A naturally occurring mutation in T cells that leads to lymphoma can be weaponized to make engineered T-cell therapies more effective against cancer, including melanoma, findings from a new study in mice suggest.
In an article published Feb. 7 in Nature, scientists from Northwestern University and the University of San Francisco (UCSF) showed that a cancerous mutation that fuses a pair of genes, CARD11 and PIK3R3, has strong anti-cancer effects when added to T cells in chimeric antigen receptor T cell (CAR-T) and T cell receptor (TCR) therapies. The study’s co-leads, Northwestern dermatologist Jaehyuk Choi, M.D., Ph.D. and UCSF scientist Kole Roybal, Ph.D., have launched a new biotech company called Moonlight Bio to take their findings to the clinic.
“The superpower that makes cancer cells so strong can be transferred into T cell therapies to make them powerful enough to eliminate what were once incurable cancers,” Choi said in a press release from the university.
Building on the basic principle that cancer cells contain gene mutations that make them more evolutionarily “fit”—that is, better at proliferating and resisting the immune system—the researchers systematically screened the impacts of 71 different mutations in cancerous T cells from patients with lymphoma. This led them to the CARD11-PIK3R3 mutation, which appeared to increase signaling by a group of proteins known as the CBM complex. CBM complex activity has been associated with malignant HER2-positive breast cancer, lymphoma and oral cancer (PDF).
When the scientists inserted the CARD11-PIK3R3 mutation into healthy T cells and tested them against a line of leukemia cells, potency was dramatically increased. While 75% to 100% of the cancer cells remained after being cultured for two weeks with regular T cells, the ones that were cultured with T cells containing the CARD11-PIK3R3 mutation were almost completely eliminated.
These results were replicated in mouse models of leukemia that were treated with CAR-Ts. In these experiments, the researchers created CARD11-PIK3R3-expressing CAR-Ts that also targeted cancer cells with the antigen CD19, which the team found was necessary for the CAR-Ts to have an effect. Mice that received CD19-CARD11-PIK3R3 CAR-Ts survived the full study periods in nearly all of the experiments—which ran between 30 and 80 days—long outliving controls as well as animals that were treated with other forms of CD19-expressing CAR-T cells, suggesting that the CARD11-PIK3R3 mutation was the differentiator.
Notably, the mice didn’t undergo lymphodepleting chemotherapy, or lymphodepletion, a step normally taken with engineered T-cell therapies that clears out a patient’s existing T cells to enhance the efficacy of the new ones.
Next, the researchers tested whether the mutation enhanced TCR therapy. They engineered CD8-expressing TCR cells with the CARD11-PIK3R3 mutation and gave them to mice with melanoma. The cells not only prevented the tumors from growing but, more than three months later, had completely cleared them in three out of the five mice in the group. One of the mice in the group died with a skin ulceration, but without tumors, the researchers noted. None of the control mice or mice treated with a different TCR therapy survived. As in the CAR-T experiments, none of the mice underwent lymphodepletion prior to treatment.
The team also carried out a dose-response study on the mice, which showed that CARD11-PIK3R3 expressing T cells could control melanoma growth at a 20-fold and even a 100-fold smaller dose than a standard T-cell therapy—once again without lymphodepletion. In addition, they tested CARD11-PIK3R3 TCR cells on mouse models that had been injected with KRAS-mutated human stomach cancer cells. All six of the mice in the experimental group had a complete response, compared to two of the five mice that received a different TCR therapy and none of the controls.
Finally, to assess long-term toxicity, the researchers followed mice that received CARD11-PIK3R3 T cell therapies, including those that were part of the dose-response study, for up to 418 days. The animals gained weight similarly to control animals—a sign that they were generally healthy—and had no signs of secondary cancer. They also noted that the cells comprised only a small portion of T cells in the blood and spleen, suggesting that they didn’t grow abnormally after doing their job against the cancer.
Still, the scientists noted in their paper, souping up therapeutic T cells with a mutation that comes from cancerous ones might sound dangerous—especially in light of recent FDA concerns about secondary cancers arising from CAR-T therapy. But their findings suggest the mutation might actually make these types of treatments safer.
“Although the source of this particular potency enhancement may suggest risk, CARD11-PIK3R3 has potential safety advantages over other approaches,” the researchers wrote in their paper. For one, the effects of the genes appear to depend on whether they are acting on cells that contain the target antigen, “minimizing the risk of autonomous proliferation,” they said. Plus, the therapy’s potency eliminates the need for pre-treatment chemotherapy to kill off the patient’s existing immune cells and make way for new ones, a process that may increase the risk of secondary cancers.
“Our long-term … studies, carried out in multiple models and at high T cell doses, showed no signs of lymphomagenesis, even at 418 after adoptive T cell transfer,” they wrote. “These data suggest that the risk of malignant transformation could be measured and managed.” They also highlighted several engineering strategies they planned to undertake to prevent cancer as well as other side effects common with T cell therapies, such as autoimmunity.
In the press release, Roybal called the finding “a starting point.”
“There’s so much to learn from nature about how we can enhance these cells and tailor them to different types of diseases,” he said.
Editor's note: A previous edition of this article misspelled Kole Roybal's last name as "Roybel".