Using yeast to break genetic 'silence'

With help from Basic Sciences and Human Biology, oncology fellow's drug has potential to reverse chromosomal shut-off in cancer
Dr. Antonio Bedalov and robot
Dr. Antonio Bedalov gazes at the robot that is used to test potential anti-cancer drugs on yeast. Photo by Clay Eals

With the announcement of this year's Nobel Prize in physiology or medicine, the world learned that a simple organism like baker's yeast has a lot to teach about the origins of cancer.

That same microbial workhorse also proves to be an ideal tool for Hutch oncology fellow Dr. Antonio Bedalov, who searches for new anti-cancer drugs.

Bedalov put yeast to work to discover a chemical compound that reverses a process called silencing, in which genes or regions of chromosomes are shut off.

A Croatian native, Bedalov named the compound "splitomicin," after his hometown, Split.

Although silencing is important for many normal developmental processes, several cancers, including some forms of acute myelogenous leukemia, have genetic abnormalities that lead to inappropriate silencing of genes critical for healthy growth.

The study appears in the Dec. 18 Proceedings of the National Academy of Sciences and involved Dr. Julian Simon, an investigator in the Clinical Research and Human Biology divisions, and Dr. Dan Gottschling in the Basic Sciences Division.

Potent inhibitors of silencing could have significant utility for treating a variety of cancers, Bedalov said. "In addition to acute myelogenous leukemia, silencing appears to play a role in a colon cancer," he said. "It also occurs in hormone-refractory forms of breast cancer." Sickle-cell-anemia patients might benefit from anti-silencing drugs as well.

"People with sickle-cell anemia have defective copies of the gene for the adult form of hemoglobin," he said. "But they possess a normal version of the fetal hemoglobin gene, which gets silenced early in life as part of normal development. Reversing silencing of fetal hemoglobin could potentially compensate for the lack of functioning hemoglobin in these patients."

Genetic hibernation

Silencing can be thought of as genetic hibernation, with gene activity - the process of making proteins - essentially quiescent for long periods of time, said Gottschling, whose laboratory studies the phenomenon in yeast.

"There are many situations in which it's beneficial for a cell to silence regions of the genome," he said. "In yeast, for example, mating can't occur unless certain genes are silenced. But there are also mechanisms, both normal and abnormal, that allow the process to be reversed."

Although multiple mechanisms for silencing exist, one form with a connection to cancer has been found in organisms as diverse as yeast, worms and humans. In fact, some of the key genetic components of this pathway are virtually identical in these organisms, which means that scientists can exploit the power of yeast genetics to study complex human processes.

Bedalov, who joined Simon's lab in 1997, recognized that this striking ubiquity made yeast an ideal system in which to look for anti-silencing - and potential anti-cancer - drugs.

Tools a short walk away

Many of the tools Bedalov needed to look for inhibitors of yeast silencing were no farther away than a short walk from the Thomas Building to the Gottschling lab in the Weintraub building. Gottschling has developed strains of yeast whose silencing ability can be evaluated quickly with a simple growth test on Petri dishes.

The reagents for drug discovery were even closer at hand: Simon is an organic chemist and has developed a high-throughput method to rapidly screen chemical compounds for anti-cancer activity in yeast.

"Toni's success demonstrates the power of a carefully chosen, cell-based drug screen," Simon said. "The question of drug specificity is minimized in a screen that uses a live cell with 6,000 other potential drug targets.

"By picking the right model system, Toni virtually guaranteed that an active compound would target a component of the silencing machinery. The same approach can be used to screen for immunosuppressive agents or anti-cancer drugs."

One target for search

Bedalov focused his drug search on one target, a silencing protein called Sir2 that has been studied extensively in yeast.

"Sir2 is required for silencing to occur and has been found in many different organisms," he said. "Human cells have seven Sir2 genes."

Although not known when Bedalov initiated his studies, Sir2 recently was found to modulate the function of p53, a well-known tumor suppressor protein.

Bedalov screened 6,000 chemical compounds to identify those that disrupt silencing in yeast. The drugs he evaluated were obtained from a chemical bank at the National Cancer Institute that consists of more than 900,000 compounds donated by chemists who have synthesized or isolated novel chemicals.

He found 11 compounds that interfered with silencing, and only one - "splitomicin" - affected all the silencing capabilities of the Sir2 protein. The Center recently filed for patent protection of the drug.

Sir2 is a type of protein known as a histone deacetylase, a molecule that strips chemical groups-called acetyl groups-from proteins that help package DNA into chromosomes. If Sir2 removes the acetyl groups from a region of the chromosome, genes in that region are silenced.

So it was not surprising for Bedalov to discover in subsequent experiments that splitomicin directly interferes with both yeast and human Sir2's ability to strip acetyl groups from chromosomal proteins.

Bedalov also used DNA microarrays - "gene chips" that allow the activity of all yeast genes to be monitored simultaneously - to determine that splitomicin's only role in the cell is to inhibit Sir2 function, which makes the drug highly effective for its target.

"We looked at the pattern of gene expression in normal yeast cells treated with splitomicin and compared that with yeast cells that contain a defective copy of the gene for Sir2," he said. "The effects on gene expression in both cases is virtually the same."

Dr. Jeff Posakony, postdoctoral fellow in Simon's lab, recently synthesized chemical derivatives of splitomicin that work more effectively than the original compound to inhibit the human form of Sir2.

More effective therapy

In other experiments, Dr. John Lamb, also a postdoc in the Simon lab, discovered that splitomicin sensitizes human cells to DNA-damaging agents, a finding that could be exploited to increase the effectiveness of cancer chemotherapy since many anti-cancer drugs inflict DNA damage.

Bedalov hopes to evaluate splitomicin and drugs like it for their therapuetic potential in cancer cells, a goal more accessible thanks to the relative ease of initial studies in yeast.

"Our hope is that this chemical-genetics approach can lead to quicker development of treatments for people with cancer and other diseases," he said.

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