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Gene Editing Technology Harnessed to Identify New, Druggable Targets in Kidney Cancer

PHILADELPHIA (November 5, 2020) – Researchers at Fox Chase Cancer Center have harnessed the power of the Nobel Prize-winning CRISPR/Cas9 technology to identify cellular factors involved in resistance to sunitinib by clear cell renal cell carcinoma.

Renal cell carcinoma is the most common type of kidney cancer and the tyrosine kinase inhibitor sunitinib is a drug that is a standard front-line therapeutic agent for the treatment of advanced disease. However, sunitinib doesn’t work for some patients with renal cell carcinoma and even those patients who initially respond to the drug will eventually develop resistance.


Peter Makhov, MD, PhD, a research assistant professor at Fox Chase, developed the idea of using CRISPR/Cas9-based high-throughput loss-of-function screening to identify factors involved in cell resistance to sunitinib.


Using this method, Makhov, who at the time of the study worked in the lab of Vladimir Kolenko, MD, PhD, an associate research professor in the Cancer Biology program, and colleagues identified the critical role of a protein called farnesyltransferase as a contributing factor of resistance to sunitinib.


“On a genetic level we can knock down the expression of farnesyltransferase, which sensitized the cancer cells to sunitinib, but to treat people, the next step was to figure out if we have any inhibitors of farnesyltransferase,” Kolenko said. “We were lucky that there are commercially available pharmacological inhibitors of farnesyltransferase that are used in the treatment of progeria.”


When the farnesyltransferase inhibitor lonafarnib and sunitinib were combined to treat renal cancer cell lines, there was a synergistic response called synthetic lethality.

Kolenko and colleagues are researching how this mechanism of resistance works. “We believe that tumor cells can accumulate sunitinib in specific organelles called lysosomes,” he said. “Eventually the concentration of sunitinib is really high and resistance occurs.”


When combined with lonafarnib, the lysosomal sequestration of sunitinib was disrupted and the drug can again act as an inhibitor. “That is why combination therapy with sunitinib and lonafarnib is much more potent than treatment with sunitinib alone,” Kolenko said.


This new CRISPR/Cas9 loss-of-function approach can be used to identify resistance mechanisms for any drug, he added.


“We plan to use the same approach for identifying potential genes whose inactivation is synthetically lethal in combination with other targeted therapeutics,” Kolenko said. “This gives us a very powerful tool.”


The paper, “CRISPR/Cas9 Genome-Wide Loss-of-Function Screening Identifies Druggable Cellular Factors Involved in Sunitinib Resistance in Renal Cell Carcinoma,” was published in the British Journal of Cancer.

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