New therapeutic strategy turns a cancer’s advantage into its downfall

Cancer cells carry a lot of genetic hiccups that can help them outgrow normal surrounding tissue. Now, researchers have developed an anti-cancer strategy that takes advantage of these glitches, rather than try to correct them.

In a proof-of-principle study published today in the journal Nature Biotechnology, a collaborative team at Fred Hutchinson Cancer Research Center and Memorial Sloan Kettering Cancer Center describe a new strategy, tested in mice and lab dishes, that uses lab-designed molecules to insert a kill switch into cancer cells — but leave healthy cells unscathed.

“We showed that we can engineer a therapy in response to the internal state of a cell,” said Hutch computational biologist Dr. Robert Bradley, who co-led the project. “We believe that we can use this exact approach to deliver therapies in a highly specific manner, even outside of the context that we focused on for our study.”

Bradley, who holds the McIlwain Family Endowed Chair in Data Science, teamed up with MSK cancer geneticist Dr. Omar Abdel-Wahab to develop and test the novel strategy.

“This kind of approach and concept is completely new,” said Abdel-Wahab. “That’s the most exciting part of it: It’s a whole new concept as well as a new form of therapy.”

Having demonstrated the principle behind their approach, the team is working to improve delivery and efficacy before testing it in the clinic.

Changes in how our cells make proteins drive cancer

Bradley and Abdel-Wahab study the processes our cells use to turn the information encoded in our genes into proteins, which do most of the work in a cell. Our cells copy a gene’s DNA sequence into a new form: molecules called messenger RNA, or mRNA. The protein-building molecular factories in our cells can then use mRNA molecules as instructions for constructing proteins out of amino acid building blocks.

Cells transcribe mRNA with bits of extra material, called introns, so each mRNA needs to be cut up and stitched (or spliced) together before it works as an instruction manual for manufacturing a protein. But if the enzymes or helper proteins called splicing regulators responsible for properly splicing mRNA get mutated, that can change how RNA is spliced and which proteins get generated. This, in turn, unbalances many cellular processes, including those that regulate cell growth and survival. In fact, mutations affecting these splicing regulators are seen in many tumor types. Recent work by Bradley, Abdel-Wahab and others is revealing how those mutations can cause cancer to develop.

Correcting splicing errors might seem the obvious approach to treating cancers caused by them — but that’s not possible right now, Bradley said.

“Currently, we can’t make the splicing errors go away, so we decided to take advantage of them,” he said. “We decided to make a therapeutic that only works when splicing errors occur.”

Turning an asset into a handicap

To take advantage of cancer cells’ splicing errors, the scientists developed mRNA molecules with lab-designed introns that can only be spliced — and then translated into protein — by cells with mutations in a specific splicing enzyme. They first tested mRNAs that encode thymidine kinase, or TK, a protein derived from herpes simplex virus. Cells carrying the TK enzyme convert the herpes treatment ganciclovir into a lethal drug.

The strategy upends the tumor cells’ upper hand: Because only cancer cells make this conversion, they’re the only cells that ganciclovir kills.

Abdel-Wahab and Bradley’s team decided to try this strategy in cancer cells that bear mutations in the gene for a splicing enzyme called SF3B1. (In 2019, the collaborators revealed how SF3B1 mutations drive cancer.) Mutations in the SF3B1 gene pop up in a lot of cancers, making it great test case for the collaborators’ counterintuitive approach.

After exhaustive studies of cells with SF3B1 mutations revealed the best sizes and sequences for the team’s synthetic introns, they tested the strategy’s effectiveness in lab dishes and mice.

Their first tests of the synthetic introns, using leukemia cells and eye-derived melanoma cells grown in dishes, showed that the viral enzyme could only be produced in cells with SF3B1 mutations. And only mutant cells treated with the synthetic mRNAs died after exposure to ganciclovir.

To test the effectiveness of their constructs in live animals, the team introduced the synthetic mRNAs into human leukemia cells which carried either a normal or mutated SF3B1 gene. The mRNA-treated tumors were then injected into mice, and the mice treated with saline or ganciclovir. Ganciclovir only suppressed tumor growth in mice injected with SF3B1-mutant leukemia cells. At day 70, nine out of 10 mice injected with an SF3B1-mutant tumor and treated with ganciclovir survived, while almost all the mice in the other groups had died from leukemia.

The team also tested their strategy against a mouse model of myelodysplastic syndrome, a group of cancers in which bone marrow cells don’t mature into healthy blood cells. They found that in mouse bone marrow, ganciclovir could selectively kill SF3B1-mutated bone marrow cells that carried the team’s specially designed mRNA.

The team found that their strategy was also successful against solid tumors carrying SF3B1 mutations, even when the specially designed mRNAs were packaged and injected into tumors already growing in the mice. All mice received the synthetic introns, but tumors only regressed in mice that also received ganciclovir. Looking more closely at the tumors and surrounding tissue, the team found the properly spliced mRNA in the SF3B1-mutated tumor tissue, but not in normal tissue surrounding the tumor, suggesting that their strategy carries little risk of harming healthy cells.

“We did the opposite of what you’d expect, and the whole approach worked better than we thought possible,” Bradley said.

Improving the strategy

Now that the team has demonstrated the promise of their approach, they’re working to make it more potent and easier to administer. There are many potential molecules they could deliver via their synthetic mRNAs, from other molecular kill switches to immunomodulatory molecules that could make a patient’s tumor susceptible to immunotherapy, Abdel-Wahab said.

Another hurdle they need to clear before the strategy can reach the clinic is the problem of delivering their synthetic mRNAs to tumors — a problem faced by all scientists working to engineer genetic solutions to disease.

“The challenge is, how do you get this [treatment] into enough of the right cells so that it would have a therapeutic impact?” Abdel-Wahab said.

The team also believes that tackling tumors with mutations in SF3B1 is just the beginning and are actively seeking industry collaborators to help advance the platform towards clinical candidates. There are other splicing factor mutations they could develop introns to address. Bradley also believes that the approach could be adapted for tumors that have splicing errors that haven’t been traced to a particular mutation.  

“I think our paper holds up the exciting possibility that perhaps we can use the same approach in cancers that don’t even have a splicing factor mutation,” Bradley said.

“We’re equally excited at the prospect of developing a new therapeutic product for the patients we focused on in this paper as for the idea that we’ve established a new technology platform that other researchers can use in many different diseases,” Bradley said.

The work was funded by the American Society of Hematology; the Leukemia & Lymphoma Society; the National Cancer Institute; the National Heart, Lung, and Blood Institute; the National Institute of Diabetes and Digestive and Kidney Diseases; the ARCS Foundation; the Washington Research Foundation and the Edward P. Evans Foundation.

Note: Scientists at Fred Hutch played a role in developing these discoveries, and Fred Hutch and certain of its scientists may benefit financially from this work in the future.