To begin their research, the researchers used an instrument called the Fluorescence in Situ Hybridization, FISH for short. Through the use of florescent tubes these machines can be used to localize DNA sequences on chromosomes. From 11 normal human breast and 14 invasive cancer tissue specimen, the researchers identified eight specific genes that have been significantly altered when comparing the spatial organization of the genes in a cancerous tissue and a normal one. Roughly around 20,000-25,000 genes are in the human body. Only eight out the total were identified to have been notably repositioned, suggesting that the changes are specific and does not reflect large scale alterations in gene organization. Neither did the repositioning of these genes reflect upon the possibility that it was due to genome instability that caused the repositioning. Genome instability is often associated with cancer because the number of genes present in the genome will often vary when the tissue is cancerous, but the repositioning of these genes did not correlate with the changes in the number of genes present in the nuclei.
Next, the researchers wanted see whether they could use the repositioned gene to distinguish cancerous human cells from healthy ones. If they were to be successful, this method could be used as a replacement to diagnose breast cancer. Tissue specimens were taken and tested. The results were satisfactory when they found that the postion of a specific gene, HES5 could distinguish between a cancerous tissue and a healthy one with almost 100 percent accuracy. The protein that this gene codes for regulates cell differentiation in multiple tissues. Disruption of this gene has been associated as a source of cancer. A few other genes out of the total eight could be used as identification for cancerous tissues with a low false-negative and false-positive rate. This means that this gene combination identified most of the cancerous tissue to be cancerous and a few of the non-cancerous tissue as cancerous.
The data that was collected for the gene HES5 is shown in the graph above. A cumulative RRDs (Relative Record Data Set) organized the data of around 88-220 nuclei per sample of HES5 gene randomly selected from regions of the tissue sample. It displays the frequency of occurrence of the gene at a specific location in the nucleus. The left side of the graph is where the genes closets to the nuclear envelope was found, and the right side of the graph consists of genes that were closer to the center. The black line indicates the genes that were from cancerous tissues, and the red from healthy tissues. A noteworthy difference between the two type of tissues can be seen.
Data was collected for several other genes using the same cumulative RRDs. Although the difference in the positioning of the genes are noticeable, several of the two colored lines overlap. This is an indication that these genes, although they show some repositioning, cannot be used to distinguish the cancerous tissues from the healthy ones.
The current breast cancer diagnostic test involves poking and prodding large needles to retrive a small amount of tissues for a biopsy. Differential repositioning of these genes gives way to a new method of identifying cancerous tissues, and possibly usage for diagnostic applications. The researchers concluded that in this study, they have identified several genes that are differently positioned in invasive breast cancer compared with normal tissue. The data and method used also show that the positioning of the genes can reliably detect cancerous tissues. "We find that the repositioning of many genes is specific to cancer and does not occur in noncancerous breast tissue nor within the normal tissue adjacent to the tumor"
These findings have significant usage for diagnostic applications. This approach reduces the current rate of false detection, and is preferable to the present method of diagnosis. A distinct advantage in using this method is that it requires a very small amount of materials. The use of spatial genome positioning can possibly reduce human errors when making the diagnosis because the approach provides pathologists with qualitative data. Subjective criteria or the individual experience of the pathologists is ruled out.
"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 (research scientist at the National Cancer Institute) "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."
MLA Citations:
"Breast Cancer." National Foundation® Official Site. Web. 30 Apr. 2012. <http://www.nationalbreastcancer.org/>.
"Gene’s Position in the Nucleus." U.S National Library of Medicine. U.S. National Library of Medicine. Web. 30 Apr. 2012. <http://www.nih.gov/news/health/dec2009/nci-07.htm>.
Meaburn, Karen J., Prabhakar R. Gudla, Sameena Khan, Stephen J. Lockett, and Tom Misteli. "Disease-specific Gene Repositioning in Breast Cancer." The Journal of Cell Biology. 7 Dec. 2009. Web. 30 Apr. 2012. <http://jcb.rupress.org/content/187/6/801.full.pdf html?sid=77645108-526c-4aa6-bafa-d494ed8708b0>.
O'Connor, Clare. "Fluorescence In Situ Hybridization." Nature.com. Nature Publishing Group. Web. 30 Apr. 2012. <http://www.nature.com/scitable/topicpage/fluorescence-in-situ-hybridization-fish-327>.
