Base editing to treat leukemia in children

Chimeric antigen receptor (CAR) T cell therapy, in which researchers engineer immune cells to target specific receptors on cancer cells, is an allied treatment for various types of blood cancers. However, its application for T-cell leukemia is challenging because the targets are other T cells that have gone rogue. “As soon as you try to arm T cells to fight against other T cell lineages, the risk is that they will fight amongst themselves,” said Waseem Qasim, a pediatric gene therapy researcher at University College London.

Eliminating the antigen shared by both the diseased and the infused T cells is one potential strategy for delivering CAR T cell therapy without committing fratricide. “In the military term, it would be hiding your flag, so you are then operating under the radar almost and are able to attack without causing friendly fire,” said Qasim.

To remove the genes coding for these flags, Qasim and his colleagues engineered CAR T cells using base editing (1). Unlike other genome editing technologies, base editing allows precise changes in single letters of the DNA code without causing breaks (2). As part of a Phase 1 study, his team is currently investigating the safety of infusing these edited cells into ten children (up to the age of 16) suffering from T-cell acute lymphoblastic leukemia, an aggressive form of blood cancer. The team published the outcome of this intervention in the first three study participants in The New England Journal of Medicine (3).

When Qasim first read about base editing, he was skeptical that it could work efficiently, but he also foresaw its potential for editing T cells. “Instead of trying to change a mutation, we’d introduce the mutation to stop a gene being expressed, and so by doing that, we can simultaneously cause three, four, more if we like, knockouts of expression of genes,” he said.

What we aim to do is clear disease within two or three weeks, and then allow the system to recover fully from a donor transplant.
- Waseem Qasim, University College London

Qasim’s team used base editing to inactivate three genes expressed on the surfaces of T cells: CD7, CD52, and TCRαβ. The removal of these “flags” on healthy donor T cells aimed to prevent fratricide and graft-versus-host disease. They then inserted a CAR gene into these edited cells to recognize CD7 in the diseased T cells of patients. The team infused the engineered T cells into the study participants and monitored their outcomes.

A 13-year-old girl and a 15-year-old boy showed no signs of leukemia cells in the bone marrow 28 days after the infusion, enabling subsequent stem cell transplantation. Bone-marrow analyses of the third patient, a 13-year-old boy, suggested ongoing remission as well. However, he experienced lung complications from a fungal infection, leading to death 33 days after receiving the infusion.

The fungus in the fatal infection likely had the chance to establish itself due to the immune depleting nature of both the CAR T cell therapy and the chemotherapy administered in combination with it, Qasim explained. “It’s important for us to bear that in mind, and we do; we screen patients very carefully to make sure there are no active infections,” he added. It is a very intensive procedure that involves hospitalization for several weeks and a high risk for infections, but if it works, patients generally rebuild immunity after the transplant, according to Qasim. “What we aim to do is clear the disease within two or three weeks, and then allow the system to recover fully from a donor transplant.”

Using base editing for knocking out multiple genes, as Qasim’s team did, is really powerful, said Luigi Naldini, a gene therapy researcher at the San Raffaele Telethon Institute for Gene Therapy who did not participate in this study. “We can see that base editing can be very efficient in these T cells, also at multiple loci, which is good,” he added.

While these results validate the efficacy of the technology for editing immune cells, they do not provide evidence on its long-term safety, Naldini cautioned. In a way, the specific application of base editing in this context is smart, he noted, since the edited cells will be cleared shortly after the infusion. However, “Some of the potential adverse effects may require longer-term monitoring,” Naldini said. “We still don't have a full understanding of the whole potential effect of base editing.”

Qasim agreed. “It’s very important ... to monitor these patients and watch very carefully what happens to the cells,” he said. Base editing carries fewer risks than its predecessors, but he is optimistic that future genome editing technologies will continue to improve. “The tools we’re using are still being developed and there will be better versions that come along,” he concluded.