Structural Breakpoint

Keck School researchers link unusual DNA structure to cancer.

by Lori Oliwenstein

USC researchers have discovered an unusual DNA structure in the chromosomes of lymphocytes that appears to create a so-called “fragile site” on the chromosome and to predispose cells carrying it to develop a common form of non-Hodgkin’s lymphoma.

“This is the first disease ever to be associated with a deviation from the Watson-Crick helix,” says Michael R. Lieber, M.D., Ph.D., Keck School of Medicine professor of pathology and biochemistry, the Rita and Edward Polusky Chair in Basic Cancer Research and the study’s principal investigator.

The paper was published in the March 4 issue of Nature.

Lieber and his colleagues at the USC/Norris Cancer Center had previously used similar techniques to uncover the first new, stable structure in DNA, which was associated with an antibody-production process called class switching. This structure, however, looks different from the previously described structure and is further distinguished by being associated with cancer.

The fragile site in question is located on the Bcl-2 gene on chromosome 18. Bcl-2 is a gene that normally plays a role in blocking apoptosis, or cellular suicide. When it is over-expressed, however, it results in a form of B-cell lymphoma (hence the name Bcl) called follicular lymphoma.

The fragile site found on the Bcl-2 gene is the most common fragile site in all of cancer, according to Lieber.
“That one break site, which is only about 120 base pairs long, is responsible for 4 percent of all cancers,” he says.

To cause follicular lymphoma, the fragile site on chromosome 18 must experience a break, and then trade bits of DNA with chromosome 14. This is a well-known phenomenon in the world of oncology research and treatment, and is called the 14:18 translocation.

“Of all the chromosomal fragile sites in cancer, this is the first one where we’ve actually understood why it’s fragile,” Lieber says. “And it’s because of this molecular quirk in the Watson-Crick helix.”

Follicular lymphoma is the second-most-common form of non-Hodgkin’s lymphoma, with somewhere between 13,000 and 22,000 cases being diagnosed each year, generally in older individuals. The five-year survival rate is about 75 percent.

Lieber credits this and related discoveries in his lab to a technique developed in conjunction with the USC/Norris laboratory of his wife, Chih-Lin Hsieh, Ph.D., associate professor of biochemistry and molecular biology and urology at the Keck School of Medicine. “It’s called the bisulfide method,” Lieber explains. “It’s based on the fact that when you treat DNA with bisulfide, the cytosine bases of the DNA undergo a transformation. But they only undergo that transformation if they’re in a single-stranded region. If they are in the normal double-stranded configuration, they do not undergo the transformation. So this has allowed us to pinpoint areas of DNA that are not arranged in a double helix and to explore them.”

There is plenty of work left to be done before the fragile site is fully understood, says Sathees Chukkurumbal Raghavan, Ph.D., a research associate in the Lieber laboratory and the paper’s first author. “While we know it deviates from the standard helix, we don’t know what the base pairing is at the fragile site.”

Lieber is equally unsure as to whether this finding will have a therapeutic application down the road. “It’s important to know how and why cancer begins,” he says. “And this is an important step to understanding why the break is happening and why the chromosomes are swapping arms.

“We already knew that this translocation throttles the Bcl-2 up, making the cell invincible—and making it a good cancer cell. But nobody knew why it was happening. Now we are beginning to understand.”

Lieber’s work is funded by the National Institutes of Health.