High-Throughput siRNA Screening Identifies Drug Targets in MYC-driven Cancers

A sophisticated high-throughput screening technique was used to search for genes able to block the activity of an oncogene that produces a protein that had traditionally been considered “undruggable” due to its lack of binding sites for low molecular weight inhibitors.

Investigators at the Fred Hutchinson Cancer Research Center (Seattle, WA, USA) focused their attention on the gene MYC, which is a strong protooncogene that it is very often found to be upregulated in many types of cancers. The Myc protein encoded by this gene is a transcription factor that activates expression of a great number of genes through binding on consensus sequences (Enhancer Box sequences (E-boxes)) and recruiting histone acetyltransferases (HATs). It can also act as a transcriptional repressor. By binding Miz-1 transcription factor and displacing the p300 coactivator, it inhibits expression of Miz-1 target genes. Myc is activated upon various mitogenic signals such as Wnt, Shh, and EGF (via the MAPK/ERK pathway). By modifying the expression of its target genes, MYC activation results in numerous biological effects. The protein encoded by MYC has been found to be highly resistant to chemotherapy mainly because it lacks efficient binding sites for drug compounds.

A paper published in the May 23, 2012, online edition of the journal Proceedings of the National Academy of Sciences of the USA described the use of high-throughput siRNA (small interfering RNA) screening to evaluate a library of 3.300 druggable genes for their possible effect on MYC. Of 49 genes selected for follow-up, 48 were confirmed by independent retesting, and approximately one-third selectively induced accumulation of cellular DNA damage. In addition, genes involved in histone acetylation and transcriptional elongation were identified, indicating that the screen had revealed known MYC-associated pathways.

For in vivo validation in a nude mouse xenograft model, the investigators selected the enzyme CSNK1e, a kinase whose expression correlated with MYC amplification in neuroblastoma (an established MYC-driven cancer). Using RNAi and available small-molecule inhibitors, they confirmed that inhibition of CSNK1e halted growth of MYC-amplified neuroblastoma xenografts.

An inhibitor for CSNK1e already exists: a compound that originally was developed to modulate sleep cycles. “It had been sitting on a shelf for years, like the thousands of other “orphan” drugs that are abandoned when they prove ineffective for their intended use,” said senior author Dr. Carla Grandori, professor of human biology at the Fred Hutchinson Cancer Research Center. “Fortunately, MYC-driven cancer cells have an Achilles heel. Their rapid growth and division damages their DNA, and they rely on other genes to repair that damage. Disabling those genes can cripple the cancer’s ability to grow.”

“It is possible that the next great breakthrough in cancer therapy is already out there, sitting on a shelf, hiding in plain view,” said Dr. Grandori. “We have barely scratched the surface. These techniques are incredibly powerful, but they are new and not widely known. There are thousands of researchers who could apply this approach to their work. In the right hands, it could speed up the development of new cancer therapies a thousand-fold.”

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Fred Hutchinson Cancer Research Center