation is required for the progression of the majority (at least 50%) of breast cancers. This is our central hypothesis. In addition, the gene inactivation seems to increase (or at least associate with) the tumor cells' ability to metastasize, and hence can be potentially used as a prognostic marker for metastasis. Obviously, identification of such a gene, which is involved in the development and progression of large number of breast tumors, is very important for understanding of tumor formation and progression (tumorigenesis), prognosis, and treatment of breast cancer.

The general methodology in non-technical terms:
We will use a candidate gene approach in the identification of the tumor suppressor gene. The human genome project provided chromosome maps with the positions of known and hypothetical genes. We know the X chromosome region (the one found deleted in breast tumors) where our gene is located, and because of the achievements of the human genome project, we have a list of genes located within this region. Now the goal is to find out which of those genes is the tumor suppressor gene. A basic criterion for a gene to be a putative tumor suppressor gene is its inactivation in tumor cells by means of mutational events or events that lead to the gene silencing. We will check the candidate genes in the region for the presence of such events.

Innovative elements of the project in non-technical terms:
The approach proposed in this study has previously been used for identification of tumor suppressor genes. The difference is that during the pre-human genome era the approach was very laborious and time consuming due to the absence of the complete knowledge of the human genome map and sequence. Currently, the approach has much more potential and promise for identification of cancer genes. Thus, it should rather be considered as "just in time" approach that may yield very important information.


Final Report (2004)
The initiation and progression of human breast cancer involves a wide spectrum of known, suspected and undiscovered genetic alterations. Nonrandom recurrent losses and gains of chromosomal segments in tumors are a consequence of mutational selection during the development and progression of neoplasia. Chromosomal deletions play a role in the abrogation of tumor suppressor gene function and are generally thought to reflect the existence of a tumor suppressor gene within the lost region.

In our previous studies, we detected frequent deletions of the q25 region on the X chromosome, which was observed in about 50% of breast tumors. The loss of the Xq25 region was significantly associated with larger tumor size, higher histologic grade, and axillary lymph node metastasis. We hypothesized that, (a) the Xq25 region harbors a tumor suppressor gene whose inactivation plays a role in tumorigenesis of the majority of breast tumors, and (b) inactivation of this tumor suppressor gene is an event that relates to breast cancer progression and increases the metastatic potential of tumor cells. The goal of this project is to identify this putative tumor suppressor gene.

During the course of this study we identified two genes in the Xq25 region, ODZ1 and a putative gene FLJ20130, whose expression was considerably downregulated in about half of the tested human tumor cell lines of different tissue origin, particularly breast cancer cell lines. The expression of the ODZ1 gene was also found to be downregulated in the majority of primary breast, ovary, colon and stomach tumors. This finding by itself is a good indication of a tumor suppressor role of these genes in the development of cancer. We did not identify any somatic mutations in the coding region of the ODZ1 gene in tumors, including those tumors with downregulated ODZ1. We conclude that the downregulation of the ODZ1 gene expression in cancer results from either mutational or epigenetic alterations in the regulatory sequences of the gene.

We performed correlation analysis between expression of ODZ1 and tumor clinico-pathological characteristics. We found that cancers with low ODZ1 expression are more prevalent in blacks and are characterized by the presence of metastasis (distant and regional lymph node), higher tumor size and a lower degree of differentiation. Thus, ODZ1 gene expression in tumors may have prognostic value for the development breast cancer disease.