Researchers have identified several genes whose spatial position inside the cell nucleus is altered in invasive breast cancer when compared to normal breast tissue. The findings suggest that cancer cells may have disease-specific, three-dimensional gene arrangements and raise the possibility that such gene positioning patterns could be used as a new diagnostic strategy to distinguish cancer tissue from normal tissue. The study, by researchers at the National Cancer Institute (NCI), part of the National Institutes of Health, appeared online Dec. 7, 2009, and will appear in print on Dec. 14, 2009 in the Journal of Cell Biology.

Chromosomes and individual genes have been found to occupy specific locations relative to one another and to landmarks within the cell nucleus. The spatial organization of genes can change during a number of normal bodily processes. Alterations of spatial organization also occur in disease states such as cancer. The distinctive changes in shape and size of the cell nucleus, which pathologists use routinely as indicators of whether or not cancer is present, suggest that major changes in spatial gene organization also occur in cancer cell nuclei.

"In our study, we set out to identify genes which are differentially positioned in breast cancer tissues and we explored the possibility that disease-specific spatial organization of genes might be used as a new diagnostic strategy to distinguish malignant from normal tissue," said senior author Tom Misteli, Ph.D., of NCI's Center for Cancer Research.

To identify genes which occupy distinct positions inside the nucleus in normal and malignant cells, the researchers visualized a set of 20 genes using fluorescent in situ hybridization (FISH), a technique to detect and localize specific DNA sequences in intact cells in a set of 11 normal human breast and 14 invasive cancer tissue specimens. The scientists identified eight genes with a high frequency of repositioning in cancer specimens. Only a minority of tested genes underwent significant repositioning in a given cancer tissue, suggesting that repositioning is gene-specific and does not reflect a large-scale alteration in gene organization. The repositioning events were also not due to a common cellular occurrence known as genomic instability, which is often associated with cancer, because repositioning did not correlate with changes in the number of copies of the gene present in the cell.

The scientists next used the tissue specimens to test whether gene repositioning could distinguish cancer from normal and non-cancerous tissues. They found that the position of a single gene, HES5, allowed identification of invasive breast cancer tissue with nearly 100 percent accuracy. HES5 is a gene commonly associated with cancer and affects biological pathways that have been implicated in cancer. Additionally, several combinations of two or three genes allowed identification of cancerous tissues with low false-negative and false-positive rates (that is, the combinations identified most cancer tissues as cancer and few non-cancerous tissues as cancer). This approach compares favorably with current standard breast cancer diagnostic tests that rely on fine needles or larger core needles to biopsy small amounts of tissue for examination.

Identification of genes that are localized differently in normal and cancer cells allows the possibility of using spatial gene positioning as a novel diagnostic tool, although the authors note that the findings will need to be replicated in a set of larger tissue samples. As required for such an application, the researchers found low variability of gene positioning among individuals. They also found that cancer tissues could accurately be identified by comparison to a standardized normal gene distribution.

A distinct advantage of this approach over existing methods is the very small quantity of material required. Differences in spatial positioning were routinely detected by analysis of 100 to 200 cells despite the lack of uniformity in cancer samples. Furthermore, this approach is suitable for adaptation in a routine laboratory setting because all individual steps of the procedure rely on standard methods, including embedding of biopsy material and FISH detection. The use of spatial genome positioning for detection of tumors could reduce human error in making a diagnosis because the method gives a quantifiable readout and is not based on subjective criteria or the individual expertise of the pathologist who performs an evaluation with a microscope.

"If validated in a larger number of samples, we envision that this approach may be a useful first molecular indicator of cancer after an abnormal mammogram," said Misteli. "Our method of cancer diagnosis is not limited to breast cancer and may be applied to any cancer type in which repositioned genes can be identified."

For more information on Dr. Misteli’s research, please go to http://ccr.cancer.gov/staff/staff.asp?profileid=5819.

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