Subtle changes in normal genes implicated in breast cancer

New search method could aid in the discovery of biomarkers

Using a super-efficient method they invented to search for a type of cancer-related change in all genes of a cell, Dana-Farber Cancer Institute researchers have discovered new evidence about how the “microenvironment” of breast cancers helps drive the cancers’ growth and migration.

The scientists found that non-cancerous cells surrounding young breast cancers — the microenvironment — undergo epigenetic modifications. (Epigenetic modifications affect genetic function and are passed along to the cell’s offspring, but they don’t alter a gene’s actual structure or DNA.) The subtly altered gene function causes the microenvironment cells to send signals to the breast tumor cells to grow fast and become more aggressive.

“This is the first demonstration that epigenetic occur in the supportive cells of a tumor, and this further emphasizes that surrounding cells play an active role in cancer formation and growth,” says Kornelia Polyak, MD, PhD. “These changes in the microenvironment may occur before breast duct cells undergo genetic changes that cause cancer, thus detecting the epigenetic alterations may be a means of early cancer diagnosis or even predicting cancer risk.”

Polyak is senior author of the paper, which was posted this week as an advance online publication on the Nature Genetics web site, http://www.nature.com/ng. The first author of the paper is Min Hu, PhD, of Dana-Farber.

Polyak and her colleagues had previously shown that the genes in the microenvironment surrounding the breast’s milk ducts were overactive, and that they continued to be overactive when their cells reproduced, even though their DNA had not been altered. She suspected that the methylation state of the cells’ DNA was being inherited. A gene’s activity can be regulated by a kind of chemical switch process, methylation, when units called methyl groups are added or removed from the gene’s DNA. The on-off pattern of methylation in a cell’s genes can be passed from one generation to another, even when the DNA remains unchanged. This is an example of an epigenetic modification.

Cancer is often associated with less-than-normal methylation of cells’ DNA. Techniques exist for checking the methylation state of a cell, gene by gene. But Polyak and her colleagues, looking to obtain the methylation pattern of a cell’s entire genome (approximately 20,000-25,000 genes) at once, devised a method called Methylation Specific Digital Karyotyping (MSDK) that can read a cell’s complete methylation profile. Polyak and her colleague obtained a profile of the entire genome in a few weeks, a task that would have taken several weeks to months, if it was even possible, using conventional methods.

Using MSDK to study breast cancer tissue, the scientists tested the epithelial and myoepithelial cells that line the breast ducts, and the surrounding cells, known as stoma, including fibroblasts. They found that in all of these cell types, gene expression was altered by epigenetic methylation changes that were not present in normal breast tissue cells.

Most breast cancers develop in the inner lining of the breast’s milk ducts. Some cancerous lesions remain confined within the ducts for years — called ductal carcinoma in situ or DCIS. Others become invasive, breaking through the walls of the duct into the breast tissue, and threatening to metastasize throughout the body. In previous work, the Dana-Farber scientists showed that the stromal cells of the microenvironment, while not malignant themselves, can goad the cancer cells within the duct into more aggressive action. This insight, the researchers commented, provide a rationale for future chemotherapy that targets the stromal cells as well as the tumors themselves.

In addition to furthering scientific understanding of how breast cancers grow, the method and the new findings could aid in the discovery of biomarkers, or physical changes that could be used in the early detection of breast cancers before they can be diagnosed by conventional means.

Polyak said that Dana-Farber has filed for a patent on the method and the genes identified as aberrantly methylated in the various cell types, and is working with a company to use it for the development of diagnostic tools for early breast cancer diagnosis.