“This indicates that RNAi promiscuity has contributed to the misidentification of cancer-essential genes and the initiation of clinical trials against nonessential targets,” wrote Dr Sheltzer, in a tweet. He and his colleagues tested 32 different cells lines from 12 different cancer types, including many of the lines where the proteins had been implicated as essential.
Although the team’s results may be compelling, it may not be time to sweep away all prior results on targeted therapies just yet.
“Some of these dependencies may be real and may depend on the particular condition in which the cell lines are grown,” said Andrea Califano, PhD, professor of systems biology at Columbia University in New York. “It also depends very much on how many relevant cell lines you have in your collection.”
As an example, Dr Califano points to his work on HDAC6, one of the essential proteins tested in the new study.4 “The HDAC6 dependency is what determines the difference between inflammatory breast cancer, which is a very aggressive type of cancer and depends on HDAC6, and noninflammatory breast cancer, a vast majority of which does not depend on it,” Dr Califano said. “None of the cell lines that were studied in the context of this study were related to inflammatory breast cancers. As a result, the new study is not inconsistent with prior results.”
Still, the work highlights the importance of validating cell-screening assays using multiple approaches. For instance, researchers can repeat their knockout experiments using different RNA constructs against the same gene, which will have different off-target effects. If the loss of viability remains, it’s more likely a true target. Another way to verify RNAi results is by using a “rescue assay,” in which the gene thought to be deactivated is returned to the cell, rescuing the cell’s viability.
But these verification steps can be difficult and time consuming. The precise genetic alterations made possible by CRISPR simplify the process of verifying a drug’s mechanism-of-action, Sheltzer said on Twitter. “I think that applying these genetic technologies in a preclinical setting will decrease the number of new drugs that get tested in cancer patients but fail to provide any clinical benefit,” he wrote.
Other examples of drug-target mismatches have begun appearing in the literature. “It’s definitely the tip of the iceberg,” said Richard Phillips, MD, PhD, a neuro-oncologist at Memorial Sloan Kettering Cancer Center in New York City. Earlier this year, Dr Phillips published evidence that a drug-target pair, originally described in leukemia, doesn’t work the same way in a rare pediatric cancer called diffuse intrinsic pontine glioma, or DIPG.5