Many cancer drugs aim at the wrong molecular targets

Analysis using CRISPR gene-editing technology suggests that drugs’ mechanism of action are misunderstood.



Lung cancer cells dividing, coloured scanning electron micrograph (SEM).

Many cancer drugs seek to stop malignant cells, such as these lung-cancer cells, from proliferating.Credit: Anne Weston, EM STP, The Francis Crick Institute/Science Photo Library



Many experimental cancer drugs might be succeeding in unintended ways, finds a study that used CRISPR–Cas9 gene editing to investigate how such drugs interact with malignant cells.

An analysis of ten drugs — including seven now in clinical trials — found that the proteins they target are not crucial for the survival of cancer cells. The results could help to explain why many cancer drugs fail in clinical trials, says William Kaelin, a cancer researcher at the Dana–Farber Cancer Institute in Boston, Massachusetts. Still, he says, “I’m not terribly surprised by the findings.”

The results, published in Science Translational Medicine1 on 11 September, do not necessarily mean that the drugs will not work at all. Some might have shown signs of success in early trials because they are acting on other, unknown targets, says the study’s lead author, cancer geneticist Jason Sheltzer of Cold Spring Harbor Laboratory in New York.

But not knowing drugs’ true mode of action could limit their prospects, he adds. In some cases, scientists can link a therapy to a molecular marker that indicates how likely that drug is to work in a given person. Scientists can then use these markers to select clinical-trial participants who are likely to benefit from the therapy, boosting the chances that it will succeed in the tests used to seek regulatory approval.

This approach is not possible if the drug’s target is uncertain, Sheltzer says. And drugs with unknown targets could harm normal cells in addition to cancer cells, raising the risk of toxic side effects.

“It’s hard enough to develop drugs when you know their mechanism of action,” says Kaelin. “It’s really difficult when you don’t know the mechanism of action.”


Missing the target

Sheltzer and his lab first stumbled onto the problem by accident: in search of a positive control for an experiment, they selected a well-studied protein thought to be important in breast-cancer cell division. But when the team used CRISPR–Cas9 to mutate the gene that controls production of the protein2they found no effect on cancer-cell growth. “We wanted to know whether that was just kind of a one-off occurrence, or whether there were other genes like it in clinical trials,” he says.

The researchers then selected ten other drugs, targeting a total of six proteins, for further evaluation. The ten drugs have been used in 29 clinical trials that aim to enrol more than 1,000 people; their protein targets have been implicated in cancer-cell survival and proliferation in over 180 publications.

But much of the evidence in support of those targets came from a technique called RNA-interference (RNAi), which allows researchers to silence specific genes — but can sometimes affect the activity of other genes.

Sheltzer’s team used multiple methods to evaluate the relationship between the drugs’ efficacy and their targets. They included CRISPR–Cas9, which disables genes in a different way — by editing them to create mutations in them. Some studies have suggested that CRISPR is more precise than RNAi, although it too can sometimes affect other genes.


Homing in

In each case, they found that the target of the ten experimental cancer drugs did not affect the growth of cancer cells grown in the laboratory, compared to controls. Furthermore, when the scientists used CRISPR to wipe out expression of proteins targeted by the drugs, the therapies still killed cancer cells. This suggests that the drugs’ effectiveness is not tied to their purported protein targets after all.

The team then examined one drug, OTS964, in more detail. They found that, although the drug had been developed to target one protein, it was exerting its effect on cancer cells through another ― CDK11, which is involved in cell division.

The findings do have limitations, notes study co-author Ann Lin, a cancer researcher at Stanford University in California. Her team′s experiments were carried out in cells grown in the lab, she notes. “It is possible that these drug targets are essential in human patients,” she says, and not in isolated cells.

And Kaelin says that there was little prior genetic data on the collection of drugs and targets that the team examined — making it hard to back up their value in mice or people. Other targets, with stronger evidence to back them up, would likely fare better, he says.

But Sheltzer hopes to use his results to track down other proteins, like CDK11, that could be exploited for new cancer treatments. “There is an unexplored world of cancer targets out there,” he says. “By using CRISPR and other technologies to examine these drugs, we might unlock new targets.”



doi: 10.1038/d41586-019-02701-6




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CRISPR reveals some cancer drugs hit unexpected targets



Cancer drug developers may be missing their molecular targets—and never knowing it. Many recent drugs take aim at specific cell proteins that drive the growth of tumors. The strategy has had marked successes, such as the leukemia drug Gleevec. But a study now finds that numerous candidate anticancer drugs still kill tumor cells after the genome editor CRISPR was used to eliminate their presumed targets. That suggests the drugs thwart cancer by interacting with different molecules than intended.

The study, published this week in Science Translational Medicine, points to problems with an older lab tool for silencing genes that has been used to identify leads for such drugs. The results also hint that the drugs in question, most of which are in clinical trials, and perhaps others could be optimized to work even better by pinning down their true mechanism.

“The work is very well done and it’s a great public service. I hope people talk about it. I don’t find any of it surprising, unfortunately,” says William Kaelin of the Dana-Farber Cancer Institute in Boston, who has written about why promising preclinical findings are often not reproducible, or fail to lead to drugs.

Leads for many recent targeted drugs emerged from experiments in which cancer cells were dosed with RNA strands that disrupt the natural RNAs that convey a gene’s protein-building instructions. After using this RNA interference (RNAi) method to zero in on genes essential to the growth of cancer cells, researchers screened libraries of molecules to find compounds that block the genes’ proteins.

A few years ago, cancer biologist Jason Sheltzer of Cold Spring Harbor Laboratory in New York and colleagues used CRISPR’s gene-disabling skills, instead of RNAi, to prevent the manufacture of a well-established growth protein, called MELK, in cancer cells. Several companies at the time were developing MELK inhibitors as anticancer agents. But to the group’s surprise, the MELK-deficient cells kept growing. And a drug thought to be aimed at MELK still stopped growth of the cells, suggesting its true target was not that protein.

That work spurred Sheltzer’s lab to collect examples of other drugs that target proteins found largely with RNAi. His group ultimately homed in on 10 drugs aimed at six proteins whose roles range from driving cell proliferation to controlling cancer gene activity. When the scientists used CRISPR to knock out the genes for those proteins in various cancer cell lines, the cells kept growing, suggesting the original RNAi assay was misleading. Yet, when the team gave the relevant drug to cancer cells now missing the target protein, they still died—apparently through some other mechanism. “Many of the previous results were replicable, but the interpretation was wrong,” Sheltzer says.

The researchers found a clue to the real mechanism for a drug, now in preclinical testing, that supposedly blocks a protein called PBK, which aids cell division. By identifying cells that developed resistance to the drug, known as OTS964, and sequencing them for mutations that confer that trait, the lab showed the drug instead blocks the protein CDK11, which plays a different role in cell proliferation. Sheltzer calls this result “exciting” because inhibitors of other CDKs work well against breast cancer, and targeting this one could be a new option. (Science could not reach the drug’s manufacturer, OncoTherapy Science, for comment.)

Sheltzer doesn’t think his group’s results cast doubt on the targeted cancer drugs already on the market, as most have other compelling evidence they’re hitting the right protein. But for the 10 candidate drugs studied by his lab, as well as others in development, it’s important to find out how they work so physicians can match patients to the best drug and fulfill the promise of precision medicine, Sheltzer says. Paul Workman of the Institute of Cancer Research in London agrees: “It clearly helps enormously if the true target is now found.”




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