Bedalov's research draws upon an emerging field of molecular biology called epigenetics. In contrast to gene therapy, a method of curing diseases by delivering new genes to problematic cells, epigenetic therapy is based upon a subtler premise. The DNA sequence itself is not changed: Instead, only the accessibility of critical genes to DNA-reading proteins is manipulated.
The human genome contains an estimated 25,000 to 30,000 genes that code for functioning proteins, but they aren't all accessible to being switched on, or expressed, at all times. Just like thousands of musicians in a vast orchestra, each waiting for a cue to perform, every individual gene should remain silent at the appropriate times. Enzymes such as silent information regulators (SIRS) can silence a gene by attaching small chemical groups, usually methyl or acetyl groups, to either the DNA or its packaging, the histone proteins. These chemical modifications cloak the gene, in a sense, putting it into a state of hibernation.
While gene silencing is a necessary and ubiquitous molecular event within healthy cells, inappropriate silencing has been associated with the development of certain forms of cancer and other diseases. Untimely silencing of the gene for a tumor-suppressor protein, for example, would have the same effect as a mutation within this gene. Either way, the role performed by that protein is unfulfilled, and a cellular transition from healthy to cancerous may result. Low levels of silencing can give rise to cancer as well, if pro-cancer proteins, called oncogenes, are not adequately silenced.
A potential anticancer strategy, therefore, is to take advantage of the proteins that silence genes. In 2001, Bedalov and collaborators discovered splitomicin, which inhibits the yeast SIR2 protein, one such gene silencer. "Toni was the intellectual force behind the idea of looking for small molecule inhibitors of gene silencing," said Dr. Dan Gottschling, faculty member in the Basic Sciences Division and collaborator on this project. "His idea was that tumor suppressor genes were being silenced in some cancers. In thinking about how to approach the problem, he took full advantage of the open nature of the Hutchinson Center and making connections between work in our lab and Julian Simon's lab."
The discovery of splitomicin, which Bedalov named in honor of Split, his hometown in Croatia, was the first drug discovered to inhibit SIR2 and helped establish that small molecules could manipulate gene-silencing proteins. Following the splitomicin discovery, the next step was to extend the anti-silencing effect from yeast to human cancer cells. Recently, Bedalov and his group identified cambinol, a splitomicin analogue that acts upon SiRT1, the human relative to yeast's SIR2. In early experiments with animals, Bedalov and his group have found that cambinol can reduce the size of small tumors. The results are currently being prepared for publication. "In proof of principle, at least, it looks very exciting," Bedalov said.
Cambinol, like splitomicin, is an attractive drug for therapeutic use because of its exquisite selectivity for the silencing protein that it inhibits. This specificity is desirable because it reduces the possibility of side effects in patients. Also, the drug sensitizes cells to DNA damage, the mechanism by which many chemotherapy drugs kill off cancer cells. Cambinol potentially could increase the vulnerability of malignant growths to chemotherapy, if administered together.
In addition to cancer, drugs that influence gene silencing may be used to address other diseases as well. Individuals with sickle cell anemia suffer the effects of a flawed hemoglobin protein, yet they possess the genes to code for a fetal form of hemoglobin — functional, but silenced in the early stages of life as part of normal development. If this gene can be woken up with anti-silencing drugs, it theoretically would produce healthy hemoglobin to replace the mutated version.
The road to drug approval is brutally selective: An estimated one-in-10,000 new drug candidates will survive the journey from test tube to FDA approval, while the remainder fail at some stage along the way. Bedalov is undaunted by these statistics, however, insisting that every "failure" can help cast light upon the various biochemical events he is targeting.
"This is the reason why I would like to keep my focus on the early phases of anticancer drug discoveries and on understanding the pathways that are affected by the drug in cancer cells," Bedalov said. Contributing to a deeper understanding of the molecular process of silencing is just as important as the more glamorous and, perhaps, more profitable success which comes with seeing a drug all the way through human clinical trials.
Though cambinol might not be the actual drug administered to patients, years down the line, it represents the next evolutionary step in the drug design process. Working with the structure of cambinol as a type of molecular template, Bedalov will explore effects of minor modifications to the structure and work towards new candidates for anti-silencing drugs.
Bedalov, A., Hirao, M., Posakony, J., Nelson, M., and Simon, J. A. (2003) NAD+-Dependent Deacetylase Hst1p Controls Biosynthesis and Cellular NAD+ Levels in Saccharomysces cerevisiae. Mol. Cell. Biol. 23, 7044-7054
Hirao M, J. Posakony, J, Nelson M, Hrubby H, Jung M, Simon J and A. Bedalov. Identification of selective inhibitors of NAD-dependent deacetylase using phenotypic screens in yeast. 2003 J Biol Chem. 278(52):52772-82
Tonibelle Gatbonton, Maria Imbesi, Melisa Nelson, Joshua M. Akey, Douglas C. Ruderfer, Leonid Kruglyak, Julian Simon, Antonio Bedalov. Telomere length as a quantitative trait: Genome-wide survey of the deletion mutants and genetic mapping of the telomere length- control genes in Saccharomyces cerevisiae. Submitted.
To view the Telomere Length Database: